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William Marsh Rice University, commonly referred to as Rice University or Rice, is a private research university located on a 295-acre campus in Houston, Texas, United States. The university is situated near the Houston Museum District and is adjacent to the Texas Medical Center. It is consistently ranked among the top 20 universities in the U.S. and the top 100 in the world.Opened in 1912 after the murder of its namesake William Marsh Rice, Rice is now a research university with an undergraduate focus. Its emphasis on education is demonstrated by a small student body and 5:1 student-faculty ratio, among the lowest in the top American universities including the Ivy League. The university has produced 101 Fulbright Scholars, 11 Truman Scholars, 24 Marshall Scholars, 12 Rhodes Scholars, 3 Nobel Laureates, 2 Pulitzer Prize winners, and at least 2 deceased and 2 living billionaires. The university has a very high level of research activity for its size, with $115.3 million in sponsored research funding in 2011. Rice is noted for its applied science programs in the fields of artificial heart research, structural chemical analysis, signal processing, space science, and nanotechnology. It was ranked first in the world in materials science research by the Times Higher Education in 2010. Rice is a member of the Association of American Universities.Rice is noted for its entrepreneurial activity, and has been recognized as the top ranked business incubator in the world by the Stockholm-based UBI Index for both 2013 and 2014.The university is organized into eleven residential colleges and eight schools of academic study, including the Wiess School of Natural science, the George R. Brown School of Engineering, the School of Social science, and the School of Humanities. Graduate programs are offered through the Jesse H. Jones Graduate School of Business, School of Architecture, Shepherd School of Music, and Susanne M. Glasscock School of Continuing Studies. Rice students are bound by the strict Honor Code, which is enforced by a uniquely student-run Honor Council.Rice competes in 14 NCAA Division I varsity sports and is a part of Conference USA, often competing with its cross-town rival the University of Houston. Intramural and club sports are offered in a wide variety of activities such as jiu jitsu, water polo, and crew. Wikipedia.

Klimchuk J.A.,NASA | Bradshaw S.J.,Rice University
Astrophysical Journal | Year: 2014

It has been suggested that the hot plasma of the solar corona comes primarily from impulsive heating events, or nanoflares, that occur in the lower atmosphere, either in the upper part of the ordinary chromosphere or at the tips of type II spicules. We test this idea with a series of hydrodynamic simulations. We find that synthetic Fe XII (195) and Fe XIV (274) line profiles generated from the simulations disagree dramatically with actual observations. The integrated line intensities are much too faint; the blueshifts are much too fast; the blue-red asymmetries are much too large; and the emission is confined to low altitudes. We conclude that chromospheric nanoflares are not a primary source of hot coronal plasma. Such events may play an important role in producing the chromosphere and powering its intense radiation, but they do not, in general, raise the temperature of the plasma to coronal values. Those cases where coronal temperatures are reached must be relatively uncommon. The observed profiles of Fe XII and Fe XIV come primarily from plasma that is heated in the corona itself, either by coronal nanoflares or a quasi-steady coronal heating process. Chromospheric nanoflares might play a role in generating waves that provide this coronal heating. © 2014. The American Astronomical Society. All rights reserved.. Source

Bradshaw S.J.,Rice University | Klimchuk J.A.,NASA
Astrophysical Journal, Supplement Series | Year: 2011

The "smoking gun" of small-scale, impulsive events heating the solar corona is expected to be the presence of hot (>5MK) plasma. Evidence for this has been scarce, but has gradually begun to accumulate due to recent studies designed to constrain the high-temperature part of the emission measure distribution. However, the detected hot component is often weaker than models predict and this is due in part to the common modeling assumption that the ionization balance remains in equilibrium. The launch of the latest generation of space-based observing instrumentation on board Hinode and the Solar Dynamics Observatory (SDO) has brought the matter of the ionization state of the plasma firmly to the forefront. It is timely to consider exactly what emission current instruments would detect when observing a corona heated impulsively on small scales by nanoflares. Only after we understand the full effects of nonequilibrium ionization can we draw meaningful conclusions about the plasma that is (or is not) present. We have therefore performed a series of hydrodynamic simulations for a variety of different nanoflare properties and initial conditions. Our study has led to several key conclusions. (1) Deviations from equilibrium are greatest for short-duration nanoflares at low initial coronal densities. (2) Hot emission lines are the most affected and are suppressed sometimes to the point of being invisible. (3) For the many scenarios we have considered, the emission detected in several of the SDO-AIA channels (131, 193, and 211 ) would be dominated by warm, overdense, cooling plasma. (4) It is difficult not to create coronal loops that emit strongly at 1.5MK and in the range 2-6MK, which are the most commonly observed kind, for a broad range of nanoflare scenarios. (5) The Fe XV (284.16 ) emission in most of our models is about 10 times brighter than the Ca XVII (192.82 ) emission, consistent with observations. Our overarching conclusion is that small-scale, impulsive heating inducing a nonequilibrium ionization state leads to predictions for observable quantities that are entirely consistent with what is actually observed. © 2011. The American Astronomical Society. All rights reserved.. Source

Barnes A.S.,Baylor College of Medicine | Kimbro R.T.,Rice University
Journal of General Internal Medicine | Year: 2012

BACKGROUND: Interventions to address obesity and weight loss maintenance among African Americans have yielded modest results. There is limited data on African Americans who have achieved successful longterm weight loss maintenance. OBJECTIVE: To identify a large sample of African American adults who intentionally achieved clinically significant weight loss of 10 %; to describe weight-loss and maintenance efforts of African Americans through a cross-sectional survey; to determine the feasibility of establishing a registry of African American adults who have successfully lost weight. DESIGN, SETTING, AND PARTICIPANTS: African American volunteers from the United States ≥ 18 years of age were invited to complete a cross-sectional survey about weight, weight-loss, weight-loss maintenance or regain. Participants were invited to submit contact information to be maintained in a secure registry. MAIN MEASURES: Percentage of participants who achieved long-term weight-loss maintenance reporting various dietary and physical activity strategies, motivations for and social-cognitive influences on weight loss and maintenance, current eating patterns, and selfmonitoring practices compared to African Americans who lost weight but regained it. Participants also completed the Short International Physical Activity Questionnaire. KEY RESULTS: Of 3,414 individuals screened, 1,280 were eligible and completed surveys. Ninety-percent were women. This descriptive analysis includes 1,110 women who lost weight through non-surgical means. Over 90 % of respondents had at least some college education. Twenty-eight percent of respondents were weight-loss maintainers. Maintainers lost an average of 24 % of their body weight and had maintained ≥ 10 % weight loss for an average of 5.1 years. Maintainers were more likely to limit their fat intake, eat breakfast most days of the week, avoid fast food restaurants, engage in moderate to high levels of physical activity, and use a scale to monitor their weight. CONCLUSIONS: Influences and practices differ among educated African American women who maintain weight loss compared to those who regain it. © Society of General Internal Medicine 2012. Source

Halas N.J.,Rice University | Moskovits M.,University of California at Santa Barbara
MRS Bulletin | Year: 2013

Discovered by Richard Van Duyne in 1976, surface-enhanced Raman spectroscopy (SERS) has enjoyed a continual expansion in interest over the past 36 years benefitting from a series of discoveries, new fields, and technological capabilities, all of which have greatly contributed to the current broad interest in this topic. The focus on nanoscience and nanotechnology that began in the early 1990s naturally put a spotlight on SERS as a quintessentially nanoscale phenomenon. This article discusses some of the key field-shaping developments in SERS from a historical and a materials perspective, providing background for the articles in this issue of MRS Bulletin. Copyright © Materials Research Society 2013. Source

Lee C.T.A.,Rice University | Morton D.M.,University of California at Riverside
Earth and Planetary Science Letters | Year: 2015

High silica (>70 wt.% SiO2) granites (HSGs) are important carriers of highly incompatible elements, thus, understanding their origin is relevant to understanding how the composition of the continental crust evolves. We examined a large-scale geochemical study of plutons in the Peninsular Ranges Batholith in southern California (USA) to better understand the petrogenetic relationships between HSGs and the batholith. Using highly incompatible and compatible elements, we show that HSGs represent residual liquids within a felsic (69-72 wt.% SiO2) magmatic crystal mush at crystal fractions of 50-60% and residual liquid fractions of 40-50%. Trace element systematics show that separation of the HSG liquid from the crystal mush is inefficient, such that no more than 70-80% of the HSG is fully extracted and the remaining greater than 20-30% remains trapped in cumulate mush. We find little evidence of more efficient liquid-crystal segregation, which suggests that compaction-induced segregation may be too slow to be important on a large scale. Instead, the terminal porosity of 20-30% coincides with theoretical maximum packing fraction of unimodal particles settled out of suspension (~0.74), which may indicate that crystal settling - perhaps in the form of hindered settling - drives segregation of viscous silicic melts and crystals. Unlike compaction, settling operates on timescales of 1-10 ky, fast enough to generate large volumes of HSG and complementary cumulates with trapped melt before magma chambers freeze. Many felsic plutons may thus be cumulates, but because of trapped melt, they are difficult to geochemically distinguish from plutons whose compositions fall along liquid lines of descent. The approach here, using a combination of highly incompatible and compatible elements, provides a way of identifying and quantifying trapped melt fractions. Finally, we show that HSGs appear to form only in the shallow crust (<10 km) and rarely in the middle to lower crust. Where HSGs are common, mafic magmas are common too, suggesting a genetic relationship between the two. If HSGs derive by crystal fractionation of basaltic parents, they represent at most 5% of the original mass of parental magma, but because they form almost exclusively at low pressures, they may be over-represented in shallowly exhumed batholiths. Why HSGs form primarily in the upper crust is unclear. © 2014 Elsevier B.V. Source

Yang L.H.,University of California at Davis | Rudolf V.H.W.,Rice University
Ecology Letters | Year: 2010

Climate change is altering the phenology of many species and the timing of their interactions with other species, but the impacts of these phenological shifts on species interactions remain unclear. Classical approaches to the study of phenology have typically documented changes in the timing of single life-history events, while phenological shifts affect many interactions over entire life histories. In this study, we suggest an approach that integrates the phenology and ontogeny of species interactions with a fitness landscape to provide a common mechanistic framework for investigating phenological shifts. We suggest that this ontogeny-phenology landscape provides a flexible method to document changes in the relative phenologies of interacting species, examine the causes of these phenological shifts, and estimate their consequences for interacting species. © 2009 Blackwell Publishing Ltd/CNRS. Source

De Giacomo G.,University of Rome La Sapienza | Vardi M.Y.,Rice University
IJCAI International Joint Conference on Artificial Intelligence | Year: 2013

In this paper we look into the assumption of interpreting LTL over finite traces. In particular we show that LTLf, i.e., LTL under this assumption, is less expressive than what might appear at first sight, and that at essentially no computational cost one can make a significant increase in expressiveness while maintaining the same intuitiveness of LTLf. Indeed, we propose a logic, LDLf for Linear Dynamic Logic over finite traces, which borrows the syntax from Propositional Dynamic Logic (PDL), but is interpreted over finite traces. Satisfiability, validity and logical implication (as well as model checking) for LDLf are PSPACE-complete as for LTLf (and LTL). Source

Hoffmann J.C.,Rice University
Integrative biology : quantitative biosciences from nano to macro | Year: 2013

In order to independently study the numerous variables that influence cell movement, it will be necessary to employ novel tools and materials that allow for exquisite control of the cellular microenvironment. In this work, we have applied advanced 3D micropatterning technology, known as two-photon laser scanning lithography (TP-LSL), to poly(ethylene glycol) (PEG) hydrogels modified with bioactive peptides in order to fabricate precisely designed microenvironments to guide and quantitatively investigate cell migration. Specifically, TP-LSL was used to fabricate cell adhesive PEG-RGDS micropatterns on the surface of non-degradable PEG-based hydrogels (2D) and in the interior of proteolytically degradable PEG-based hydrogels (3D). HT1080 cell migration was guided down these adhesive micropatterns in both 2D and 3D, as observed via time-lapse microscopy. Differences in cell speed, cell persistence, and cell shape were observed based on variation of adhesive ligand, hydrogel composition, and patterned area for both 2D and 3D migration. Results indicated that HT1080s migrate faster and with lower persistence on 2D surfaces, while HT1080s migrating in 3D were smaller and more elongated. Further, cell migration was shown to have a biphasic dependence on PEG-RGDS concentration and cells moving within PEG-RGDS micropatterns were seen to move faster and with more persistence over time. Importantly, the work presented here begins to elucidate the multiple complex factors involved in cell migration, with typical confounding factors being independently controlled. The development of this unique platform will allow researchers to probe how cells behave within increasingly complex 3D microenvironments that begin to mimic specifically chosen aspects of the in vivo landscape. Source

Wickham H.,Rice University
Journal of Statistical Software | Year: 2011

Many data analysis problems involve the application of a split-apply-combine strategy, where you break up a big problem into manageable pieces, operate on each piece inde- pendently and then put all the pieces back together. This insight gives rise to a new R package that allows you to smoothly apply this strategy, without having to worry about the type of structure in which your data is stored. The paper includes two case studies showing how these insights make it easier to work with batting records for veteran baseball players and a large 3d array of spatio-temporal ozone measurements. Source

Ouyang M.,Huazhong University of Science and Technology | Duenas-Osorio L.,Rice University
Structural Safety | Year: 2014

Electric power systems are critical to economic prosperity, national security, public health and safety. However, in hurricane-prone areas, a severe storm may simultaneously cause extensive component failures in a power system and lead to cascading failures within it and across other power-dependent utility systems. Hence, the hurricane resilience of power systems is crucial to ensure their rapid recovery and support the needs of the population in disaster areas. This paper introduces a probabilistic modeling approach for quantifying the hurricane resilience of contemporary electric power systems. This approach includes a hurricane hazard model, component fragility models, a power system performance model, and a system restoration model. These coupled four models enable quantifying hurricane resilience and estimating economic losses. Taking as an example the power system in Harris County, Texas, USA, along with real outage and restoration data after Hurricane Ike in 2008, the proposed resilience assessment model is calibrated and verified. In addition, several dimensions of resilience as well as the effectiveness of alternative strategies for resilience improvement are simulated and analyzed. Results show that among technical, organizational and social dimensions of resilience, the organizational resilience is the highest with a value of 99.964% (3.445 in a proposed logarithmic scale) while the social resilience is the lowest with a value of 99.760% (2.620 in the logarithmic scale). Although these values seem high in absolute terms due to the reliability of engineered systems, the consequences of departing from ideal resilience are still high as economic losses can add up to $83 million per year. © 2014 Elsevier Ltd. Source

Whitney K.D.,Rice University | Randell R.A.,Indiana University Bloomington | Rieseberg L.H.,University of British Columbia
New Phytologist | Year: 2010

Summary: •Adaptive trait introgression is increasingly recognized as common. However, it is unclear whether adaptive genetic exchanges typically affect only a single trait, or instead affect multiple aspects of the phenotype. Here, we examine introgression of abiotic tolerance traits between two hybridizing North American sunflower species, Helianthus annuus and Helianthus debilis.•In two common gardens in the hybrid range, we measured 10 ecophysiological, phenological, and architectural traits for parents and their natural and artificial hybrids, and examined how fitness covaried with trait values.•Eight of the 10 traits showed patterns consistent with introgression from H. debilis into H. annuus, and suggested that H. debilis-like traits allowing rapid growth and reproduction before summer heat and drought have been favored in the hybrid range. Natural selection currently favors BC1 hybrids with H. debilis-like branching traits.•We demonstrate that introgression has altered multiple aspects of the H. annuus phenotype in an adaptive manner, has affected traits relevant to both biotic and abiotic environments, and may have aided expansion of the H. annuus range into central Texas, USA. © The Authors (2010). Journal compilation © New Phytologist Trust (2010). Source

Yu R.,Renmin University of China | Yu R.,Shanghai JiaoTong University | Si Q.,Rice University
Physical Review Letters | Year: 2015

Motivated by the properties of the iron chalcogenides, we study the phase diagram of a generalized Heisenberg model with frustrated bilinear-biquadratic interactions on a square lattice. We identify zero-temperature phases with antiferroquadrupolar and Ising-nematic orders. The effects of quantum fluctuations and interlayer couplings are analyzed. We propose the Ising-nematic order as underlying the structural phase transition observed in the normal state of FeSe, and discuss the role of the Goldstone modes of the antiferroquadrupolar order for the dipolar magnetic fluctuations in this system. Our results provide a considerably broadened perspective on the overall magnetic phase diagram of the iron chalcogenides and pnictides, and are amenable to tests by new experiments. © 2015 American Physical Society. Source

Karl N.J.,Rice University
Nature Photonics | Year: 2015

The idea of using radiation in the 0.1–1.0 THz range as carrier waves for free-space wireless communications has attracted growing interest in recent years, due to the promise of the large available bandwidth. Recent research has focused on system demonstrations, as well as the exploration of new components for modulation, beam steering and polarization control. However, the multiplexing and demultiplexing of terahertz signals remains an unaddressed challenge, despite the importance of such capabilities for broadband networks. Using a leaky-wave antenna based on a metal parallel-plate waveguide, we demonstrate frequency-division multiplexing and demultiplexing over more than one octave of bandwidth. We show that this device architecture offers a unique method for controlling the spectrum allocation, by variation of the waveguide plate separation. This strategy, which is distinct from those previously employed in either the microwave or optical regimes, enables independent control of both the centre frequency and bandwidth of multiplexed terahertz channels. © 2015 Nature Publishing Group Source

Manjavacas A.,CSIC - Institute of Optics | Abajo F.J.G.D.,CSIC - Institute of Optics | Nordlander P.,Rice University
Nano Letters | Year: 2011

We present a fully quantum mechanical approach to describe the coupling between plasmons and excitonic systems such as molecules or quantum dots. The formalism relies on Zubarev's Green functions, which allow us to go beyond the perturbative regime within the internal evolution of a plasmonic nanostructure and to fully account for quantum aspects of the optical response and Fano resonances in plasmon - excition (plexcitonic) systems. We illustrate this method with two examples consisting of an exciton-supporting quantum emitter placed either in the vicinity of a single metal nanoparticle or in the gap of a nanoparticle dimer. The optical absorption of the combined emitter - dimer structure is shown to undergo dramatic changes when the emitter excitation level is tuned across the gap-plasmon resonance. Our work opens a new avenue to deal with strongly interacting plasmon - excition hybrid systems. © 2011 American Chemical Society. Source

Cech E.A.,Rice University
Science Technology and Human Values | Year: 2014

Much has been made of the importance of training ethical, socially conscious engineers, but does US engineering education actually encourage neophytes to take seriously their professional responsibility to public welfare? Counter to such ideals of engagement, I argue that students' interest in public welfare concerns may actually decline over the course of their engineering education. Using unique longitudinal survey data of students at four colleges, this article examines (a) how students' public welfare beliefs change during their engineering education, (b) whether engineering programs emphasize engagement, and (c) whether these program emphases are related to students' public welfare beliefs. I track four specific public welfare considerations: the importance to students of professional/ethical responsibilities, understanding the consequences of technology, understanding how people use machines, and social consciousness. Suggesting a culture of disengagement, I find that the cultural emphases of students' engineering programs are directly related to their public welfare commitments and students' public welfare concerns decline significantly over the course of their engineering education. However, these findings also suggest that if engineering programs can dismantle the ideological pillars of disengagement in their local climates, they may foster more engaged engineers. © The Author(s) 2013. Source

Goldman R.,Rice University
Graphical Models | Year: 2011

Quaternion multiplication can be applied to rotate vectors in 3-dimensions. Therefore in Computer Graphics, quaternions are sometimes used in place of matrices to represent rotations in 3-dimensions. Yet while the formal algebra of quaternions is well-known in the Graphics community, the derivations of the formulas for this algebra and the geometric principles underlying this algebra are not well understood. The goals of this paper are: To provide a fresh, geometric interpretation of quaternions, appropriate for contemporary Computer Graphics;To derive the formula for quaternion multiplication from first principles;To present better ways to visualize quaternions, and the effect of quaternion multiplication on points and vectors in 3-dimensions based on insights from the algebra and geometry of multiplication in the complex plane;To develop simple, intuitive proofs of the sandwiching formulas for rotation and reflection;To show how to apply sandwiching to compute perspective projections. In Part I of this paper, we investigate the algebra of quaternion multiplication and focus in particular on topics i and ii. In Part II we apply our insights from Part I to analyze the geometry of quaternion multiplication with special emphasis on topics iii, iv and v. © 2010 Elsevier Inc. All rights reserved. Source

Kushwaha M.S.,Rice University
Applied Physics Letters | Year: 2013

We investigate a two-component, cylindrical, quasi-one-dimensional quantum plasma subjected to a radial confining harmonic potential and an applied magnetic field in the symmetric gauge. It is demonstrated that such a system as can be realized in semiconducting quantum wires offers an excellent medium for observing the quantum pinch effect at low temperatures. An exact analytical solution of the problem allows us to make significant observations: surprisingly, in contrast to the classical pinch effect, the particle density as well as the current density displays a determinable maximum before attaining a minimum at the surface of the quantum wire. The effect will persist as long as the equilibrium pair density is sustained. Therefore, the technological promise that emerges is the route to the precise electronic devices that will control the particle beams at the nanoscale. © 2013 AIP Publishing LLC. Source

Schmidt T.L.,Yale University | Imambekov A.,Rice University | Glazman L.I.,Yale University
Physical Review Letters | Year: 2010

We consider the dynamic response functions of interacting one dimensional spin-12 fermions at arbitrary momenta. We build a nonperturbative zero-temperature theory of the threshold singularities using mobile impurity Hamiltonians. The interaction induced low-energy spin-charge separation and power-law threshold singularities survive away from Fermi points. We express the threshold exponents in terms of the spinon spectrum. © 2010 The American Physical Society. Source

Halas N.J.,Rice University
Nano Letters | Year: 2010

While studies of surface plasmons on metals have been pursued for decades, the more recent appearance of nanoscience has created a revolution in this field with "Plasmonics" emerging as a major area of research. The direct optical excitation of surface plasmons on metallic nanostructures provides numerous ways to control and manipulate light at nanoscale dimensions. This has stimulated the development of novel optical materials, deeper theoretical insight, innovative new devices, and applications with potential for significant technological and societal impact. Nano Letters has been instrumental in the emergence of plasmonics, providing its readership with rapid advances in this dynamic field. © 2010 American Chemical Society. Source

Miller J.S.,Rice University
PLoS Biology | Year: 2014

How structure relates to function-across spatial scales, from the single molecule to the whole organism-is a central theme in biology. Bioengineers, however, wrestle with the converse question: will function follow form? That is, we struggle to approximate the architecture of living tissues experimentally, hoping that the structure we create will lead to the function we desire. A new means to explore the relationship between form and function in living tissue has arrived with three-dimensional printing, but the technology is not without limitations. © 2014 Jordan S. Source

Kougioumtzoglou I.A.,University of Liverpool | Spanos P.D.,Rice University
Mechanical Systems and Signal Processing | Year: 2013

A novel identification approach for linear and nonlinear time-variant systems subject to non-stationary excitations based on the localization properties of the harmonic wavelet transform is developed. Specifically, a single-input/single-output (SISO) structural system model is transformed into an equivalent multiple-input/single-output (MISO) system in the wavelet domain. Next, time and frequency dependent generalized harmonic wavelet based frequency response functions (GHW-FRFs) are appropriately defined. Finally, measured (non-stationary) input-output (excitation-response) data are utilized to identify the unknown GHW-FRFs and related system parameters. The developed approach can be viewed as a generalization of the well established reverse MISO spectral identification approach to account for non-stationary inputs and time-varying system parameters. Several linear and nonlinear time-variant systems are used to demonstrate the reliability of the approach. The approach is found to perform satisfactorily even in the case of noise-corrupted data. © 2013 Elsevier Ltd. Source

Kougioumtzoglou I.A.,University of Liverpool | Spanos P.D.,Rice University
Computers and Structures | Year: 2013

An approximate analytical dimension reduction approach is developed for determining the response of a multi-degree-of-freedom (MDOF) nonlinear/hysteretic system subject to a non-stationary stochastic excitation vector. The approach is based on the concepts of statistical linearization and of stochastic averaging. It is readily applicable even for excitations possessing evolutionary in time power spectra. Further, it can be potentially used in conjunction with design spectrum based analyses to obtain peak system response estimates. Numerical examples include MDOF systems comprising the versatile Bouc-Wen (hysteretic) model. The reliability of the approach is demonstrated by pertinent Monte Carlo simulations. © 2012 Elsevier Ltd. Source

Xu Y.,Rice University
Mathematical Programming Computation | Year: 2015

Multi-way data arises in many applications such as electroencephalography classification, face recognition, text mining and hyperspectral data analysis. Tensor decomposition has been commonly used to find the hidden factors and elicit the intrinsic structures of the multi-way data. This paper considers sparse nonnegative Tucker decomposition (NTD), which is to decompose a given tensor into the product of a core tensor and several factor matrices with sparsity and nonnegativity constraints. An alternating proximal gradient method is applied to solve the problem. The algorithm is then modified to sparse NTD with missing values. Per-iteration cost of the algorithm is estimated scalable about the data size, and global convergence is established under fairly loose conditions. Numerical experiments on both synthetic and real world data demonstrate its superiority over a few state-of-the-art methods for (sparse) NTD from partial and/or full observations. The MATLAB code along with demos are accessible from the author’s homepage. © 2014, Springer-Verlag Berlin Heidelberg and Mathematical Optimization Society. Source

Stevenson P.M.,Rice University
Nuclear Physics B | Year: 2013

Physical quantities in QCD are independent of renormalization scheme (RS), but that exact invariance is spoiled by truncations of the perturbation series. "Optimization" corresponds to making the perturbative approximant, at any given order, locally invariant under small RS changes. A solution of the resulting optimization equations is presented. It allows an efficient algorithm for finding the optimized result. Example results for Re+e-=3∑qi2(1+R) to fourth order (NNNLO) are given that show nice convergence, even down to arbitrarily low energies. The Q=. 0 "freezing" behavior, R=0.3±0.3, found at third order is confirmed and made more precise; R=0.2±0.1. Low-energy results in the MS- scheme, by contrast, show the typical pathologies of a non-convergent asymptotic series. © 2012 Elsevier B.V. Source

Stevenson P.M.,Rice University
Nuclear Physics B | Year: 2013

Perturbative QCD, when optimized by the principle of minimal sensitivity at fourth order, yields finite results for Re+e-(Q) down to Q=0. For two massless flavors (nf=2) this occurs because the couplant "freezes" at a fixed-point of the optimized β function. However, for larger nf's, between 6.7 and 15.2, the infrared limit arises by a novel mechanism in which the evolution of the optimized β function with energy Q is crucial. The evolving β function develops a minimum that, as Q→0, just touches the axis at ap (the "pinch point"), while the infrared limit of the optimized couplant is at a larger value, a{star operator} (the "unfixed point"). This phenomenon results in R approaching its infrared limit not as a power law, but as R→R{star operator}-const/|lnQ|2. Implications for the phase structure of QCD as a function of nf are briefly considered. © 2013 Elsevier B.V. Source

Studer C.,Rice University | Larsson E.G.,Linkoping University
IEEE Journal on Selected Areas in Communications | Year: 2013

We investigate an orthogonal frequency-division multiplexing (OFDM)-based downlink transmission scheme for large-scale multi-user (MU) multiple-input multiple-output (MIMO) wireless systems. The use of OFDM causes a high peak-to-average (power) ratio (PAR), which necessitates expensive and power-inefficient radio-frequency (RF) components at the base station. In this paper, we present a novel downlink transmission scheme, which exploits the massive degrees-of-freedom available in large-scale MU-MIMO-OFDM systems to achieve low PAR. Specifically, we propose to jointly perform MU precoding, OFDM modulation, and PAR reduction by solving a convex optimization problem. We develop a corresponding fast iterative truncation algorithm (FITRA) and show numerical results to demonstrate tremendous PAR-reduction capabilities. The significantly reduced linearity requirements eventually enable the use of low-cost RF components for the large-scale MU-MIMO-OFDM downlink. © 2012 IEEE. Source

Gilbert O.M.,Rice University
Proceedings. Biological sciences / The Royal Society | Year: 2012

A major challenge for social theory is to explain the importance of kin discrimination for the evolution of altruism. One way to assess the importance of kin discrimination is to test its effects on increasing relatedness within groups. The social amoeba Dictyostelium discoideum aggregates to form a fruiting body composed of dead stalk and live spores. Previous studies of a natural population showed that where D. discoideum occurs in the soil, multiple clones are often found in the same small soil samples. However, actual fruiting bodies usually contain only one clone. We here performed experiments to gauge the effect of kin-discriminatory segregation on increasing relatedness. We mixed co-occurring clones from this population using a relatedness level found in small soil samples. We found a lower proportion of uniclonal fruiting bodies and a lower level of relatedness compared with natural fruiting bodies. We found that the amount of relatedness increase attributable to kin-discriminatory segregation was small. These findings suggest a relatively minor influence of kin-discriminatory segregation on relatedness in D. discoideum. We discuss our results comparing with the results of previous studies, including those of wild clones and laboratory mutants. We ask why wild clones of D. discoideum exhibit a low degree of kin-discriminatory segregation, and what alternative factors might account for high relatedness in D. discoideum. Source

Rahmati A.,Broadcom Corporation | Zhong L.,Rice University
IEEE Transactions on Mobile Computing | Year: 2013

Many emerging mobile applications and services are based on smartphones. We have performed a four-month field study of the adoption and usage of smartphone-based services by 14 novice teenage users. From the field study, we present the application usage and usage characteristics of our participants. We show that their usage is highly mobile, location-dependent, and serves multiple social purposes. Furthermore, we report qualitative lessons regarding the evaluation of smartphone-based services. In particular, we highlight the cases that an accurate evaluation would require a long-term and/or field study instead of a short or lab-based study, and the cases where studying a particular application independently is insufficient and a holistic study, i.e., involving the whole device, is necessary. We further present guidelines on effectively shortening the length of a study. These lessons are supported in part by five identified contributing factors to usage evolution. © 2002-2012 IEEE. Source

Hotez P.J.,Baylor College of Medicine | Hotez P.J.,The Texas Institute | Hotez P.J.,Rice University
PLoS Neglected Tropical Diseases | Year: 2013

The concept of the neglected tropical diseases (NTDs) was established in the aftermath of the Millennium Development Goals. Here, we summarize the emergence of several new post-2010 global health documents and policies, and how they may alter the way we frame the world's major NTDs since they were first highlighted. These documents include a new Global Burden of Disease 2010 Study that identifies visceral leishmaniasis and food-borne trematode infections as priority diseases beyond the seven NTDs originally targeted by preventive chemotherapy, a London Declaration for access to essential medicines, and a 2013 World Health Assembly resolution on NTDs. Additional information highlights an emerging dengue fever pandemic. New United Nations resolutions on women and the non-communicable diseases (NCDs) have not yet embraced NTDs, which may actually be the most common afflictions of girls and women and represent a stealth cause of NCDs. NTDs also have important direct and collateral effects on HIV/AIDS and malaria, and there is now a robust evidence base and rationale for incorporating NTDs into the Global Fund to Fight AIDS, Tuberculosis, and Malaria. "Blue marble health" is an added concept that recognizes a paradoxical NTD disease burden among the poor living in G20 (Group of Twenty) and other wealthy countries, requiring these nations to take greater ownership for both disease control and research and development. As we advance past the year 2015, it will be essential to incorporate global NTD elimination into newly proposed Sustainable Development Goals. © 2013 Peter J. Hotez. Source

Tour J.M.,Rice University
Chemistry of Materials | Year: 2014

Graphene electronic devices can be made by top-down (TD) or bottom-up (BU) approaches. This Perspective defines and explains those two approaches and discusses the advantages and limitations of each, particularly in the context of graphene fabrication. It is further exemplified using graphene nanoribbons as the prototypical graphene structure that can be prepared using either a TD or BU approach. The TD approach is well-suited for placement of large arrays of devices on a chip using standard patterning tools. However, the TD approach severely compromises the edges of the graphene since present fabrication tools are coarse relative to the ∼0.1 nm definition of a C-C bond. The BU approach can afford exquisite control of the graphene edges; however, placing the structures, en mass, in the locations of interest is often impossible. Also, using the BU approach, it can be very difficult to make device structures long enough for integration with TD-derived probe electrodes. Specific examples are shown, along with an outlook for optimization of future graphene devices in order to capitalize upon the advantages of both TD and BU fabrication methodologies. © 2013 American Chemical Society. Source

Jiang L.,California Institute of Technology | Imambekov A.,Rice University
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2011

We study the dynamical decoupling of multiqubit states from environment. For a system of m qubits, the nested Uhrig dynamical decoupling (NUDD) sequence can efficiently suppress generic decoherence induced by the system-environment interaction to order N using (N +1 )2m pulses. We prove that the NUDD sequence is universal, i.e., it can restore the coherence of an m-qubit quantum system independent of the details of the system-environment interaction. We also construct a general mapping between dynamical decoupling problems and discrete quantum walks in certain functional spaces. © 2011 American Physical Society. Source

Alvarez-Puebla R.A.,University of Vigo | Zubarev E.R.,Rice University | Kotov N.A.,University of Michigan | Liz-Marzan L.M.,University of Vigo
Nano Today | Year: 2012

The fabrication of highly optically active supercrystals of anisotropic nanorods exploiting the electric field concentration and the nanoantenna effects provides a new family of optical sensors with the potential to maximize the SERS signal and thereby the possibility of detecting and quantifying the disease markers with low SERS cross-sections at ultralow concentrations. The capabilities of the new self-assembled nanorod SERS substrates have been demonstrated for real-time sensing of prions in real blood. It may also be possible to functionalize the top layers of supercrystals with specific recognition molecules for sensing many other disease markers, or even its integration into on-line devices, for the ultrasensitive screening of analytical targets relevant to medical science, environment, and homeland security. © 2011 Elsevier Ltd. All rights reserved. Source

Jia L.,Massachusetts Institute of Technology | Thomas E.L.,Rice University
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2011

We present a set of two-dimensional aperiodic structures with a large complete photonic band gap (PBG), which are named two-pattern photonic crystals. By superposing two substructures without regard to registration, we designed six new aperiodic PBG structures having a complete PBG larger than 15% for ε2/ε2ε1ε1=11.4. The rod-honeycomb two-pattern photonic crystal provides the largest complete PBG to date. An aperiodic structure becomes the champion structure with the largest PBG. Surprisingly, the TM and TE gaps of a two-pattern photonic crystal are much less interdependent than the PBGs of conventional photonic crystals proposed before, affording interesting capabilities for us to tune the TM and TE PBGs separately. By altering the respective substructures, optical devices for different polarizations (TE, TM, or both) can readily be designed. © 2011 American Physical Society. Source

He X.,Rice University
Nature Nanotechnology | Year: 2016

The one-dimensional character of electrons, phonons and excitons in individual single-walled carbon nanotubes leads to extremely anisotropic electronic, thermal and optical properties. However, despite significant efforts to develop ways to produce large-scale architectures of aligned nanotubes, macroscopic manifestations of such properties remain limited. Here, we show that large (>cm2) monodomain films of aligned single-walled carbon nanotubes can be prepared using slow vacuum filtration. The produced films are globally aligned within ±1.5° (a nematic order parameter of ∼1) and are highly packed, containing 1 × 106 nanotubes in a cross-sectional area of 1 μm2. The method works for nanotubes synthesized by various methods, and film thickness is controllable from a few nanometres to ∼100 nm. We use the approach to create ideal polarizers in the terahertz frequency range and, by combining the method with recently developed sorting techniques, highly aligned and chirality-enriched nanotube thin-film devices. Semiconductor-enriched devices exhibit polarized light emission and polarization-dependent photocurrent, as well as anisotropic conductivities and transistor action with high on/off ratios. © 2016 Nature Publishing Group Source

Yeung L.Y.,Rice University
Geochimica et Cosmochimica Acta | Year: 2016

The arrangement of isotopes within a collection of molecules records their physical and chemical histories. Clumped-isotope analysis interrogates these arrangements, i.e., how often rare isotopes are bound together, which in many cases can be explained by equilibrium and/or kinetic isotope fractionation. However, purely combinatorial effects, rooted in the statistics of pairing atoms in a closed system, are also relevant, and not well understood. Here, I show that combinatorial isotope effects are most important when two identical atoms are neighbors on the same molecule (e.g., O2, N2, and D-D clumping in CH4). When the two halves of an atom pair are either assembled with different isotopic preferences or drawn from different reservoirs, combinatorial effects cause depletions in clumped-isotope abundance that are most likely between zero and -1‰, although they could potentially be -10‰ or larger for D-D pairs. These depletions are of similar magnitude, but of opposite sign, to low-temperature equilibrium clumped-isotope effects for many small molecules. Enzymatic isotope-pairing reactions, which can have site-specific isotopic fractionation factors and atom reservoirs, should express this class of combinatorial isotope effect, although it is not limited to biological reactions. Chemical-kinetic isotope effects, which are related to a bond-forming transition state, arise independently and express second-order combinatorial effects related to the abundance of the rare isotope. Heteronuclear moeties (e.g., CO and CH), are insensitive to direct combinatorial influences, but secondary combinatorial influences are evident. In general, both combinatorial and chemical-kinetic factors are important for calculating and interpreting clumped-isotope signatures of kinetically controlled reactions. I apply this analytical framework to isotope-pairing reactions relevant to geochemical oxygen, carbon, and nitrogen cycling that may be influenced by combinatorial clumped-isotope effects. These isotopic signatures, manifest as either directly bound isotope "clumps" or as features of a molecule's isotopic anatomy, are linked to molecular mechanisms and may eventually provide additional information about biogeochemical cycling on environmentally relevant spatial scales. © 2015 Elsevier Ltd. Source

Gopal A.,University of Maryland University College | Koka B.R.,Rice University
MIS Quarterly: Management Information Systems | Year: 2012

In this paper, the interacting effect of formal contracts and relational governance on vendor profitability and quality in the software outsourcing industry are examined. We focus on a critical manifestation of relational governance-The presence of relational flexibility in the exchange relationship-and argue that the enacted observation of relational flexibility is driven by perceptions of exchange hazards. In a departure from extant literature, however, we propose that the benefits accruing from it are asymmetric and depend on how the exchange risks are apportioned by the formal contract. Formally, we hypothesize that relational flexibility provides greater benefits to an exchange partner that faces the greater proportion of risk in a project, induced through the contract. In addition, we hypothesize that these benefits manifest on the performance dimensions that are of importance to the risk-exposed partner. We test our hypotheses on 105 software projects completed by a software outsourcing vendor for multiple clients. The results show that relational flexibility positively affects profitability in only fixed price contracts, where the vendor faces greater risk, while positively affecting quality only in time and materials contracts, where the client is at greater risk. We thus provide evidence for the asymmetric benefits from relational governance, thereby arguing for a more contingent and limited view of the value of relational governance, based on risk-exposure, rather than the more expansive view prevalent in the literature contending that relational governance provides benefits for all parties to an exchange. We conclude with a discussion of the research and managerial implications of our findings. Source

Marti A.A.,Rice University | Colon J.L.,University of Puerto Rico at San Juan
Inorganic Chemistry | Year: 2010

We studied the structures, luminescence, and self-quenching properties of tris(2,2′-bipyridyl)ruthenium(II) (Ru(bpy)32+) two-dimensional arrangements within the layers of zirconium phosphate (ZrP). The intercalation of Ru(bpy)32+ was accomplished using a hydrated form of zirconium phosphate ZrP. Varying the Ru(bpy)32+/ZrP intercalation ratio, different Ru(bpy)32+-exchanged ZrP loading levels were achieved. The ion exchange of Ru(bpy)32+ within ZrP produces a red shift in the metal-to-ligand charge-transfer (MLCT) absorption band of the complex from 452 nm in aqueous solution to 460 nm in ZrP. Steady state luminescence spectra of the Ru(bpy)32+-exchanged ZrP materials show an increase in the luminescence intensity with an increase in the Ru(bpy)32+ loading level until about 0.77 M, where subsequent increases in the loading level produce a decrease in the luminescence (self-quenching region). Time-resolved luminescence measurements are consistent with the steady state luminescence measurements. Analysis of the time domain luminescence measurements in loadings higher than 0.77 M leads to the determination of a collisional quenching rate constant of (1.67 ± 0.05) -106 M-1 s-1. Stern-Volmer analysis of the luminescence quantum yield of Ru(bpy)32+-exchanged ZrP materials indicates that static quenching is also involved in the Ru(bpy)32+ self-quenching mechanism. The quantum yield data behavior might be explained by a model that takes into account collisional quenching and the quasi-static Perrin mechanism. The calculation yields a quenching sphere of action of 14.8 Å, which is slightly larger than the collisional radii of two Ru(bpy) 32+ ions (12.2 Å), as predicted by the model. © 2010 American Chemical Society. Source

Sanchez-Adams J.,Rice University | Athanasiou K.A.,University of California at Davis
Biomaterials | Year: 2012

Adult stem cells from the dermal layer of skin are an attractive alternative to primary cells for meniscus engineering, as they may be easily obtained and used autologously. Recently, chondroinducible dermis cells from caprine skin have shown promising characteristics for cartilage tissue engineering. In this study, their multilineage differentiation capacity is determined, and methods of expanding and tissue engineering these cells are investigated. It was found that these cells could differentiate along adipogenic, osteogenic, and chondrogenic lineages, allowing them to be termed dermis isolated adult stem cells (DIAS cells). Focusing on cartilage tissue engineering, it was found that passaging these cells in chondrogenic medium and forming them into self-assembled tissue engineered constructs caused upregulation of collagen type II and COMP gene expression. Further investigation showed that applying transforming growth factor β1 (TGF-β1) or bone morphogenetic protein 2 (BMP-2) to DIAS constructs caused increased sulfated glycosaminoglycan content. Additionally, TGF-β1 treatment caused significant increases in compressive properties and construct contraction. In contrast, BMP-2 treatment resulted in the largest constructs, but did not increase compressive properties. These results show that DIAS cells can be easily manipulated for cartilage tissue engineering strategies, and may also be a useful cell source for other mesenchymal tissues. © 2011 Elsevier Ltd. Source

Koushanfar F.,Rice University
Proceedings of the ACM Great Lakes Symposium on VLSI, GLSVLSI | Year: 2011

Almost all of today's security systems rely on cryptographic primitives as core components which are usually considered the most trusted part of the system. The realization of these primitives on the underlying processing platform plays a crucial role for any real-world deployment. In this work, we discuss new trends in public-key cryptography that could potentially establish as alternatives to the currently used RSA and ECC cryptosystems. Analyzing these trends from a developer's perspective, we identify the requirements for optimal processing architectures. Moreover, we investigate if these requirements are already satisfied with latest processing platforms, i.e., which of the streaming, hybrid, multi-core or application-specific instructions processors provide a most promising target architecture. Copyright © 2011 by ASME. Source

Yang H.,Rice University | Johns-Krull C.M.,University of Colorado at Boulder
Astrophysical Journal | Year: 2011

We present an analysis of high-resolution (R 50, 000) infrared K-band echelle spectra of 14 T Tauri stars (TTSs) in the Orion Nebula Cluster. We model Zeeman broadening in three magnetically sensitive Ti I lines near 2.2 μm and consistently detect kilogauss-level magnetic fields in the stellar photospheres. The data are consistent in each case with the entire stellar surface being covered with magnetic fields, suggesting that magnetic pressure likely dominates over gas pressure in the photospheres of these stars. These very strong magnetic fields might themselves be responsible for the underproduction of X-ray emission of TTSs relative to what is expected based on main-sequence star calibrations. We combine these results with previous measurements of 14 stars in Taurus and 5 stars in the TW Hydrae association to study the potential variation of magnetic field properties during the first 10 million years of stellar evolution, finding a steady decline in total magnetic flux with age. © 2011. The American Astronomical Society. All rights reserved. Source

Rao R.,Air Force Research Lab | Rao R.,Honda Research Institute United States Inc. | Liptak D.,Air Force Research Lab | Liptak D.,UES, Inc. | And 3 more authors.
Nature Materials | Year: 2012

Chiral-selective growth of single-walled carbon nanotubes (SWNTs) remains a great challenge that hinders their use in applications such as electronics and medicine. Recent experimental and theoretical reports have begun to address this problem by suggesting that selectivity may be achieved during nucleation by changing the catalyst composition or structure. Nevertheless, to establish a rational basis for chiral-selective synthesis, the underlying mechanisms governing nucleation, growth, and termination of SWNTs must be better understood. To this end, we report the first measurements of growth rates of individual SWNTs through in situ Raman spectroscopy and correlate them with their chiral angles. Our results show that the growth rates are directly proportional to the chiral angles, in agreement with recent theoretical predictions. Importantly, the evidence singles out the growth stage as responsible for the chiral distribution-distinct from nucleation and termination which might also affect the final product distribution. Our results suggest a route to chiral-selective synthesis of SWNTs through rational synthetic design strategies based on kinetic control. © 2012 Macmillan Publishers Limited. All rights reserved. Source

Zhu H.,Rice University
Nanotechnology | Year: 2010

Methods for synthesizing quantum dots generally rely on very high temperatures to both nucleate and grow core and core-shell semiconductor nanocrystals. In this work, we generate highly monodisperse ZnS and CdZnS shells on CdSe semiconductor nanocrystals at temperatures as low as 65 degrees C by enhancing the precursor solubility. Relatively small amounts of trioctylphosphine and trioctylphosphine oxide have marked effects on the solubility of the metal salts used to form shells; their inclusion in the precursor solutions, which use thiourea as a sulfur source, can lead to homogeneous and fully dissolved solutions. Upon addition to suspensions of quantum dot cores, these precursors deposit as uniform shells; the lowest temperature for shell growth (65 degrees C) yields the thinnest shells (d < 1 nm) while the same process at higher temperatures (180 degrees C) forms thicker shells (d approximately 1-2 nm). The growth of the shell structures, average particle size, size distribution, and shape were examined using optical spectroscopy, transmission electron microscopy, x-ray diffraction, and transmittance small angle x-ray scattering. The photoluminescence quantum yield (QY) of the as-prepared CdSe/ZnS quantum dots ranged from 26% to 46% as compared to 10% for the CdSe cores. This method was further generalized to CdZnS shells by mixing cadmium and zinc acetate precursors. The CdSe/CdZnS nanocrystals have a thicker shell and higher QY (40% versus 36%) as compared to the CdSe/ZnS prepared under similar conditions. These low temperature methods for shell growth are readily amenable to scale-up and can provide a route for economical and less energy intensive production of quantum dots. Source

Moghaddasie B.,Ferdowsi University of Mashhad | Stanciulescu I.,Rice University
International Journal of Non-Linear Mechanics | Year: 2013

The structural behaviour of shallow arches is complex and can be influenced by many parameters. In this paper, the response of a half-sine shallow arch under static loading in a thermal environment is investigated. The arch has pinned supports and the material behaviour is assumed elastic. The exact displacement field, load-bearing capacity and the locus of critical points are obtained. Boundaries of domains with different stability behaviours (e.g., different number of limit and bifurcation points) are also determined. Three types of loading (concentrated, uniform and asymmetrical uniform) are examined. The primary equilibrium paths are verified against results obtained from finite element simulations. The proposed method is robust and accurate. © 2013 Elsevier Ltd. Source

Liao X.,Rice University | Rong S.,Washington University in St. Louis | Queller D.C.,Washington University in St. Louis
PLoS Biology | Year: 2015

The evolution of sterile worker castes in eusocial insects was a major problem in evolutionary theory until Hamilton developed a method called inclusive fitness. He used it to show that sterile castes could evolve via kin selection, in which a gene for altruistic sterility is favored when the altruism sufficiently benefits relatives carrying the gene. Inclusive fitness theory is well supported empirically and has been applied to many other areas, but a recent paper argued that the general method of inclusive fitness was wrong and advocated an alternative population genetic method. The claim of these authors was bolstered by a new model of the evolution of eusociality with novel conclusions that appeared to overturn some major results from inclusive fitness. Here we report an expanded examination of this kind of model for the evolution of eusociality and show that all three of its apparently novel conclusions are essentially false. Contrary to their claims, genetic relatedness is important and causal, workers are agents that can evolve to be in conflict with the queen, and eusociality is not so difficult to evolve. The misleading conclusions all resulted not from incorrect math but from overgeneralizing from narrow assumptions or parameter values. For example, all of their models implicitly assumed high relatedness, but modifying the model to allow lower relatedness shows that relatedness is essential and causal in the evolution of eusociality. Their modeling strategy, properly applied, actually confirms major insights of inclusive fitness studies of kin selection. This broad agreement of different models shows that social evolution theory, rather than being in turmoil, is supported by multiple theoretical approaches. It also suggests that extensive prior work using inclusive fitness, from microbial interactions to human evolution, should be considered robust unless shown otherwise. © 2015 Liao et al. Source

Ferreiro D.U.,CONICET | Komives E.A.,University of California at San Diego | Wolynes P.G.,Rice University
Quarterly Reviews of Biophysics | Year: 2014

Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their own structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of frustration in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and especially how biomolecular structure connects to function by means of localized frustration. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding mechanisms. We review here how the biological functions of proteins are related to subtle local physical frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. In this review, we also emphasize that frustration, far from being always a bad thing, is an essential feature of biomolecules that allows dynamics to be harnessed for function. In this way, we hope to illustrate how Frustration is a fundamental concept in molecular biology. © Cambridge University Press 2014. Source

Laska J.N.,Dropcam Inc. | Baraniuk R.G.,Rice University
IEEE Transactions on Signal Processing | Year: 2012

The recently introduced compressive sensing (CS) framework enables digital signal acquisition systems to take advantage of signal structures beyond bandlimitedness. Indeed, the number of CS measurements required for stable reconstruction is closer to the order of the signal complexity than the Nyquist rate. To date, the CS theory has focused on real-valued measurements, but in practice measurements are mapped to bits from a finite alphabet. Moreover, in many potential applications the total number of measurement bits is constrained, which suggests a tradeoff between the number of measurements and the number of bits per measurement. We study this situation in this paper and show that there exist two distinct regimes of operation that correspond to high/low signal-to-noise ratio (SNR). In the measurement compression (MC) regime, a high SNR favors acquiring fewer measurements with more bits per measurement; in the quantization compression (QC) regime, a low SNR favors acquiring more measurements with fewer bits per measurement. A surprise from our analysis and experiments is that in many practical applications it is better to operate in the QC regime, even acquiring as few as 1 bit per measurement. © 2012 IEEE. Source

Qu L.,Boise State University | Yin W.,Rice University
Computational Statistics and Data Analysis | Year: 2012

A copula density is the joint probability density function (PDF) of a random vector with uniform marginals. An approach to bivariate copula density estimation is introduced that is based on maximum penalized likelihood estimation (MPLE) with a total variation (TV) penalty term. The marginal unity and symmetry constraints for copula density are enforced by linear equality constraints. The TV-MPLE subject to linear equality constraints is solved by an augmented Lagrangian and operator-splitting algorithm. It offers an order of magnitude improvement in computational efficiency over another TV-MPLE method without constraints solved by the log-barrier method for the second order cone program. A data-driven selection of the regularization parameter is through K-fold cross-validation (CV). Simulation and real data application show the effectiveness of the proposed approach. The MATLAB code implementing the methodology is available online. © 2011 Elsevier Inc. All rights reserved. Source

Takizawa K.,Waseda University | Tezduyar T.E.,Rice University
Archives of Computational Methods in Engineering | Year: 2012

The computational challenges posed by fluid-structure interaction (FSI) modeling of parachutes include the lightness of the parachute canopy compared to the air masses involved in the parachute dynamics, in the case of "ringsail" parachutes the geometric complexities created by the construction of the canopy from "rings" and "sails" with hundreds of ring "gaps" and sail "slits", and in the case of parachute clusters the contact between the parachutes. The Team for Advanced Flow Simulation and Modeling (T*AFSM) has successfully addressed these computational challenges with the Stabilized Space-Time FSI (SSTFSI) technique, which was developed and improved over the years by the T*AFSM and serves as the core numerical technology, and a number of special techniques developed in conjunction with the SSTFSI technique. The quasi-direct and direct coupling techniques developed by the T*AFSM, which are applicable to cases with incompatible fluid and structure meshes at the interface, yield more robust algorithms for FSI computations where the structure is light and therefore more sensitive to the variations in the fluid dynamics forces. The special technique used in dealing with the geometric complexities of the rings and sails is the Homogenized Modeling of Geometric Porosity, which was developed and improved in recent years by the T*AFSM. The Surface-Edge-Node Contact Tracking (SENCT) technique was introduced by the T*AFSM as a contact algorithm where the objective is to prevent the structural surfaces from coming closer than a minimum distance in an FSI computation. The recently-introduced conservative version of the SENCT technique is more robust and is now an essential technology in the parachute cluster computations carried out by the T*AFSM. We provide an overview of the core and special techniques developed by the T*AFSM, present single-parachute FSI computations carried out for design-parameter studies, and report FSI computation and dynamical analysis of two-parachute clusters. © 2012 CIMNE, Barcelona, Spain. Source

Damanik D.,Rice University | Gorodetski A.,University of California at Irvine
Communications in Mathematical Physics | Year: 2011

We consider the spectrum of the Fibonacci Hamiltonian for small values of the coupling constant. It is known that this set is a Cantor set of zero Lebesgue measure. Here we study the limit, as the value of the coupling constant approaches zero, of its thickness and its Hausdorff dimension. We prove that the thickness tends to infinity and, consequently, the Hausdorff dimension of the spectrum tends to one. We also show that at small coupling, all gaps allowed by the gap labeling theorem are open and the length of every gap tends to zero linearly. Moreover, for a sufficiently small coupling, the sum of the spectrum with itself is an interval. This last result provides a rigorous explanation of a phenomenon for the Fibonacci square lattice discovered numerically by Even-Dar Mandel and Lifshitz. Finally, we provide explicit upper and lower bounds for the solutions to the difference equation and use them to study the spectral measures and the transport exponents. © The Author(s) 2011. Source

Koushanfar F.,Rice University
IEEE Transactions on Information Forensics and Security | Year: 2012

In the horizontal semiconductor business model where the designer's intellectual property (IP) is transparent to foundry and to other entities on the production chain, integrated circuits (ICs) overbuilding and IP piracy are prevalent problems. Active metering is a suite of methods enabling the designers to control their chips postfabrication. We provide a comprehensive description of the first known active hardware metering method and introduce new formal security proofs. The active metering method uniquely and automatically locks each IC upon manufacturing, such that the IP rights owner is the only entity that can provide the specific key to unlock or otherwise control each chip. The IC control mechanism exploits: 1) the functional description of the design, and 2) unique and unclonable IC identifiers. The locks are embedded by modifying the structure of the hardware computation model, in the form of a finite state machine (FSM). We show that for each IC hiding the locking states within the modified FSM structure can be constructed as an instance of a general output multipoint function that can be provably efficiently obfuscated. The hidden locks within the FSM may also be used for remote enabling and disabling of chips by the IP rights owner during the IC's normal operation. An automatic synthesis method for low overhead hardware implementation is devised. Attacks and countermeasures are addressed. Experimental evaluations demonstrate the low overhead of the method. Proof-of-concept implementation on the H.264 MPEG decoder automatically synthesized on a Xilinix Virtex-5 field-programmable gate array (FPGA) further shows the practicality, security, and the low overhead of the new method. © 2011 IEEE. Source

Davenport M.A.,Georgia Institute of Technology | Laska J.N.,Dropcam Inc. | Treichler J.R.,Applied Signal Technology | Baraniuk R.G.,Rice University
IEEE Transactions on Signal Processing | Year: 2012

Compressive sensing (CS) exploits the sparsity present in many signals to reduce the number of measurements needed for digital acquisition. With this reduction would come, in theory, commensurate reductions in the size, weight, power consumption, and/or monetary cost of both signal sensors and any associated communication links. This paper examines the use of CS in the design of a wideband radio receiver in a noisy environment. We formulate the problem statement for such a receiver and establish a reasonable set of requirements that a receiver should meet to be practically useful. We then evaluate the performance of a CS-based receiver in two ways: via a theoretical analysis of its expected performance, with a particular emphasis on noise and dynamic range, and via simulations that compare the CS receiver against the performance expected from a conventional implementation. On the one hand, we show that CS-based systems that aim to reduce the number of acquired measurements are somewhat sensitive to signal noise, exhibiting a 3 dB SNR loss per octave of subsampling, which parallels the classic noise-folding phenomenon. On the other hand, we demonstrate that since they sample at a lower rate, CS-based systems can potentially attain a significantly larger dynamic range. Hence, we conclude that while a CS-based system has inherent limitations that do impose some restrictions on its potential applications, it also has attributes that make it highly desirable in a number of important practical settings. © 1991-2012 IEEE. Source

Davydycheva S.,Rice University
Leading Edge (Tulsa, OK) | Year: 2010

Electromagnetic (EM) logging is an im-portant method of formation evaluation because of its sensitivity to resistivity, which is a function of fluid saturation and fluid properties. Conventional induction and propagation resistivity logging tools excite the geological formation by axial magnetic dipole transmitter(s). Axial re-ceivers measure the formation response, reflecting the medium resistivity. Such axial measurement has no azimuthal sensitivity and is insensitive to the anisotropy and many other details of the formation. © 2010 Society of Exploration Geophysicists. Source

The cell population balance, ensemble and continuum modeling frameworks are widely used for the mathematical description of microbial populations. Each of these approaches focuses on different aspects of the processes of growth, division and intracellular reaction occurrence. Therefore, each framework can output different information at different computational expense. Continuum models assume lumped biomasses, capture the dynamics of bulk intracellular concentrations and are easy to simulate. Ensemble models account for heterogeneity due to different initial conditions or kinetic constants, and are more computationally expensive. Finally, cell population balances capture the partitioning of the intracellular contents in detail, but can quickly become intractable, as the number of biochemical species taken into consideration increases. It is thus natural to ask whether one can adequately simulate cell populations with a simpler approach. In this paper, starting from an (n+1) cell population balance, for n biochemical species and the cell volume, we investigate biologically plausible conditions, under which two exact hybrid models are derived. Provided that the conditions hold true, both hybrid models are exact but much simpler alternatives of the cell population balance; no approximation is involved. In the first, the evolution of the species concentrations is captured by an ensemble model, and in the second by a continuum model. Both hybrid models also contain a 1-dimensional population balance for the cell volume. This work should provide a guideline for choosing the modeling approach which is the most appropriate for the particular application. © 2009 Elsevier Ltd. All rights reserved. Source

Vershik and Kerov gave asymptotical bounds for the maximal and the typical dimensions of irreducible representations of symmetric groups S n. It was conjectured by Olshanski that the maximal and the typical dimensions of the isotypic components of tensor representations of the symmetric group admit similar asymptotical bounds. The main result of this article is the proof of this conjecture. Consider the natural representation of S n on (CN)⊗n. Its isotypic components are parametrized by Young diagrams with n cells and at most N rows. Biane found the limit shape of Young diagrams when n→∞,n/N→c. By showing that this limit shape is the unique solution to a variational problem, it is proven here, that after scaling, the maximal and the typical dimensions of isotypic components lie between positive constants. A new proof of Biane's limit-shape theorem is obtained. © 2012 Elsevier Ltd. Source

Engelhardt Jr. H.T.,Rice University
Journal of Medicine and Philosophy | Year: 2011

In the face of the moral pluralism that results from the death of God and the abandonment of a God's eye perspective in secular philosophy, bioethics arose in a context that renders it essentially incapable of giving answers to substantive moral questions, such as concerning the permissibility of abortion, human embryonic stem cell research, euthanasia, etc. Indeed, it is only when bioethics understands its own limitations and those of secular moral philosophy in general can it better appreciate those tasks that it can actually usefully perform in both the clinical and academic setting. It is the task of this paper to understand and reevaluate bioethics by understanding these limits. Academic bioethicists can analyze ideas, concepts, and claims necessary to understanding the moral questions raised in health care, assessing the arguments related to these issues, and provide an understanding of the different moral perspectives on bioethical issues. In the clinical setting, bioethicists can provide legal advice, serve as experts on IRBs, mediating disputes, facilitating decision-making and risk management, and clarifying normative issues. However, understanding this is only possible when one understands the history, genesis, and foundations of bioethics and its inability to provide a resolution to postmodern moral pluralism. © The Author 2011. Source

Levine H.,Rice University
Physical Biology | Year: 2014

Unlike a new generation of scientists that are being trained directly to work on the physics of living systems, most of us more senior members of the community had to find our way from other research areas. We all have our own stories as to how we made this transition. Here, I describe how a chance encounter with the eukaryotic microorganism Dictyostelium discoideum led to a decades-long research project and taught me valuable lessons about how physics and biology can be mutually supportive disciplines. © 2014 IOP Publishing Ltd. Source

Ferreiro D.U.,Protein Physiology Laboratory | Komives E.A.,University of California at San Diego | Wolynes P.G.,Rice University
Quarterly Reviews of Biophysics | Year: 2014

Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their own structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of frustration in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and especially how biomolecular structure connects to function by means of localized frustration. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding mechanisms. We review here how the biological functions of proteins are related to subtle local physical frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. In this review, we also emphasize that frustration, far from being always a bad thing, is an essential feature of biomolecules that allows dynamics to be harnessed for function. In this way, we hope to illustrate how Frustration is a fundamental concept in molecular biology. Copyright © 2014 Cambridge University Press. Source

Barone V.,Central Michigan University | Hod O.,Tel Aviv University | Peralta J.E.,Central Michigan University | Scuseria G.E.,Rice University
Accounts of Chemical Research | Year: 2011

Over the last several years, low-dimensional graphene derivatives, such as carbon nanotubes and graphene nanoribbons, have played a central role in the pursuit of a plausible carbon-based nanotechnology. Their electronic properties can be either metallic or semiconducting depending purely on morphology, but predicting their electronic behavior has proven challenging. The combination of experimental efforts with modeling of these nanometer-scale structures has been instrumental in gaining insight into their physical and chemical properties and the processes involved at these scales. Particularly, approximations based on density functional theory have emerged as a successful computational tool for predicting the electronic structure of these materials. In this Account, we review our efforts in modeling graphitic nanostructures from first principles with hybrid density functionals, namely the Heyd-Scuseria-Ernzerhof (HSE) screened exchange hybrid and the hybrid meta-generalized functional of Tao, Perdew, Staroverov, and Scuseria (TPSSh).These functionals provide a powerful tool for quantitatively studying structure-property relations and the effects of external perturbations such as chemical substitutions, electric and magnetic fields, and mechanical deformations on the electronic and magnetic properties of these low-dimensional carbon materials. We show how HSE and TPSSh successfully predict the electronic properties of these materials, providing a good description of their band structure and density of states, their work function, and their magnetic ordering in the cases in which magnetism arises. Moreover, these approximations are capable of successfully predicting optical transitions (first and higher order) in both metallic and semiconducting single-walled carbon nanotubes of various chiralities and diameters with impressive accuracy. This versatility includes the correct prediction of the trigonal warping splitting in metallic nanotubes.The results predicted by HSE and TPSSh provide excellent agreement with existing photoluminescence and Rayleigh scattering spectroscopy experiments and Green's function-based methods for carbon nanotubes. This same methodology was utilized to predict the properties of other carbon nanomaterials, such as graphene nanoribbons. Graphene nanoribbons may be viewed as unrolled (and passivated) carbon nanotubes. However, the emergence of edges has a crucial impact on the electronic properties of graphene nanoribbons. Our calculations have shown that armchair nanoribbons are predicted to be nonmagnetic semiconductors with a band gap that oscillates with their width. In contrast, zigzag graphene nanoribbons are semiconducting with an electronic ground state that exhibits spin polarization localized at the edges of the carbon nanoribbon. The spatial symmetry of these magnetic states in graphene nanoribbons can give rise to a half-metallic behavior when a transverse external electric field is applied. Our work shows that these properties are enhanced upon different types of oxidation of the edges. We also discuss the properties of rectangular graphene flakes, which present spin polarization localized at the zigzag edges. © 2011 American Chemical Society. Source

Mkrtchyan S.,Rice University
Communications in Mathematical Physics | Year: 2011

The paper studies scaling limits of random skew plane partitions confined to a box when the inner shapes converge uniformly to a piecewise linear function V of arbitrary slopes in [-1, 1]. It is shown that the correlation kernels in the bulk are given by the incomplete Beta kernel, as expected. As a consequence it is established that the local correlation functions in the scaling limit do not depend on the particular sequence of discrete inner shapes that converge to V. A detailed analysis of the correlation kernels at the top of the limit shape, and of the frozen boundary is given. It is shown that depending on the slope of the linear section of the back wall, the system exhibits behavior observed in either Okounkov and Reshetikhin (Commun Math Phys 269(3):571-609, 2007) or Boutillier et al. (http://arXiv.org/abs/0912.3968v2 [math-ph], 2009). © 2011 Springer-Verlag. Source

Miller T.E.X.,Rice University | Rudgers J.A.,University of New Mexico
American Naturalist | Year: 2014

Heritable symbioses can have important ecological effects and have triggered important evolutionary innovations. Current predictions for long-term symbiont prevalence are based on their fitness benefits and vertical transmission rates but ignore nonlinear competitive feedbacks among symbiotic and symbiont-free hosts. We hypothesized that such feedbacks function as stabilizing mechanisms, promoting coexistence of host types and maintaining intermediate symbiont frequency at the population scale. Using a model grass/endophyte symbiosis, we manipulated competition within and between endophyte-symbiotic (E+) and endophyte-free (E-) hosts and fit competition models to experimental data. We show for the first time that symbiont-structured competition can generate stable coexistence of E+ and E- hosts, even under perfect vertical transmission. Niche differentiation was the key to coexistence, causing hosts of each type to limit themselves more strongly than each other. These results establish roles for nonlinear competitive dynamics and niche differentiation in the ecology and evolution of heritable symbionts. © 2014 by The University of Chicago. Source

Shifrer D.,Rice University
Journal of Health and Social Behavior | Year: 2013

Poorer outcomes for youth labeled with learning disabilities (LDs) are often attributed to the student's own deficiencies or cumulative disadvantage; but the more troubling possibility is that special education placement limits rather than expands these students' opportunities. Labeling theory partially attributes the poorer outcomes of labeled persons to stigma related to labels. This study uses data on approximately 11,740 adolescents and their schools from the Education Longitudinal Survey of 2002 to determine if stigma influences teachers' and parents' educational expectations for students labeled with LDs and labeled adolescents' expectations for themselves. Supporting the predictions of labeling theory, teachers and parents are more likely to perceive disabilities in, and hold lower educational expectations for labeled adolescents than for similarly achieving and behaving adolescents not labeled with disabilities. The negative effect of being labeled with LDs on adolescents' educational expectations is partially mechanized through parents' and particularly teachers' lower expectations. © American Sociological Association 2013. Source

Engelhardt H.T.,Rice University
Journal of Medicine and Philosophy (United Kingdom) | Year: 2012

A complex interaction of ideological, financial, social, and moral factors makes the financial sustainability of health care systems a challenge across the world. One difficulty is that some of the moral commitments of some health care systems collide with reality. In particular, commitments to equality in access to health care and to fair equality of opportunity undergird an unachievable promise, namely, to provide all with the best of basic health care. In addition, commitments to fair equality of opportunity are in tension with the existence of families, because families are aimed at advantaging their own members in preference to others. Because the social-democratic state is committed to fair equality of opportunity, it offers a web of publicly funded entitlements that make it easier for persons to exit the family and to have children outside of marriage. In the United States, in 2008, 41% of children were born outside of wedlock, whereas, in 1940, the percentage was only 3.8%, and in 1960, 5%, with the further consequence that the social and financial capital generated through families, which aids in supporting health care in families, is diminished. In order to explore the challenge of creating a sustainable health care system that also supports the traditional family, the claims made for fair equality of opportunity in health care are critically reconsidered. This is done by engaging the expository device of John Rawls's original position, but with a thin theory of the good that is substantively different from that of Rawls, one that supports a health care system built around significant copayments, financial counseling, and compulsory savings, with a special focus on enhancing the financial and social capital of the family. This radical recasting of Rawls, which draws inspiration from Singapore, is undertaken as a heuristic to aid in articulating an approach to health care allocation that can lead past the difficulties of social-democratic policy. © The Author 2012. Source

Baring M.G.,Rice University
Advances in Space Research | Year: 2011

It is widely accepted that the prompt transient signal in the 10 keV-10 GeV band from gamma-ray bursts (GRBs) arises from multiple shocks internal to the ultra-relativistic expansion. The detailed understanding of the dissipation and accompanying acceleration at these shocks is a currently topical subject. This paper explores the relationship between GRB prompt emission spectra and the electron (or ion) acceleration properties at the relativistic shocks that pertain to GRB models. The focus is on the array of possible high-energy power-law indices in accelerated populations, highlighting how spectra above 1 MeV can probe the field obliquity in GRB internal shocks, and the character of hydromagnetic turbulence in their environs. It is emphasized that diffusive shock acceleration theory generates no canonical spectrum at relativistic MHD discontinuities. This diversity is commensurate with the significant range of spectral indices discerned in prompt burst emission. Such system diagnostics are now being enhanced by the broad-band spectral coverage of bursts by the Fermi Gamma-Ray Space Telescope; while the Gamma-Ray Burst Monitor (GBM) provides key diagnostics on the lower energy portions of the particle population, the focus here is on constraints in the non-thermal, power-law regime of the particle distribution that are provided by the Large Area Telescope (LAT). © 2010 COSPAR. Published by Elsevier Ltd. All rights reserved. Source

Crosnoe R.,University of Texas at Austin | Lopez Turley R.N.,Rice University
Future of Children | Year: 2011

The children from immigrant families in the United States make up a historically diverse population, and they are demonstrating just as much diversity in their experiences in the K-12 educational system. Robert Crosnoe and Ruth Lo ́pez Turley summarize these K-12 patterns, paying special attention to differences in academic functioning across segments of the immigrant population defined by generational status, race and ethnicity, and national origin. A good deal of evidence points to an immigrant advantage in multiple indicators of academic progress, meaning that many youths from immigrant families outperform their peers in school. This apparent advantage is often referred to as the immigrant paradox, in that it occurs despite higher-than-average rates of social and economic disadvantages in this population as a whole. The immigrant paradox, however, is more pronounced among the children of Asian and African immigrants than other groups, and it is stronger for boys than for girls. Furthermore, evidence for the paradox is far more consistent in secondary school than in elementary school. Indeed, school readiness appears to be one area of potential risk for children from immigrant families, especially those of Mexican origin. For many groups, including those from Latin America, any evidence of the immigrant paradox usually emerges after researchers control for family socioeconomic circumstances and youths' English language skills. For others, including those from Asian countries, it is at least partially explained by the tendency for more socioeconomically advantaged residents of those regions to leave their home country for the United States. Bilingualism and strong family ties help to explain immigrant advantages in schooling; school, community, and other contextual disadvantages may suppress these advantages or lead to immigrant risks. Crosnoe and Turley also discuss several policy efforts targeting young people from immigrant families, especially those of Latin American origin. One is the DREAM Act, proposed federal legislation to create a pathway to citizenship for undocumented youth who meet certain criteria. Another effort includes culturally grounded programs to support the college preparation of immigrant adolescents and the educational involvement of immigrant parents of young children. Source

Goswami P.,Rice University | Chakravarty S.,University of California at Los Angeles
Physical Review Letters | Year: 2011

Four-component massive and massless Dirac fermions in the presence of long range Coulomb interaction and chemical potential disorder exhibit striking fermionic quantum criticality. For an odd number of flavors of Dirac fermions, the sign of the Dirac mass distinguishes the topological and the trivial band insulator phases, and the gapless semimetallic phase corresponds to the quantum critical point that separates the two. Up to a critical strength of disorder, the semimetallic phase remains stable, and the universality class of the direct phase transition between two insulating phases is unchanged. Beyond the critical strength of disorder the semimetallic phase undergoes a phase transition into a disorder controlled diffusive metallic phase, and there is no longer a direct phase transition between the two types of insulating phases. © 2011 American Physical Society. Source

Lenardic A.,Rice University | Crowley J.W.,Harvard University
Astrophysical Journal | Year: 2012

A model of coupled mantle convection and planetary tectonics is used to demonstrate that history dependence can outweigh the effects of a planet's energy content and material parameters in determining its tectonic state. The mantle convection-surface tectonics system allows multiple tectonic modes to exist for equivalent planetary parameter values. The tectonic mode of the system is then determined by its specific geologic and climatic history. This implies that models of tectonics and mantle convection will not be able to uniquely determine the tectonic mode of a terrestrial planet without the addition of historical data. Historical data exists, to variable degrees, for all four terrestrial planets within our solar system. For the Earth, the planet with the largest amount of observational data, debate does still remain regarding the geologic and climatic history of Earth's deep past but constraints are available. For planets in other solar systems, no such constraints exist at present. The existence of multiple tectonic modes, for equivalent parameter values, points to a reason why different groups have reached different conclusions regarding the tectonic state of extrasolar terrestrial planets larger than Earth ("super-Earths"). The region of multiple stable solutions is predicted to widen in parameter space for more energetic mantle convection (as would be expected for larger planets). This means that different groups can find different solutions, all potentially viable and stable, using identical models and identical system parameter values. At a more practical level, the results argue that the question of whether extrasolar terrestrial planets will have plate tectonics is unanswerable and will remain so until the temporal evolution of extrasolar planets can be constrained. © 2012. The American Astronomical Society. All rights reserved. Source

Kolomeisky A.B.,Rice University
Journal of Physical Chemistry Letters | Year: 2011

Concentration profiles of signaling molecules, known as morphogen gradients, determine polarity and spatial patterning in the development of all multicellular organisms. A widely used approach to explain the establishment of morphogen concentration gradients assumes that signaling molecules are produced locally, then spread via a free diffusion along the line of developing cells and degraded uniformly. However, recent experiments have produced controversial observations concerning the feasibility of this theoretical description. Some experimentally measured dispersions for morphogens cannot support fast formation of stationary concentration profiles. In addition, the latest theoretical analyses of times to establish the morphogen gradient yield a surprising linear scaling as a function of length from the source that is not expected for the unbiased diffusion process. We propose here a theoretical approach that provides a possible physical-chemical mechanism to explain these observations. It is argued that relaxation times to establish morphogen gradients are mostly determined by first arrival times, and the degradation plays a critical role in this mechanism by effectively accelerating diffusion of signaling molecules via removal of slow moving particles. This coupling between diffusion and degradation is analogous to the action of the effective field that drives particles away from the local source. © 2011 American Chemical Society. Source

Engelhardt Jr. H.T.,Rice University
Christian Bioethics | Year: 2014

Many have regarded the 1970's, rich as they were with the works of such as Paul Ramsey and Richard McCormick, as the golden age of Bioethics. As Stanley Hauerwas has pointed out, the claim is false. This article argues that Ramsey and others, by creating a Christian bioethics that was not founded in Christ and in distinctly Christian commitments, contribute to the auto-demolition of Christian bioethics. After all if Christian bioethics contributed to bioethical reflection only what a good secular bioethics can offer, why bother. However, now a distinctly Christian bioethics is growing. © The Author 2014. Source

Enormous amounts of 13C-depleted carbon rapidly entered the exogenic carbon cycle during the onset of the Paleocene-Eocene thermal maximum (PETM), as attested to by a prominent negative carbon isotope (δ 13C) excursion and deep-sea carbonate dissolution. A widely cited explanation for this carbon input has been thermal dissociation of gas hydrate on continental slopes, followed by release of CH 4 from the seafloor and its subsequent oxidation to CO 2 in the ocean or atmosphere. Increasingly, papers have argued against this mechanism, but without fully considering existing ideas and available data. Moreover, other explanations have been presented as plausible alternatives, even though they conflict with geological observations, they raise major conceptual problems, or both. Methane release from gas hydrates remains a congruous explanation for the δ 13C excursion across the PETM, although it requires an unconventional framework for global carbon and sulfur cycling, and it lacks proof. These issues are addressed here in the hope that they will prompt appropriate discussions regarding the extraordinary carbon injection at the start of the PETM and during other events in Earth's history. © Author(s) 2011. Source

A snapshot Image Mapping Spectrometer (IMS) with high sampling density is developed for hyperspectral microscopy, measuring a datacube of dimensions 285 x 285 x 60 (x, y, lambda). The spatial resolution is approximately 0.45 microm with a FOV of 100 x 100 microm(2). The measured spectrum is from 450 nm to 650 nm and is sampled by 60 spectral channels with average sampling interval approximately 3.3 nm. The channel's spectral resolution is approximately 8nm. The spectral imaging results demonstrate the potential of the IMS for real-time cellular fluorescence imaging. Source

Foster M.S.,Rice University | Gurarie V.,University of Colorado at Boulder | Dzero M.,Kent State University | Yuzbashyan E.A.,Rutgers University
Physical Review Letters | Year: 2014

Ultracold atomic gases in two dimensions tuned close to a p-wave Feshbach resonance were expected to exhibit topological superfluidity, but these were found to be experimentally unstable. We show that one can induce a topological Floquet superfluid if weakly interacting atoms are brought suddenly close ("quenched") to such a resonance, in the time before the instability kicks in. The resulting superfluid possesses Majorana edge modes, yet differs from a conventional Floquet system as it is not driven externally. Instead, the periodic modulation is self-generated by the dynamics. © 2014 American Physical Society. Source

Mitra R.,University of California at San Diego | Tauxe L.,University of California at San Diego | Keech McIntosh S.,Rice University
Earth and Planetary Science Letters | Year: 2013

This study presents 17 archeointensity estimates from Senegal and Mali, two neighboring countries in West Africa, for the period 1000 BCE to 1000 CE. The archeological artifacts used in this study were collected during the course of two separate projects, together spanning 22 years and across 8 separate excavations. A primary objective of this study was to get accurate dates, hence, only samples with independent age constraints from pottery style, detailed stratigraphy and 14C dates were used. A total of 236 specimens from 63 samples were subjected to a double heating paleointensity experiment (IZZI method) from which 95 specimens were selected using a set of very strict selection criteria. The paleointensity results were corrected for differential cooling rate effects and remanence anisotropy. Additionally, we demonstrate the equivalence of using tensors derived from anhysteretic and thermal remanences for correcting remanent anisotropy of the specimens and use the former for the anisotropy correction. Our data show good agreement with the most recent paleosecular variation model but are lower than the pre-existing data, which are mostly from Egypt and Morocco. The presence of substantial non-axial-dipolar contributions in the region is evident when virtual axial dipole moments (VADMs) from the published literature are calculated for 20° latitudinal bands and compared with our data-the average VADM values show a distinct latitudinal gradient. A prominent feature of this dataset is an intensity high observed prior to 700 CE in both Senegal and Mali. Comparing this peak with existing records from regions further to the north suggests a small but significant temporal offset and is interpreted to be additional evidence for a geomagnetic field with a significant and rapidly changing non-axial-dipolar contribution. © 2013 Elsevier B.V. Source

West J.L.,Rice University
Nature Materials | Year: 2011

Wylie et al. have demonstrate the simultaneous immobilization of multiple proteins in hydrogels with three-dimensional (3D) spatial control. The growth of cells in 3D gels made of collagen or reconstituted extracellular matrix (ECM) proteins has shown that cellular responses in such systems are different from observations made on polystyrene surfaces. By using two-photon chemistry, Wylie and colleagues show the feasibility of patterning two proteins, the stem-cell differentiation factors sonic hedgehog (SHH) and ciliary neurotrophic factor (CNTF), as opposed to the shorter bioactive peptides that have been previously immobilized in two-photon patterning studies. As a result of this experiment, stacks of patterned agarose hydrogel layers are fabricated and that the pair of fusion proteins barstar SSH and biotin CNTF remain bioactive after immobilization. Source

Chidyagwai P.,Temple University | Riviere B.,Rice University
Advances in Water Resources | Year: 2011

This paper presents a two-grid method for solving systems of partial differential equations modelling incompressible free flow coupled with porous media flow. This work considers both the coupled Stokes and Darcy as well as the coupled Navier-Stokes and Darcy problems. The numerical schemes proposed are based on combinations of the continuous finite element method and the discontinuous Galerkin method. Numerical errors and convergence rates for solutions obtained from the two-grid method are presented. CPU times for the two-grid algorithm are shown to be significantly less than those obtained by solving the fully coupled problem. © 2011 Elsevier Ltd. Source

Acosta S.,Rice University | Acosta S.,Baylor College of Medicine
Computer Methods in Applied Mechanics and Engineering | Year: 2015

The formulation of the on-surface radiation condition (OSRC) is extended to handle wave scattering problems in the presence of multiple obstacles. The new multiple-OSRC simultaneously accounts for the outgoing behavior of the wave fields, as well as, the multiple wave reflections between the obstacles. Like boundary integral equations (BIE), this method leads to a reduction in dimensionality (from volume to surface) of the discretization region. However, as opposed to BIE, the proposed technique leads to boundary integral equations with smooth kernels. Hence, these Fredholm integral equations can be handled accurately and robustly with standard numerical approaches without the need to remove singularities. Moreover, under weak scattering conditions, this approach renders a convergent iterative method which bypasses the need to solve single scattering problems at each iteration.Inherited from the original OSRC, the proposed multiple-OSRC is generally a crude approximate method. If accuracy is not satisfactory, this approach may serve as a good initial guess or as an inexpensive pre-conditioner for Krylov iterative solutions of BIE. © 2014 Elsevier B.V. Source

Penczek P.A.,University of Houston | Kimmel M.,Rice University | Spahn C.M.T.,Charite - Medical University of Berlin
Structure | Year: 2011

We present the codimensional principal component analysis (PCA), a novel and straightforward method for resolving sample heterogeneity within a set of cryo-EM 2D projection images of macromolecular assemblies. The method employs PCA of resampled 3D structures computed using subsets of 2D data obtained with a novel hypergeometric sampling scheme. PCA provides us with a small subset of dominating "eigenvolumes" of the system, whose reprojections are compared with experimental projection data to yield their factorial coordinates constructed in a common framework of the 3D space of the macromolecule. Codimensional PCA is unique in the dramatic reduction of dimensionality of the problem, which facilitates rapid determination of both the plausible number of conformers in the sample and their 3D structures. We applied the codimensional PCA to a complex data set of Thermus thermophilus 70S ribosome, and we identified four major conformational states and visualized high mobility of the stalk base region. © 2011 Elsevier Ltd. All rights reserved. Source

Tristram Engelhardt Jr. H.,Rice University
Theoretical Medicine and Bioethics | Year: 2012

Given intractable moral pluralism, what ought one to make of the bioethics that arose in the early 1970s, grounded as it was in the false assumption that there is a common secular morality that secular bioethics ought to apply? It is as if bioethics developed without recognition of the crisis at the heart of secular morality itself. Secular moral rationality cannot of itself provide the foundations to identify a particular morality and its bioethics as canonical. One is not just confronted with intractable moral and bioethical pluralism, but with the absence of a secular ground that can show why one should act morally rather than self-interestedly. The result is not merely the deflation of much of traditional Western morality to life-style and death-style choices, but the threat of deflating to political slogans the now-dominant secular morality, including its affirmation of human autonomy, equality, social justice, and human dignity. All of this invites one critically to reconsider the meaning and force of secular bioethics. © Springer Science+Business Media B.V. 2012. Source

Wickham H.,Rice University
Journal of Statistical Software | Year: 2014

A huge amount of effort is spent cleaning data to get it ready for analysis, but there has been little research on how to make data cleaning as easy and effective as possible. This paper tackles a small, but important, component of data cleaning: data tidying. Tidy datasets are easy to manipulate, model and visualize, and have a specific structure: each variable is a column, each observation is a row, and each type of observational unit is a table. This framework makes it easy to tidy messy datasets because only a small set of tools are needed to deal with a wide range of un-tidy datasets. This structure also makes it easier to develop tidy tools for data analysis, tools that both input and output tidy datasets. The advantages of a consistent data structure and matching tools are demonstrated with a case study free from mundane data manipulation chores. © 2014 Journal of Statistical Software. All right reserved. Source

Esadze A.,University of Texas Medical Branch | Kemme C.A.,University of Texas Medical Branch | Kolomeisky A.B.,Rice University | Iwahara J.,University of Texas Medical Branch
Nucleic Acids Research | Year: 2014

The inducible transcription factor Egr-1, which recognizes a 9-bp target DNA sequence via three zinc-finger domains, rapidly activates particular genes upon cellular stimuli such as neuronal signals and vascular stresses. Here, using the stopped-flow fluorescence method, we measured the target search kinetics of the Egr-1 zinc-finger protein at various ionic strengths between 40 and 400 mM KCl and found the most efficient search at 150 mM KCl. We further investigated the kinetics of intersegment transfer, dissociation, and sliding of this protein on DNA at distinct concentrations of KCl. Our data suggest that Egr-1's kinetic properties are well suited for efficient scanning of chromosomal DNA in vivo. Based on a newly developed theory, we analyzed the origin of the optimal search efficiency at physiological ionic strength. Target association is accelerated by nonspecific binding to nearby sites and subsequent sliding to the target as well as by intersegment transfer. Although these effects are stronger at lower ionic strengths, such conditions also favor trapping of the protein at distant nonspecific sites, decelerating the target association. Our data demonstrate that Egr-1 achieves the optimal search at physiological ionic strength through a compromise between the positive and negative impacts of nonspecific interactions with DNA. © 2014 The Author(s) 2014. Source

Summary: Because of their small size, bacterial cells have long kept details about their inner workings a secret. We are starting to decipher their mechanistic secrets, in no small part due to the development of single-molecule and super-resolution fluorescence imaging, the subject of the 2014 Nobel Prize in Chemistry. These new methods have yielded a surge of discoveries about the subcellular organization and dynamics inside microbes. One example is an increased understanding of the virulence pathway within the cholera-causing microbe, Vibrio cholerae. Here, expression of the cholera toxin is regulated by an unusual step: transcription is activated by two inner-membrane proteins. Relating potential cooperative mechanisms between these two membrane-bound proteins and transcription activation is difficult using ensemble methods, which could obfuscate any underlying heterogeneity. Recent efforts using single-molecule tracking and super-resolution imaging have begun to unravel the heterogeneity. The results support a mechanism in which one membrane protein recruits the other in order to activate transcription. The study helps to explain the relationship between the two proteins in cholera replication and also sheds light on the broader process of membrane-bound transcription activation which, although uncommon, has been observed in other organisms. The mechanistic secrets of bacterial cells are being deciphered through single-molecule and super-resolution fluorescence imaging, the subject of the 2014 Nobel Prize in Chemistry. The virulence pathway within the cholera-causing microbe, Vibrio cholera, is regulated by unusual transcription activation by two inner-membrane proteins. Using single molecule techniques, Hass, et al. reports a mechanism in which one protein recruits the other to activate transcription, shedding light on the heterogeneity in microbe subcellular organization and the broader process of membrane-bound transcription activation. © 2015 John Wiley & Sons Ltd. Source

Christodoulides N.,Rice University
Methodist DeBakey cardiovascular journal | Year: 2012

Cardiovascular disease remains the leading cause of death in the world and continues to serve as the major contributor to healthcare costs. Likewise, there is an ever-increasing need and demand for novel and more efficient diagnostic tools for the early detection of cardiovascular disease, especially at the point-of-care (POC). This article reviews the programmable bio-nanochip (P-BNC) system, a new medical microdevice approach with the capacity to deliver both high performance and reduced cost. This fully integrated, total analysis system leverages microelectronic components, microfabrication techniques, and nanotechnology to noninvasively measure multiple cardiac biomarkers in complex fluids, such as saliva, while offering diagnostic accuracy equal to laboratory-confined reference methods. This article profiles the P-BNC approach, describes its performance in real-world testing of clinical samples, and summarizes new opportunities for medical microdevices in the field of cardiac diagnostics. Source

Kolomeisky A.B.,Rice University | Feng X.,University of Southern California | Krylov A.I.,University of Southern California
Journal of Physical Chemistry C | Year: 2014

A simple three-state model for the dynamics of the singlet fission (SF) process is developed. The model facilitates the analysis of the relative significance of different factors, such as electronic energies, couplings, and the entropic contributions. The entropic contributions to the rates are important; they drive the SF process in endoergic cases (such as tetracene). The anticipated magnitude of entropic contributions is illustrated by simple calculations. By considering a series of three acenes (tetracene, pentacene, and hexacene), we explained the experimentally observed 3 orders of magnitude difference in the rate of SF in tetracene and pentacene and predicted that the rate in hexacene will be slightly faster than in pentacene. This trend is driven by the increased thermodynamic drive for SF (Gibbs free energy difference of the initial excitonic state and two separated triplets). The model also explains experimentally observed fast SF in 5,12-diphenyltetracene. Consistently with the experimental observations, the model predicts weak temperature dependence of the multiexciton formation rate in tetracene as well as a reduced rate of this step in solutions and in isolated dimers. © 2014 American Chemical Society. Source

Hibbing J.R.,University of Nebraska - Lincoln | Smith K.B.,University of Nebraska - Lincoln | Alford J.R.,Rice University
Behavioral and Brain Sciences | Year: 2014

Disputes between those holding differing political views are ubiquitous and deep-seated, and they often follow common, recognizable lines. The supporters of tradition and stability, sometimes referred to as conservatives, do battle with the supporters of innovation and reform, sometimes referred to as liberals. Understanding the correlates of those distinct political orientations is probably a prerequisite for managing political disputes, which are a source of social conflict that can lead to frustration and even bloodshed. A rapidly growing body of empirical evidence documents a multitude of ways in which liberals and conservatives differ from each other in purviews of life with little direct connection to politics, from tastes in art to desire for closure and from disgust sensitivity to the tendency to pursue new information, but the central theme of the differences is a matter of debate. In this article, we argue that one organizing element of the many differences between liberals and conservatives is the nature of their physiological and psychological responses to features of the environment that are negative. Compared with liberals, conservatives tend to register greater physiological responses to such stimuli and also to devote more psychological resources to them. Operating from this point of departure, we suggest approaches for refining understanding of the broad relationship between political views and response to the negative. We conclude with a discussion of normative implications, stressing that identifying differences across ideological groups is not tantamount to declaring one ideology superior to another. © 2014 Cambridge University Press. Source

Ball Z.T.,Rice University
Current Opinion in Chemical Biology | Year: 2015

Chemical manipulation of natural, unengineered proteins is a daunting challenge which tests the limits of reaction design. By combining transition-metal or other catalysts with molecular recognition ideas, it is possible to achieve site-selective protein reactivity without the need for engineered recognition sequences or reactive sites. Some recent examples in this area have used ruthenium photocatalysis, pyridine organocatalysis, and rhodium(II) metallocarbene catalysis, indicating that the fundamental ideas provide opportunities for using diverse reactivity on complex protein substrates and in complex cell-like environments. © 2014 Elsevier Ltd. Source

Lefteriu S.,Rice University | Antoulas A.C.,Jacobs University Bremen
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems | Year: 2010

This paper addresses the problem of modeling systems from measurements of their frequency response. For multiport devices, currently available techniques are expensive. We propose a new approach which is based on a system-theoretic tool, the Loewner matrix pencil constructed in the context of tangential interpolation. Several implementations are presented. They are fast, accurate, they build low order models and are especially designed for a large number of terminals. Moreover, they identify the underlying system, rather than merely fitting the measurements. The numerical results show that our algorithms yield smaller models in less time, when compared to vector fitting. © 2009 IEEE. Source

Huerga D.,CSIC - Institute for the Structure of Matter | Dukelsky J.,CSIC - Institute for the Structure of Matter | Scuseria G.E.,Rice University
Physical Review Letters | Year: 2013

We present a canonical mapping transforming physical boson operators into quadratic products of cluster composite bosons that preserves matrix elements of operators when a physical constraint is enforced. We map the 2D lattice Bose-Hubbard Hamiltonian into 2×2 composite bosons and solve it within a generalized Hartree-Bogoliubov approximation. The resulting Mott insulator-superfluid phase diagram reproduces well quantum Monte Carlo results. The Higgs boson behavior in the superfluid phase along the unit density line is unraveled and in remarkable agreement with experiments. Results for the properties of the ground and excited states are competitive with other state-of-the-art approaches, but at a fraction of their computational cost. The composite boson mapping here introduced can be readily applied to frustrated many-body systems where most methodologies face significant hurdles. © 2013 American Physical Society. Source

Ling Q.,Anhui University of Science and Technology | Wen Z.,Shanghai JiaoTong University | Yin W.,Rice University
IEEE Transactions on Signal Processing | Year: 2013

A set of vectors (or signals) are jointly sparse if all their nonzero entries are found on a small number of rows (or columns). Consider a network of agents {i} that collaboratively recover a set of jointly sparse vectors {x (i)} from their linear measurements {y(i)}. Assume that every agent i collects its own measurement y(i) and aims to recover its own vector x(i) taking advantages of the joint sparsity structure. This paper proposes novel decentralized algorithms to recover these vectors in a way that every agent runs a recovery algorithm and exchanges with its neighbors only the estimated joint support of the vectors. The agents will obtain their solutions through collaboration while keeping their vectors' values and measurements private. As such, the proposed approach finds applications in distributed human action recognition, cooperative spectrum sensing, decentralized event detection, as well as collaborative data mining. We use a non-convex minimization model and propose algorithms that alternate between support consensus and vector update. The latter step is based on reweighted ℓq iterations, where q can be 1 or 2. We numerically compare the proposed decentralized algorithms with existing centralized and decentralized algorithms. Simulation results demonstrate that the proposed decentralized approaches have strong recovery performance and converge reasonably fast. © 1991-2012 IEEE. Source

Summerlin E.J.,NASA | Baring M.G.,Rice University
Astrophysical Journal | Year: 2012

Diffusive shock acceleration (DSA) at relativistic shocks is expected to be an important acceleration mechanism in a variety of astrophysical objects including extragalactic jets in active galactic nuclei and gamma-ray bursts. These sources remain good candidate sites for the generation of ultrahigh energy cosmic rays. In this paper, key predictions of DSA at relativistic shocks that are germane to the production of relativistic electrons and ions are outlined. The technique employed to identify these characteristics is a Monte Carlo simulation of such diffusive acceleration in test-particle, relativistic, oblique, magnetohydrodynamic (MHD) shocks. Using a compact prescription for diffusion of charges in MHD turbulence, this approach generates particle angular and momentum distributions at any position upstream or downstream of the shock. Simulation output is presented for both small angle and large angle scattering scenarios, and a variety of shock obliquities including superluminal regimes when the de Hoffmann-Teller frame does not exist. The distribution function power-law indices compare favorably with results from other techniques. They are found to depend sensitively on the mean magnetic field orientation in the shock, and the nature of MHD turbulence that propagates along fields in shock environs. An interesting regime of flat-spectrum generation is addressed; we provide evidence for it being due to shock drift acceleration, a phenomenon well known in heliospheric shock studies. The impact of these theoretical results on blazar science is outlined. Specifically, Fermi Large Area Telescope gamma-ray observations of these relativistic jet sources are providing significant constraints on important environmental quantities for relativistic shocks, namely, the field obliquity, the frequency of scattering, and the level of field turbulence. © 2012 The American Astronomical Society. All rights reserved. Source

Noe F.,Free University of Berlin | Clementi C.,Rice University
Journal of Chemical Theory and Computation | Year: 2015

Characterizing macromolecular kinetics from molecular dynamics (MD) simulations requires a distance metric that can distinguish slowly interconverting states. Here, we build upon diffusion map theory and define a kinetic distance metric for irreducible Markov processes that quantifies how slowly molecular conformations interconvert. The kinetic distance can be computed given a model that approximates the eigenvalues and eigenvectors (reaction coordinates) of the MD Markov operator. Here, we employ the time-lagged independent component analysis (TICA). The TICA components can be scaled to provide a kinetic map in which the Euclidean distance corresponds to the kinetic distance. As a result, the question of how many TICA dimensions should be kept in a dimensionality reduction approach becomes obsolete, and one parameter less needs to be specified in the kinetic model construction. We demonstrate the approach using TICA and Markov state model (MSM) analyses for illustrative models, protein conformation dynamics in bovine pancreatic trypsin inhibitor and protein-inhibitor association in trypsin and benzamidine. We find that the total kinetic variance (TKV) is an excellent indicator of model quality and can be used to rank different input feature sets. © 2015 American Chemical Society. Source

Palem K.V.,Rice University
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences | Year: 2014

As pressures, Notably from energy consumption, Start impeding the growth and scale of computing systems, inevitably, designers and users are increasingly considering the prospect of trading accuracy or exactness. This paper is a perspective on the progress in embracing this somewhat unusual philosophy of innovating computing systems that are designed to be inexact or approximate, in the interests of realizing extreme efficiencies. With our own experience in designing inexact physical systems including hardware as a backdrop, we speculate on the rich potential for considering inexactness as a broad emerging theme if not an entire domain for investigation for exciting research and innovation. If this emerging trend to pursuing inexactness persists and grows, then we anticipate an increasing need to consider system co-design where application domain characteristics and technology features interplay in an active manner. A noteworthy early example of this approach is our own excursion into tailoring and hence co-designing floating point arithmetic units guided by the needs of stochastic climatemodels. This approach requires a unified effort between software and hardware designers that does away with the normal clean abstraction layers between the two. © 2014 The Author(s) Published by the Royal Society. All rights reserved. Source

Stevenson P.M.,Rice University
Nuclear Physics B | Year: 2016

Perturbative QCD with nf flavours of massless quarks becomes simple in the hypothetical limit nf→1612, where the leading β-function coefficient vanishes. The Banks–Zaks (BZ) expansion in a0≡8321(1612−nf) is straightforward to obtain from perturbative results in MS‾ or any renormalization scheme (RS) whose nf dependence is ‘regular’. However, ‘irregular’ RS's are perfectly permissible and should ultimately lead to the same BZ results. We show here that the ‘optimal’ RS determined by the Principle of Minimal Sensitivity does yield the same BZ-expansion results when all orders of perturbation theory are taken into account. The BZ limit provides an arena for exploring optimized perturbation theory at arbitrarily high orders. These explorations are facilitated by a ‘master equation’ expressing the optimization conditions in the fixed-point limit. We find an intriguing strong/weak coupling duality a→a⁎ 2/a about the fixed point a⁎. © 2016 The Author(s) Source

Vardi M.Y.,Rice University
Proceedings of the ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems | Year: 2016

A major theme in relational database theory is navigating the tradeoff between expressiveness and tractability for query languages, where the query-containment problem is considered a benchmark of tractability. The query class UCQ, consisting off unions of conjunctive queries, is a fragment of first-order logic that has a decidable query containment problem, but its expressiveness is limited. Extending UCQ with recursion yields Datalog, an expressive query language that has been studied extensively and has recently become popular in application areas such as declarative networking. Unfortunately, Datalog has an undecidable query containment problem. Identifying a fragment of Datalog that is expressive enough for applications but has a decidable query-containment problem has been an open problem for several years. In the area of graph databases, there has been a similar search for a query language that combines expressiveness and tractability. Because of the need to navigate along graph paths of unspecified length, transitive closure has been considered a fundamental operation. Query classes of increasing complexity - using the operations of disjunction, conjunction, projection, and transitive closure - have been studied, but the classes lacked natural closure properties. The class RQ of regular queries has emerged only recently as a natural query class that is closed under all of its operations and has a decidable query-containment problem. RQ turned out to be a fragment of Datalog where recursion can be used only to express transitive closure. Furthermore, it turns out that applying this idea to Datalog, that is, restricting recursion to the expression of transitive closure, does yield the long-sought goal - an expressive fragment of Datalog with a decidable query-optimization problem. © 2016 ACM. Source

Parry R.,Rice University | Nishino S.,Georgia Institute of Technology | Spain J.,Georgia Institute of Technology
Natural Product Reports | Year: 2011

Naturally-occurring nitro compounds display great structural diversity, and a wide range of biological activities. This review summarizes current information on the structures of naturally-occurring nitro compounds and on the biosynthesis of the nitro group. © The Royal Society of Chemistry 2011. Source

Chiang S.,Rice University | Haneef Z.,Baylor College of Medicine | Haneef Z.,Medical Center
Clinical Neurophysiology | Year: 2014

Temporal lobe epilepsy (TLE) is the most common form of adult epilepsy. Accumulating evidence has shown that TLE is a disorder of abnormal epileptogenic networks, rather than focal sources. Graph theory allows for a network-based representation of TLE brain networks, and has potential to illuminate characteristics of brain topology conducive to TLE pathophysiology, including seizure initiation and spread. We review basic concepts which we believe will prove helpful in interpreting results rapidly emerging from graph theory research in TLE. In addition, we summarize the current state of graph theory findings in TLE as they pertain its pathophysiology. Several common findings have emerged from the many modalities which have been used to study TLE using graph theory, including structural MRI, diffusion tensor imaging, surface EEG, intracranial EEG, magnetoencephalography, functional MRI, cell cultures, simulated models, and mouse models, involving increased regularity of the interictal network configuration, altered local segregation and global integration of the TLE network, and network reorganization of temporal lobe and limbic structures. As different modalities provide different views of the same phenomenon, future studies integrating data from multiple modalities are needed to clarify findings and contribute to the formation of a coherent theory on the pathophysiology of TLE. © 2014 International Federation of Clinical Neurophysiology. Source

Boufounos P.T.,MItsubishi Electric | Boufounos P.T.,Rice University
IEEE Transactions on Information Theory | Year: 2012

Scalar quantization is the most practical and straightforward approach to signal quantization. However, it has been shown that scalar quantization of oversampled or compressively sensed signals can be inefficient in terms of the rate-distortion tradeoff, especially as the oversampling rate or the sparsity of the signal increases. In this paper, we modify the scalar quantizer to have discontinuous quantization regions. We demonstrate that with this modification it is possible to achieve exponential decay of the quantization error as a function of the oversampling rate instead of the quadratic decay exhibited by current approaches. Our approach is universal in the sense that prior knowledge of the signal model is not necessary in the quantizer design, only in the reconstruction. Thus, we demonstrate that it is possible to reduce the quantization error by incorporating side information on the acquired signal, such as sparse signal models or signal similarity with known signals. In doing so, we establish a relationship between quantization performance and the Kolmogorov entropy of the signal model. © 2011 IEEE. Source

Schnur T.T.,Rice University
Journal of Memory and Language | Year: 2014

Naming semantically related pictures (e.g., "goat" "cow" "mouse") becomes increasingly slower when repeatedly naming from a semantic category even when several unrelated trials intervene (Howard, Nickels, Coltheart, & Cole-Virtue, 2006). The aim of this study was to test whether cumulative semantic interference is independent of time and unrelated trials between naming occurrences as predicted if interference is the result of learning reflected by persistent changes to semantic-lexical connection strength (Oppenheim, Dell, & Schwartz, 2010). Consistent with this account, changes in response stimulus intervals did not affect cumulative interference, allowing rejection of a temporary residual activation account of interference, suggesting that persistence of cumulative interference in this paradigm is similar to when exemplars are repeatedly named in the blocked-cyclic naming paradigm. However, cumulative interference disappeared when intervening unrelated trials increased (8-50) except when a short lag occurred (2) in the sequence. Critically, when a short lag occurred in the sequence, interference extended to new categories separated by long lags (8-14) which were not previously named. To account for results, modifications of learning models of naming should include a mechanism by which interference dissipates, and a mechanism which biases learning to create persistence in contexts where semantic relationships are amplified. © 2014 Elsevier Inc. Source

Lee C.T.A.,Rice University | Bachmann O.,ETH Zurich
Earth and Planetary Science Letters | Year: 2014

Most magmatism on Earth forms by direct melting of the mantle, generating basalts at the low silica end of the terrestrial compositional spectrum. However, most subduction zone magmas erupted or sampled at the surface are basalt-andesitic to andesitic and hence have higher Si contents. Endmember hypotheses for the origin of andesites are: (1) direct melting of the mantle at water-saturated conditions, (2) partial re-melting of altered basaltic crust, (3) crystal fractionation of arc basalts in crustal magma chambers, and (4) mixing of mafic magmas with high Si crust or magmas, e.g., dacite-rhyolite. Here, we explore the possibility of using Zr and P systematics to evaluate the importance of some of these processes. Direct melting of the mantle generates magmas with low Zr (<50 ppm) and P2O5 (<0.2 wt.%). Crystal-liquid segregation should drive an increase in P and Zr in the residual magma because the magma is initially undersaturated in zircon and apatite. With further cooling and crystallization, apatite followed by zircon will saturate, causing P and Zr to decrease so that most rhyolites and granites will have low P and Zr (high temperature rhyolites may never saturate in zircon and will maintain high Zr contents). Mixing of basalts with rhyolites having low P and Zr should generate coupled decreases in Zr and P with increasing SiO2. Here, we show that Zr (>100 ppm) and P2O5 (>0.2 wt.%) in island- and continental-arc magmas initially increase to levels higher than what can be achieved if andesites form by direct mantle melting. As Si increases, both Zr and P decrease with Zr decreasing at higher Si, and hence lagging the decrease in P. These systematics, particularly the decoupled decrease in Zr and P, cannot be explained by mixing, and instead, are more easily explained if andesites are dominantly formed by crystal-liquid segregation from moderately hydrous basalt, wherein P and Zr are controlled, respectively, by early and later saturation in apatite and zircon. Although there is clear isotopic and outcrop (enclaves) evidence for mixing in magmatic systems, crystal-liquid segregation appears to be the dominant process in generating intermediate magmas, with mixing playing a secondary role.Finally, recent studies have suggested that the abundance of certain magma compositions in a given volcanic setting may be dictated by the optimal crystallinity window for efficient crystal-liquid separation (50-70 vol%). We show that the SiO2 content of the residual liquid in this crystallinity window increases with increasing water content. We thus speculate that high water contents (>2 wt.% H2O) may favor extraction of andesitic and dacitic liquids while lower water contents favor extraction of more basaltic magmas. If continental arc magmas tend to be more andesitic, as often believed, it follows that they may begin more water-rich than island arc magmas, which are basaltic. In any case, if intermediate arc magmas are formed dominantly by crystal-liquid fractionation, large volumes of complementary mafic cumulates must be generated during the formation of andesitic magmas, as is seen in well-exposed crustal sections. © 2014 Elsevier B.V. Source

Llope W.J.,Rice University
Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment | Year: 2012

A large-area (50 m 2) Time-of-Flight system has recently been installed in the STAR experiment at RHIC. The detectors are Multigap Resistive Plate Chambers (MRPCs) and are digitized using custom electronics based on the CERN NINO and HPTDC chips. Several different prototype systems were built and operated in STAR from 2002 to 2006. The design and performance of the prototypes and the ∼70% installed final system during the 2009 RHIC Run will be presented. A possible future upgrade to the STAR experiment is the Muon Telescope Detector (MTD). This system will use very large MRPCs with double-ended read-out to identify via time of flight the muons that pass through steel back-legs of the STAR magnet. The design of this system and the performance of MTD prototype systems will also be presented. © 2010 Elsevier B.V. All rights reserved. Source

Glazer E.S.,University of Texas M. D. Anderson Cancer Center | Curley S.A.,University of Texas M. D. Anderson Cancer Center | Curley S.A.,Rice University
Cancer | Year: 2010

BACKGROUND: Nonionizing radiation, such as radiofrequency field and near infrared laser, induces thermal cytotoxicity in cancer cells treated with gold nanoparticles. Quantum dots are fluorescent semiconducting nanoparticles that were hypothesized to induce similar injury after radiofrequency field irradiation. METHODS: Gold nanoparticles and 2 types of quantum dot (cadmium-selenide and indium-gallium-phosphide) conjugated to cetuximab (C225), a monoclonal antibody against human epidermal growth factor receptor (EGFR)-1, demonstrated concentration-dependent heating in a radiofrequency field. The authors investigated the effect of radiofrequency field exposure after targeted nanoparticle treatment in a coculture of 2 human cancer cell lines that have differential EGFR-1 expression (a high-expressing pancreatic carcinoma, Panc-1, and a low-expressing breast carcinoma, Cama-1). RESULTS: Radiofrequency revealed that Panc-1 or Cama-1 cells not containing gold nanoparticles or quantum dots had a viability of >92%. The viability of Panc-1 cells exposed to the radiofrequency field after treatment with 50 nM Au-C225 was 39.4% ± 8.3% without injury to bystander Cama-1 cells (viability was 93.7% ± 1.0%; P ∼ .0006). Panc-1 cells treated with targeted cadmium-selenide quantum dots were only 47.5% viable after radiofrequency field exposure (P<.0001 compared with radiofrequency only Panc-1 control cells). Targeted indium-gallium- phosphide quantum dots decreased Panc-1 viability to 58.2% ± 3.4% after radiofrequency field exposure (P = ∼.0004 compared with Cama-1 and Panc-1 controls). CONCLUSIONS: The authors selectively induced radiofrequency field cytotoxicity in Panc-1 cells without injury to bystander Cama-1 cells using EGFR-1-targeted nanoparticles, and demonstrated an interesting bifunctionality of fluorescent nanoparticles as agents for both cancer cell imaging and treatment. © 2010 American Cancer Society. Source

Nicolo M.J.,Royal Dutch Shell | Dickens G.R.,Rice University | Hollis C.J.,Institute of Geological & Nuclear Sciences
Paleoceanography | Year: 2010

Extreme global warming and massive input of 13C-depleted carbon into the exogenic carbon cycle characterize the Paleocene-Eocene thermal maximum (PETM) circa 55.5 Ma. Previous work indicates that dissolved O 2 concentrations dropped in some regions of the ocean during this event, but spatial, temporal, and causal relationships between warming, carbon input, and O 2 deficiency remain elusive. We present lithologic, carbon isotopic, and trace fossil results from outcrops in New Zealand that clarify this issue. Sections exposed at Mead and Dee Streams in eastern Marlborough, South Island, contain expanded sedimentary intervals that were deposited before, during, and after the PETM on an upper continental slope. The PETM in these intervals is characterized by enhanced siliciclastic deposition, a hallmark negative carbon isotope excursion, and a loss of bioturbation. Importantly, however, the latter only occurs during the prominent drop in δ 13C and not during its recovery. Our results suggest that South Pacific intermediate waters became hypoxic coincident to carbon injection at the start of the PETM. While higher sea surface temperatures throughout the PETM would have decreased the dissolved oxygen content of sinking surface waters, we argue here that oxygen depletion was driven by some combination of elevated temperature, water column stratification, and intermediate water methane oxidation. © 2010 by the American Geophysical Union. Source

Wang S.,Cameron International Corporation | Liu C.,Pall Corporation | Li Q.,Rice University
Water Research | Year: 2013

Organic polymers are widely used as flocculants in pretreatment for microfiltration. However, their impact on microfiltration system performance was not well understood. In this study, the effects of three types of polymer flocculants on microfiltration permeate water quality and membrane fouling were evaluated using a hollow fiber membrane under two different operation modes, coagulation/flocculation-sedimentation-microfiltration (CFSM) and coagulation/flocculation-microfiltration (CFM). Interestingly, the effect of polymers on membrane fouling did not appear to reflect their impact on dissolved organic matter content or floc particle properties in the membrane feed water. The addition of polymer flocculants resulted in floc particles of larger size and smaller fractal dimension and slightly enhanced the removal of dissolved organic matter, both of which were expected to reduce membrane fouling. However, it significantly aggravated membrane fouling in all cases except when the positively charged poly(diallyldimethylammonium) chloride was used in the CFSM process. In particular, all polymers greatly increased hydraulically irreversible fouling in the CFM mode. The increased fouling in the CFSM mode is attributed to the residual polymer, while that in the CFM mode is attributed to the enhanced irreversible floc particle attachment on the membrane surface. Considering the potential severe membrane fouling and the small improvement in treated water quality when polymers are used, the application of polymers in microfiltration pretreatment needs to be carefully evaluated. © 2013. Source

Tapia R.,Rice University
Mathematical Programming | Year: 2015

In this paper we present several representation theorems and averaging theorems for members of the difference class of secant updates introduced by Brodlie et al. (J Inst Math Appl 11:73–82, 1973). Major contributions are that the integral form of the mean-value theorem leads to a proof that the BFGS update is pointwise the infinite average of all the updates on the one-dimension manifold in the Dennis class that connects the DFP secant update to the Greenstadt update, and that it can be expressed as the pointwise average of these latter two updates. Analogous results hold for all secant updates that belong to the difference class. These results contribute new understanding of the structural properties of the highly popular BFGS secant update and other updates from the difference class. © 2014, Springer-Verlag Berlin Heidelberg and Mathematical Optimization Society. Source

Pettigrew C.,Johns Hopkins University | Martin R.C.,Rice University
Psychology and Aging | Year: 2014

The present study tested the hypothesis that older adults show age-related deficits in interference resolution, also referred to as inhibitory control. Although oftentimes considered as a unitary aspect of executive function, various lines of work support the notion that interference resolution may be better understood as multiple constructs, including resistance to proactive interference (PI) and responsedistractor inhibition (e.g., Friedman&Miyake, 2004). Using this dichotomy, the present study assessed whether older adults (relative to younger adults) show impaired performance across both, 1, or neither of these interference resolution constructs. To do so, we used multiple tasks to tap each construct and examined age effects at both the single task and latent variable levels. Older adults consistently demonstrated exaggerated interference effects across resistance to PI tasks. Although the results for the response-distractor inhibition tasks were less consistent at the individual task level analyses, age effects were evident on multiple tasks, as well as at the latent variable level. However, results of the latent variable modeling suggested declines in interference resolution are best explained by variance that is common to the 2 interference resolution constructs measured herein. Furthermore, the effect of age on interference resolution was found to be both distinct from declines in working memory, and independent of processing speed. These findings suggest multiple cognitive domains are independently sensitive to age, but that declines in the interference resolution constructs measured herein may originate from a common cause. © 2014 American Psychological Association. Source

Whitney K.D.,Rice University | Garland Jr. T.,University of California at Riverside
PLoS Genetics | Year: 2010

Mechanisms underlying the dramatic patterns of genome size variation across the tree of life remain mysterious. Effective population size (Ne) has been proposed as a major driver of genome size: selection is expected to efficiently weed out deleterious mutations increasing genome size in lineages with large (but not small) Ne. Strong support for this model was claimed from a comparative analysis of Neu and genome size for ≈30 phylogenetically diverse species ranging from bacteria to vertebrates, but analyses at that scale have so far failed to account for phylogenetic nonindependence of species. In our reanalysis, accounting for phylogenetic history substantially altered the perceived strength of the relationship between Neu and genomic attributes: there were no statistically significant associations between Neu and gene number, intron size, intron number, the half-life of gene duplicates, transposon number, transposons as a fraction of the genome, or overall genome size. We conclude that current datasets do not support the hypothesis of a mechanistic connection between Ne and these genomic attributes, and we suggest that further progress requires larger datasets, phylogenetic comparative methods, more robust estimators of genetic drift, and a multivariate approach that accounts for correlations between putative explanatory variables. © 2010 Whitney, Garland. Source

Fischer-Baum S.,Rice University | McCloskey M.,Johns Hopkins University
Journal of Experimental Psychology: Learning Memory and Cognition | Year: 2015

In immediate serial recall, participants are asked to recall novel sequences of items in the correct order. Theories of the representations and processes required for this task differ in how order information is maintained; some have argued that order is represented through item-to-item associations, while others have argued that each item is coded for its position in a sequence, with position being defined either by distance from the start of the sequence, or by distance from both the start and the end of the sequence. Previous researchers have used error analyses to adjudicate between these different proposals. However, these previous attempts have not allowed researchers to examine the full set of alternative proposals. In the current study, we analyzed errors produced in 2 immediate serial recall experiments that differ in the modality of input (visual vs. aural presentation of words) and the modality of output (typed vs. spoken responses), using new analysis methods that allow for a greater number of alternative hypotheses to be considered. We find evidence that sequence positions are represented relative to both the start and the end of the sequence, and show a contribution of the end-based representation beyond the final item in the sequence. We also find limited evidence for item-to-item associations, suggesting that both a start-end positional scheme and item-to-item associations play a role in representing item order in immediate serial recall. © 2015 American Psychological Association. Source

Zhang Z.,Nanjing University of Aeronautics and Astronautics | Zhang Z.,Rice University | Guo W.,Nanjing University of Aeronautics and Astronautics
Nano Letters | Year: 2012

We show by density functional theory calculations with both hybrid and semilocal functionals that cubic boron nitride (111) nanofilms are intrinsically metallic and even turn into semiconductors once the thickness is less than 0.69 nm, which is in sharp contrast to the known insulating nature of boron nitride materials. The exceptional metallic or semiconducting band gap is due to a combined effect of thickness-dependent inbuilt electric polarization and labile near-gap states unique in the polar nanofilms. The band gap and dipole moment of the nanofilms can be further significantly tuned by applying an in-plane strain. These distinguished features of the boron nitride nanofilms are robust to surface passivation and can be enhanced by hybridizing with diamond films, thereby opening an exciting prospect of using the versatile cubic nanofilms in future electronic and piezoelectric devices. © 2012 American Chemical Society. Source

Nicolaou K.C.,Rice University
Chemistry and Biology | Year: 2014

Admirable as it is, the drug discovery and development process is continuously undergoing changes and adjustments in search of further improvements in efficiency, productivity, and profitability. Recent trends in academic-industrial partnerships promise to provide new opportunities for advancements of this process through transdisciplinary collaborations along the entire spectrum of activities involved in this complex process. This perspective discusses ways to promote the emerging academic paradigm of the chemistry-biology-medicine continuum as a means to advance the drug discovery and development process. ©2014 Elsevier Ltd All rights reserved. Source

Hentschel M.,University of Stuttgart | Hentschel M.,Max Planck Institute for Solid State Research | Schaferling M.,University of Stuttgart | Weiss T.,University of Stuttgart | And 2 more authors.
Nano Letters | Year: 2012

The living world is chiral. Chirality or the handedness of a structure or molecule is at the heart of life itself. Recently, it has been shown that plasmonic structures exhibit unprecedented and gigantic chiral optical responses. Here we show that truly three-dimensional arrangements of plasmonic "meta-atoms" only exhibit a chiral optical response if similar plasmonic "atoms" are arranged in a handed fashion as we require resonant plasmonic coupling. Moreover, we demonstrate that such particle groupings, similarly to molecular systems, possess the capability to encode their three-dimensional arrangement in unique and well-modulated spectra making them ideal candidates for a three-dimensional chiral plasmon ruler. Our results are crucial for the future design and improvement of plasmonic chiral optical systems, for example, for ultrasensitive enantiomer sensing on the single molecule level. © 2012 American Chemical Society. Source

Jia L.,Massachusetts Institute of Technology | Bita I.,Qualcomm | Thomas E.L.,Rice University
Advanced Functional Materials | Year: 2012

A systematic study of the photonic band gap (PBG) properties of 8-, 10- and 12-fold rotational symmetric quasicrystals (QCs) defined by level set equations with various phase parameters is reported. The optimized filling ratios corresponding to the largest PBGs for 19 types of QCs are found, which are useful for photonic QC fabrication design. The impact of filling ratio, rotational symmetry, and experimental fabrication parameters on the resultant PBGs are studied via PBG maps calculated by finite-difference time-domain (FDTD). Large area, high quality 8-, 10-, and 12-fold quasicrystalline pattern fabrication using multiple exposure interference lithography (MEIL) is also demonstrated. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Lukianova-Hleb E.Y.,Rice University
Nature Nanotechnology | Year: 2016

Failure of cancer surgery to intraoperatively detect and eliminate microscopic residual disease (MRD) causes lethal recurrence and metastases, and the removal of important normal tissues causes excessive morbidity. Here, we show that a plasmonic nanobubble (PNB), a non-stationary laser pulse-activated nanoevent, intraoperatively detects and eliminates MRD in the surgical bed. PNBs were generated in vivo in head and neck cancer cells by systemically targeting tumours with gold colloids and locally applying near-infrared, low-energy short laser pulses, and were simultaneously detected with an acoustic probe. In mouse models, between 3 and 30 residual cancer cells and MRD (undetectable with current methods) were non-invasively detected up to 4 mm deep in the surgical bed within 1 ms. In resectable MRD, PNB-guided surgery prevented local recurrence and delivered 100% tumour-free survival. In unresectable MRD, PNB nanosurgery improved survival twofold compared with standard surgery. Our results show that PNB-guided surgery and nanosurgery can rapidly and precisely detect and remove MRD in simple intraoperative procedures. © 2016 Nature Publishing Group Source

Dai P.,Rice University
Reviews of Modern Physics | Year: 2015

High-transition temperature (high-Tc) superconductivity in the iron pnictides or chalcogenides emerges from the suppression of the static antiferromagnetic order in their parent compounds, similar to copper oxide superconductors. This raises a fundamental question concerning the role of magnetism in the superconductivity of these materials. Neutron scattering, a powerful probe to study the magnetic order and spin dynamics, plays an essential role in determining the relationship between magnetism and superconductivity in high-Tc superconductors. The rapid development of modern neutron time-of-flight spectrometers allows a direct determination of the spin dynamical properties of iron-based superconductors throughout the entire Brillouin zone. In this paper, an overview is presented of the neutron scattering results on iron-based superconductors, focusing on the evolution of spin-excitation spectra as a function of electron and hole doping and isoelectronic substitution. Spin dynamical properties of iron-based superconductors are compared with those of copper oxide and heavy fermion superconductors and the common features of spin excitations in these three families of unconventional superconductors and their relationship with superconductivity are discussed. © 2015 American Physical Society. Source

Lapotko D.,Rice University
Cancers | Year: 2011

This review is focused on a novel cellular probe, the plasmonic nanobubble (PNB), which has the dynamically tunable and multiple functions of imaging, diagnosis, delivery, therapy and, ultimately, theranostics. The concept of theranostics was recently introduced in order to unite the clinically important stages of treatment, namely diagnosis, therapy and therapy guidance, into one single, rapid and highly accurate procedure. Cell level theranostics will have far-reaching implications for the treatment of cancer and other diseases at their earliest stages. PNBs were developed to support cell level theranostics as a new generation of on-demand tunable cellular probes. A PNB is a transient vapor nanobubble that is generated within nanoseconds around an overheated plasmonic nanoparticle with a short laser pulse. In the short term, we expect that PNB technology will be rapidly adaptable to clinical medicine, where the single cell resolution it provides will be critical for diagnosing incipient or residual disease and eliminating cancer cells, while leaving healthy cells intact. This review discusses mechanisms of plasmonic nanobubbles and their biomedical applications with the focus on cancer cell theranostics. © 2011 by the authors; licensee MDPI, Basel, Switzerland. Source

Gupta M.,Columbia University | Agrawal A.,MItsubishi Electric | Veeraraghavan A.,Rice University | Narasimhan S.G.,Carnegie Mellon University
International Journal of Computer Vision | Year: 2013

Global or indirect illumination effects such as interreflections and subsurface scattering severely degrade the performance of structured light-based 3D scanning. In this paper, we analyze the errors in structured light, caused by both long-range (interreflections) and short-range (subsurface scattering) indirect illumination. The errors depend on the frequency of the projected patterns, and the nature of indirect illumination. In particular, we show that long-range effects cause decoding errors for low-frequency patterns, whereas short-range effects affect high-frequency patterns. Based on this analysis, we present a practical 3D scanning system which works in the presence of a broad range of indirect illumination. First, we design binary structured light patterns that are resilient to individual indirect illumination effects using simple logical operations and tools from combinatorial mathematics. Scenes exhibiting multiple phenomena are handled by combining results from a small ensemble of such patterns. This combination also allows detecting any residual errors that are corrected by acquiring a few additional images. Our methods can be readily incorporated into existing scanning systems without significant overhead in terms of capture time or hardware. We show results for several scenes with complex shape and material properties. © 2012 Springer Science+Business Media, LLC. Source

Rudolf V.H.,Rice University
Proceedings. Biological sciences / The Royal Society | Year: 2014

Efforts to characterize food webs have generated two influential approaches that reduce the complexity of natural communities. The traditional approach groups individuals based on their species identity, while recently developed approaches group individuals based on their body size. While each approach has provided important insights, they have largely been used in parallel in different systems. Consequently, it remains unclear how body size and species identity interact, hampering our ability to develop a more holistic framework that integrates both approaches. We address this conceptual gap by developing a framework which describes how both approaches are related to each other, revealing that both approaches share common but untested assumptions about how variation across size classes or species influences differences in ecological interactions among consumers. Using freshwater mesocosms with dragonfly larvae as predators, we then experimentally demonstrate that while body size strongly determined how predators affected communities, these size effects were species specific and frequently nonlinear, violating a key assumption underlying both size- and species-based approaches. Consequently, neither purely species- nor size-based approaches were adequate to predict functional differences among predators. Instead, functional differences emerged from the synergistic effects of body size and species identity. This clearly demonstrates the need to integrate size- and species-based approaches to predict functional diversity within communities. Source

Kinard L.A.,Rice University
Nature protocols | Year: 2012

This protocol describes the synthesis of oligo(poly(ethylene glycol) fumarate) (OPF; 1-35 kDa; a polymer useful for tissue engineering applications) by a one-pot reaction of poly(ethylene glycol) (PEG) and fumaryl chloride. The procedure involves three parts: dichloromethane and PEG are first dried; the reaction step follows, in which fumaryl chloride and triethylamine are added dropwise to a solution of PEG in dichloromethane; and finally, the product solution is filtered to remove by-product salt, and the OPF product is twice crystallized, washed and dried under vacuum. The reaction is affected by the molecular weight of PEG and reactant molar ratio. The OPF product is cross-linked by radical polymerization by either a thermally induced or ultraviolet-induced radical initiator, and the physical properties of the OPF oligomer and resulting cross-linked hydrogel are easily tailored by varying PEG molecular weight. OPF hydrogels are injectable, they polymerize in situ and they undergo biodegradation by hydrolysis of ester bonds. The expected time required to complete this protocol is 6 d. Source

Pimpinelli A.,Rice University | Tumbek L.,University of Graz | Winkler A.,University of Graz
Journal of Physical Chemistry Letters | Year: 2014

It is known in thin-film deposition that the density of nucleated clusters N varies with the deposition rate F as a power law, N ∼ Fα. The exponent α is a function of the critical nucleus size i in a way that changes with the aggregation limiting process. We extend here the derivation of the analytical capture-zone distribution function Pβ(s) = aß·sβ·exp(-b βs2) of Pimpinelli and Einstein to generic aggregation-limiting processes. We show that the parameter β is generally related to the critical nucleus size i and to the exponent α by the equality α·β = i, in the case of compact islands. This remarkable result allows one to measure i with no a priori knowledge of the actual aggregation mechanism. We apply this equality to measuring the critical nucleus size for pentacene deposition on mica. This system shows a crossover from diffusion-limited to attachment-limited aggregation with increasing deposition rates. © 2014 American Chemical Society. Source

Asif M.S.,Rice University | Romberg J.,Georgia Institute of Technology
IEEE Transactions on Signal Processing | Year: 2014

Most of the existing sparse-recovery methods assume a static system: the signal is a finite-length vector for which a fixed set of measurements and sparse representation are available and an l1 problem is solved for the reconstruction. However, the same representation and reconstruction framework is not readily applicable in a streaming system: the signal changes over time, and it is measured and reconstructed sequentially over small intervals. This is particularly desired when dividing signals into disjoint blocks and processing each block separately is infeasible or inefficient. In this paper, we discuss two streaming systems and a new homotopy algorithm for quickly solving the associated l1 problems: 1) recovery of smooth, time-varying signals for which, instead of using block transforms, we use lapped orthogonal transforms for sparse representation and 2) recovery of sparse, time-varying signals that follows a linear dynamic model. For both systems, we iteratively process measurements over a sliding interval and solve a weighted l1-norm minimization problem for estimating sparse coefficients. Since we estimate overlapping portions of the signal while adding and removing measurements, instead of solving a new l1 program as the system changes, we use available signal estimates as starting point in a homotopy formulation and update the solution in a few simple steps. We demonstrate with numerical experiments that our proposed streaming recovery framework provides better reconstruction compared to the methods that represent and reconstruct signals as independent, disjoint blocks, and that our proposed homotopy algorithm updates the solution faster than the current state-of-the-art solvers. © 1991-2012 IEEE. Source

Takizawa K.,Waseda University | Tezduyar T.E.,Rice University
Computational Mechanics | Year: 2014

We introduce space-time computation techniques with continuous representation in time (ST-C), using temporal NURBS basis functions. This gives us a temporally smooth, NURBS-based solution, which is desirable in some cases, and a more efficient way of dealing with the computed data. We propose two versions of ST-C. In the first version, the smooth solution is extracted by projection from a solution computed with a different temporal representation, typically a discontinuous one. We use a successive projection technique with a small number of temporal NURBS basis functions at each projection, and therefore the extraction can take place as the solution with discontinuous temporal representation is being computed, without storing a large amount of time-history data. This version is not limited to solutions computed with ST techniques. In the second version, the solution with continuous temporal representation is computed directly by using a small number of temporal NURBS basis functions in the variational formulation associated with each time step. © 2013 Springer-Verlag Berlin Heidelberg. Source

Fagan M.B.,Rice University
Biology and Philosophy | Year: 2012

Stem cell biology and systems biology are two prominent new approaches to studying cell development. In stem cell biology, the predominant method is experimental manipulation of concrete cells and tissues. Systems biology, in contrast, emphasizes mathematical modeling of cellular systems. For scientists and philosophers interested in development, an important question arises: how should the two approaches relate? This essay proposes an answer, using the model of Waddington's landscape to triangulate between stem cell and systems approaches. This simple abstract model represents development as an undulating surface of hills and valleys. Originally constructed by C. H. Waddington to visually explicate an integrated theory of genetics, development and evolution, the landscape model can play an updated unificatory role. I examine this model's structure, representational assumptions, and uses in all three contexts, and argue that explanations of cell development require both mathematical models and concrete experiments. On this view, the two approaches are interdependent, with mathematical models playing a crucial but circumscribed role in explanations of cell development. © 2011 Springer Science+Business Media B.V. Source

Aggarwal V.,AT&T | Sabharwal A.,Rice University
IEEE Transactions on Information Theory | Year: 2011

Most communication systems use some form of feedback, often related to channel state information. In this paper, we study diversity multiplexing tradeoff for both frequency division duplex (FDD) and time division duplex (TDD) systems, when both receiver and transmitter knowledge about the channel is noisy and potentially mismatched. For FDD systems, we first extend the achievable tradeoff region for 1.5 rounds of message passing to get higher diversity compared to the best known scheme, in the regime of higher multiplexing gains. We then break the mold of all current channel state based protocols by using multiple rounds of conferencing to extract more bits about the actual channel. This iterative refinement of the channel increases the diversity order with every round of communication. The protocols are on-demand in nature, using high powers for training and feedback only when the channel is in poor states. The key result is that the diversity multiplexing tradeoff with perfect training and K levels of perfect feedback can be achieved, even when there are errors in training the receiver and errors in the feedback link, with a multiround protocol which has K rounds of training and K-1 rounds of binary feedback. The above result can be viewed as a generalization of Zheng and Tse, and Aggarwal and Sabharwal, where the result was shown to hold for K=1 and K=2, respectively. For TDD systems, we also develop new achievable strategies with multiple rounds of communication between the transmitter and the receiver, which use the reciprocity of the forward and the feedback channel. The multiround TDD protocol achieves a diversity-multiplexing tradeoff which uniformly dominates its FDD counterparts, where no channel reciprocity is available. © 2011 IEEE. Source

Xu Q.,Rice University | Soref R.,Air Force Research Lab
Optics Express | Year: 2011

We present a reconfigurable optical directed logic architecture that offers several significant improvements over the original directed logic presented by Hardy and Shamir. Specific embodiments of on-chip, waveguided, large-scale-integrated, cellular optical directed logic fabrics are proposed and analyzed. Five important logic functions are presented as examples to show that the same switch fabric can be reconfigured to perform different logic functions. © 2011 Optical Society of America. Source

In part to search for a possible critical point (CP) in the phase diagram of hot nuclear matter, a Beam Energy Scan was performed at the Relativistic Heavy-Ion Collider at Brookhaven National Laboratory. The STAR experiment collected significant Au + Au data sets at beam energies, sNN, of 7.7, 11.5, 19.6, 27, 39, 62.4, and 200 GeV. Lattice and phenomenological calculations suggest that the presence of a CP might result in divergences of the thermodynamic susceptibilities and correlation length. The statistical moments of the multiplicity distributions of particles reflecting conserved quantities, such as net-charge and net-strangeness, are expected to depend sensitively on these correlation lengths, making them attractive tools in the search for a possible critical point. The centrality and beam-energy dependence of the statistical moments of the netcharge multiplicity distributions will be discussed. The observables studied include the lowest four statistical moments (mean, variance, skewness, kurtosis) and the products of these moments. The measured moments of the net-kaon multiplicity distributions will also be presented. These will be compared to the predictions from approaches lacking critical behavior, such as the Hadron Resonance Gas model and Poisson statistics. © 2013. Source

Geurts F.,Rice University
Nuclear Physics A | Year: 2013

Dileptons provide ideal penetrating probes of the evolution of strongly interacting matter. With the Time-of-Flight upgrade, STAR is in a unique position to provide large-acceptance dielectron measurements. We discuss preliminary dielectron results for Au + Au collisions at sNN=19.6-200GeV, and compare to recent model calculations. With upcoming detector upgrades STAR will further improve its dielectron measurements as well as include dimuon measurements. © 2013 Elsevier B.V. Source

Luo Z.,National University of Singapore | Yuan X.,National University of Singapore | Yu Y.,National University of Singapore | Zhang Q.,Rice University | And 3 more authors.
Journal of the American Chemical Society | Year: 2012

A fundamental understanding of the luminescence of Au-thiolate nanoclusters (NCs), such as the origin of emission and the size effect in luminescence, is pivotal to the development of efficient synthesis routes for highly luminescent Au NCs. This paper reports an interesting finding of Au(I)-thiolate complexes: strong luminescence emission by the mechanism of aggregation-induced emission (AIE). The AIE property of the complexes was then used to develop a simple one-pot synthesis of highly luminescent Au-thiolate NCs with a quantum yield of ∼15%. Our key strategy was to induce the controlled aggregation of Au(I)-thiolate complexes on in situ generated Au(0) cores to form Au(0)@Au(I)-thiolate core-shell NCs where strong luminescence was generated by the AIE of Au(I)-thiolate complexes on the NC surface. We were able to extend the synthetic strategy to other thiolate ligands with added functionalities (in the form of custom-designed peptides). The discovery (e.g., identifying the source of emission and the size effect in luminescence) and the synthesis protocols in this study can contribute significantly to better understanding of these new luminescence probes and the development of new synthetic routes. © 2012 American Chemical Society. Source

Kougioumtzoglou I.A.,University of Liverpool | Spanos P.D.,Rice University
Probabilistic Engineering Mechanics | Year: 2012

A novel approximate analytical technique for determining the non-stationary response probability density function (PDF) of a class of randomly excited nonlinear oscillators is developed. Specifically, combining the concepts of statistical linearization and of stochastic averaging the evolution of the response amplitude of oscillators with nonlinear damping is captured by a first-order stochastic differential equation (SDE). This equation has nonlinear drift but constant diffusion coefficients. This convenient feature of the SDE along with the concept of the Wiener path integral is utilized in conjunction with a variational formulation to derive an approximate closed form solution for the response amplitude PDF. Notably, the determination of the non-stationary response PDF is accomplished without the need to advance the solution in short time steps as it is required by the existing alternative numerical path integral solution schemes. In this manner, an analytical Wiener path integral based technique is developed for treating certain stochastic dynamics problems for the first time. Further, the technique can be used as a convenient tool for assessing the accuracy of alternative, more general, approximate solution methods. The accuracy of the technique is demonstrated by pertinent Monte Carlo simulations. © 2011 Elsevier Ltd. All rights reserved. Source

Bajwa W.U.,Princeton University | Haupt J.,Rice University | Sayeed A.M.,University of Wisconsin - Madison | Nowak R.,University of Wisconsin - Madison
Proceedings of the IEEE | Year: 2010

High-rate data communication over a multipath wireless channel often requires that the channel response be known at the receiver. Training-based methods, which probe the channel in time, frequency, and space with known signals and reconstruct the channel response from the output signals, are most commonly used to accomplish this task. Traditional training-based channel estimation methods, typically comprising linear reconstruction techniques, are known to be optimal for rich multipath channels. However, physical arguments and growing experimental evidence suggest that many wireless channels encountered in practice tend to exhibit a sparse multipath structure that gets pronounced as the signal space dimension gets large (e.g., due to large bandwidth or large number of antennas). In this paper, we formalize the notion of multipath sparsity and present a new approach to estimating sparse (or effectively sparse) multipath channels that is based on some of the recent advances in the theory of compressed sensing. In particular, it is shown in the paper that the proposed approach, which is termed as compressed channel sensing (CCS), can potentially achieve a target reconstruction error using far less energy and, in many instances, latency and bandwidth than that dictated by the traditional least-squares-based training methods. © 2010 IEEE. Source

Tehranipoor M.,University of Texas at Dallas | Koushanfar F.,Rice University
IEEE Design and Test of Computers | Year: 2010

Editor's note: Today's integrated circuits are vulnerable to hardware Trojans, which are malicious alterations to the circuit, either during design or fabrication. This article presents a classification of hardware Trojans and a survey of published techniques for Trojan detection. -Krish Chakrabarty, Editor in Chief. © 2010 IEEE. Source

Geurts F.,Rice University
Journal of Physics: Conference Series | Year: 2013

In the study of hot and dense nuclear matter, created in relativistic heavy-ion collisions, dilepton measurements play an essential role. Leptons, when compared to hadrons, have only little interaction with the strongly interacting system. Thus, dileptons provide ideal penetrating probes that allow the study of such a system throughout its space-time evolution. In the low mass range (Mll < 1.1 GeV/c2), the dominant source of dileptons originates from the decay of vector mesons which may see effects from chiral symmetry restoration. In the intermediate mass range (1.1 < M ll < 3.0 GeV/c2), the main contributions to the mass spectrum are expected to originate from the thermal radiation of a quark-gluon plasma as well as the decays of charm mesons. In the high mass range (M ll > 3.0 GeV/c2), dilepton measurements are expected to see contributions from primordial processes involving heavy quarks, and Drell-Yan production. With the introduction of the Time-of-Flight detector, the STAR detector has been able to perform large acceptance, high purity electron identification. In this contribution, we will present STAR's recent dielectron measurements in the low and intermediate mass range for RHIC beam energies ranging between 19.6 and 200 GeV. Compared to electrons, muon measurements have the advantage of reduced bremsstrahlung radiation in the surrounding detector materials. With the upcoming detector upgrades, specifically the muon detector (MTD), STAR will be able to include such measurements in its (di-)lepton studies. We will discuss the future dilepton program at STAR and the physics cases for these upgrades. © Published under licence by IOP Publishing Ltd. Source

Wolynes P.G.,Rice University
Biochimie | Year: 2015

Protein folding has been viewed as a difficult problem of molecular self-organization. The search problem involved in folding however has been simplified through the evolution of folding energy landscapes that are funneled. The funnel hypothesis can be quantified using energy landscape theory based on the minimal frustration principle. Strong quantitative predictions that follow from energy landscape theory have been widely confirmed both through laboratory folding experiments and from detailed simulations. Energy landscape ideas also have allowed successful protein structure prediction algorithms to be developed. The selection constraint of having funneled folding landscapes has left its imprint on the sequences of existing protein structural families. Quantitative analysis of co-evolution patterns allows us to infer the statistical characteristics of the folding landscape. These turn out to be consistent with what has been obtained from laboratory physicochemical folding experiments signaling a beautiful confluence of genomics and chemical physics. © 2014 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). Source

Ferrari M.,University of Texas Health Science Center at Houston | Ferrari M.,University of Houston | Ferrari M.,Rice University
Trends in Biotechnology | Year: 2010

The physics of mass transport within body compartments and across biological barriers differentiates cancers from healthy tissues. Variants of nanoparticles can be manufactured in combinatorially large sets, varying by only one transport-affecting design parameter at a time. Nanoparticles can also be used as building blocks for systems that perform sequences of coordinated actions, in accordance with a prescribed logic. We refer to these as Logic-Embedded Vectors (LEVs). Nanoparticles and LEVs are ideal probes for the determination of mass transport laws in tumors, acting as imaging contrast enhancers, and can be employed for lesion-selective delivery of therapy. Their size, shape, density and surface chemistry dominate convective transport in the bloodstream, margination, cell adhesion, selective cellular uptake, as well as sub-cellular trafficking and localization. As argued here, the understanding of transport differentials in cancer, termed 'transport oncophysics', reveals a promising new frontier in oncology: the development of lesion-specific delivery particulates that exploit mass transport differentials to deploy treatment of greater efficacy and reduced side effects. © 2009 Elsevier Ltd. Source

Balasundaram B.,Oklahoma State University | Butenko S.,Texas A&M University | Hicks I.V.,Rice University
Operations Research | Year: 2011

This paper introduces and studies the maximum k-plex problem, which arises in social network analysis and has wider applicability in several important areas employing graph-based data mining. After establishing NP-completeness of the decision version of the problem on arbitrary graphs, an integer programming formulation is presented, followed by a polyhedral study to identify combinatorial valid inequalities and facets. A branch-and-cut algorithm is implemented and tested on proposed benchmark instances. An algorithmic approach is developed exploiting the graph-theoretic properties of a k-plex that is effective in solving the problem to optimality on very large, sparse graphs such as the power law graphs frequently encountered in the applications of interest. © 2011 INFORMS. Source

Zheng X.,University of Houston | Carstens J.L.,University of Houston | Kim J.,University of Houston | Scheible M.,University of Houston | And 7 more authors.
Nature | Year: 2015

Diagnosis of pancreatic ductal adenocarcinoma (PDAC) is associated with a dismal prognosis despite current best therapies; therefore new treatment strategies are urgently required. Numerous studies have suggested that epithelial-to-mesenchymal transition (EMT) contributes to early-stage dissemination of cancer cells and is pivotal for invasion and metastasis of PDAC. EMT is associated with phenotypic conversion of epithelial cells into mesenchymal-like cells in cell culture conditions, although such defined mesenchymal conversion (with spindle-shaped morphology) of epithelial cells in vivo is rare, with quasi-mesenchymal phenotypes occasionally observed in the tumour (partial EMT). Most studies exploring the functional role of EMT in tumours have depended on cell-culture-induced loss-of-function and gain-of-function experiments involving EMT-inducing transcription factors such as Twist, Snail and Zeb1 (refs 2, 3, 7, 8, 9, 10). Therefore, the functional contribution of EMT to invasion and metastasis remains unclear, and genetically engineered mouse models to address a causal connection are lacking. Here we functionally probe the role of EMT in PDAC by generating mouse models of PDAC with deletion of Snail or Twist, two key transcription factors responsible for EMT. EMT suppression in the primary tumour does not alter the emergence of invasive PDAC, systemic dissemination or metastasis. Suppression of EMT leads to an increase in cancer cell proliferation with enhanced expression of nucleoside transporters in tumours, contributing to enhanced sensitivity to gemcitabine treatment and increased overall survival of mice. Collectively, our study suggests that Snail- or Twist-induced EMT is not rate-limiting for invasion and metastasis, but highlights the importance of combining EMT inhibition with chemotherapy for the treatment of pancreatic cancer. © 2015 Macmillan Publishers Limited. All rights reserved. Source

Moulin H.,Rice University
International Game Theory Review | Year: 2013

The fertile application of cooperative game techniques to cost sharing problems on networks has so far concentrated on the Stand Alone core test of fairness and/or stability, and ignored many combinatorial optimization problems where this core can be empty. I submit there is much room for an axiomatic discussion of fair division in the latter problems, where Stand Alone objections are not implementable. But the computational complexity of optimal solutions is still a very severe obstacle to this approach. © 2013 World Scientific Publishing Company. Source

Shi H.,Institute of High Performance Computing of Singapore | Pan H.,Institute of High Performance Computing of Singapore | Zhang Y.-W.,Institute of High Performance Computing of Singapore | Yakobson B.I.,Rice University
Physical Review B - Condensed Matter and Materials Physics | Year: 2013

The quasiparticle (QP) band structures of both strainless and strained monolayer MoS2 are investigated using more accurate many-body perturbation GW theory and maximally localized Wannier functions (MLWFs) approach. By solving the Bethe-Salpeter equation (BSE) including excitonic effects on top of the partially self-consistent GW0 (scGW 0) calculation, the predicted optical gap magnitude is in good agreement with available experimental data. With increasing strain, the exciton binding energy is nearly unchanged, while optical gap is reduced significantly. The scGW0 and BSE calculations are also performed on monolayer WS2, similar characteristics are predicted and WS2 possesses the lightest effective mass at the same strain among monolayers Mo(S,Se) and W(S,Se). Our results also show that the electron effective mass decreases as the tensile strain increases, resulting in an enhanced carrier mobility. The present calculation results suggest a viable route to tune the electronic properties of monolayer transition-metal dichalcogenides (TMDs) using strain engineering for potential applications in high performance electronic devices. © 2013 American Physical Society. Source

1.Theory suggests that the relationship between predator diversity and prey suppression should depend on variation in predator traits such as body size, which strongly influences the type and strength of species interactions. Prey species often face a range of different sized predators, and the composition of body sizes of predators can vary between communities and within communities across seasons. 2.Here, I test how variation in size structure of predator communities influences prey survival using seasonal changes in the size structure of a cannibalistic population as a model system. Laboratory and field experiments showed that although the per-capita consumption rates increased at higher predator-prey size ratios, mortality rates did not consistently increase with average size of cannibalistic predators. Instead, prey mortality peaked at the highest level of predator body size diversity. 3.Furthermore, observed prey mortality was significantly higher than predictions from the null model that assumed no indirect interactions between predator size classes, indicating that different sized predators were not substitutable but had more than additive effects. Higher predator body size diversity therefore increased prey mortality, despite the increased potential for behavioural interference and predation among predators demonstrated in additional laboratory experiments. 4.Thus, seasonal changes in the distribution of predator body sizes altered the strength of prey suppression not only through changes in mean predator size but also through changes in the size distribution of predators. In general, this indicates that variation (i.e. diversity) within a single trait, body size, can influence the strength of trophic interactions and emphasizes the importance of seasonal shifts in size structure of natural food webs for community dynamics. © 2011 The Author. Journal of Animal Ecology © 2011 British Ecological Society. Source

Manjavacas A.,CSIC - Institute of Physical Chemistry "Rocasolano" | Nordlander P.,Rice University | Garcia De Abajo F.J.,CSIC - Institute of Physical Chemistry "Rocasolano" | Garcia De Abajo F.J.,University of Southampton
ACS Nano | Year: 2012

Among the many extraordinary properties of graphene, its optical response allows one to easily tune its interaction with nearby molecules via electrostatic doping. The large confinement displayed by plasmons in graphene nanodisks makes it possible to reach the strong-coupling regime with a nearby quantum emitter, such as a quantum dot or a molecule. In this limit, the quantum emitter can introduce a significant plasmon-plasmon interaction, which gives rise to a plasmon blockade effect. This produces, in turn, strongly nonlinear absorption cross sections and modified statistics of the bosonic plasmon mode. We characterize these phenomena by studying the equal-time second-order correlation function g (2)(0), which plunges below a value of 1, thus revealing the existence of nonclassical plasmon states. The plasmon-emitter coupling, and therefore the plasmon blockade, can be efficiently controlled by tuning the doping level of the graphene nanodisks. The proposed system emerges as a new promising platform to realize quantum plasmonic devices capable of commuting optical signals at the single-photon/plasmon level. © 2012 American Chemical Society. Source

Ahmed E.,University of California at Irvine | Eltawil A.M.,University of California at Irvine | Sabharwal A.,Rice University
IEEE Transactions on Wireless Communications | Year: 2013

In this paper, we analytically study the regime in which practical full-duplex systems can achieve larger rates than an equivalent half-duplex systems. The key challenge in practical full-duplex systems is uncancelled self-interference signal, which is caused by a combination of hardware and implementation imperfections. Thus, we first present a signal model which captures the effect of significant impairments such as oscillator phase noise, low-noise amplifier noise figure, mixer noise, and analog-to-digital converter quantization noise. Using the detailed signal model, we study the rate gain region, which is defined as the region of received signal-of-interest strength where full-duplex systems outperform half-duplex systems in terms of achievable rate. The rate gain region is derived as a piecewise linear approximation in log-domain, and numerical results show that the approximation closely matches the exact region. Our analysis shows that when phase noise dominates mixer and quantization noise, full-duplex systems can use either active analog cancellation or baseband digital cancellation to achieve near-identical rate gain regions. Finally, as a design example, we numerically investigate the full-duplex system performance and rate gain region in typical indoor environments for practical wireless applications. © 2002-2012 IEEE. Source

Thapar R.,Rice University
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms | Year: 2015

The high-mobility group (HMG) domain containing proteins regulate transcription, DNA replication and recombination. They adopt L-shaped folds and are structure-specific DNA binding motifs. Here, I define the L-motif super-family that consists of DNA-binding HMG-box proteins and the L-motif of the histone mRNA binding domain of stem-loop binding protein (SLBP). The SLBP L-motif and HMG-box domains adopt similar L-shaped folds with three α-helices and two or three small hydrophobic cores that stabilize the overall fold, but have very different and distinct modes of nucleic acid recognition. A comparison of the structure, dynamics, protein-protein and nucleic acid interactions, and regulation by PTMs of the SLBP and the HMG-box L-motifs reveals the versatile and diverse modes by which L-motifs utilize their surfaces for structure-specific recognition of nucleic acids to regulate gene expression. © 2015 Elsevier B.V. Source

Gonnermann H.M.,Rice University | Houghton B.F.,University of Hawaii at Manoa
Geochemistry, Geophysics, Geosystems | Year: 2012

We have modeled the nucleation and isothermal growth of bubbles in dacite from the 1912 Plinian eruption of Novarupta, Alaska. Bubble growth calculations account for the exsolution of H 2O and CO 2, beginning with bubble nucleation and ending when bubble sizes reproduced the observed size distribution of vesicles in Novarupta pumice clasts. Assuming classical nucleation theory, bubbles nucleated with a diameter of the order of 10 -8 m and grew to sizes ranging from 10 -6 m to greater than 10 -3 m, the typical range of vesicle sizes found in Novarupta pumice. The smallest vesicles in Novarupta pumices are also the most abundant and bubbles with radii of 10 -6 m to 10 -5 m comprise almost 90% of the entire bubble population. We find that these bubbles must have nucleated and grown to their final size within a few 100 milliseconds. Despite these extremely fast growth rates, the pressures of exsolved volatiles contained within the bubbles remained high, up to about 10 7 Pa in excess of ambient pressure. Assuming a closed-system, the potential energy of these compressed volatiles was sufficient to cause magma fragmentation, even though only a fraction of the pre-eruptive volatiles had exsolved. Unless the matrix glasses of Novarupta pyroclasts retains a large fraction of pre-eruptive volatiles, the majority of magmatic volatiles (80-90%) was likely lost by open-system degassing between magma fragmentation and quenching. © 2012. American Geophysical Union. All Rights Reserved. Source

Duenas-Osorio L.,Rice University | Kwasinski A.,University of Texas at Austin
Earthquake Spectra | Year: 2012

Data on lifeline system service restoration is seldom exploited for the calibration of performance prediction models or for response comparisons across systems and events. This study explores utility restoration curves after the 2010 Chilean earthquake through a time series method to quantify coupling strengths across lifeline systems. When consistent with field information, cross-correlations from restoration curves without significant lag times quantify operational interdependence, whereas those with significant lags reveal logistical interdependence. Synthesized coupling strengths are also proposed to incorporate cross-correlations and lag times at once. In the Chilean earthquake, coupling across fixed and mobile phones was the strongest per region followed by coupling within and across telecommunication and power systems in adjacent regions. Unapparent couplings were also revealed among telecommunication and power systems with water networks. The proposed methodology can steer new protocols for post-disaster data collection, including anecdotal information to evaluate causality, and inform infrastructure interdependence effect prediction models. © 2012, Earthquake Engineering Research Institute. Source

Niu F.,China University of Petroleum - Beijing | Niu F.,Rice University
Earth and Planetary Science Letters | Year: 2014

We observe a clear seismic arrival at ~35-45. s after the direct P wave in USArray recordings of two deep earthquakes occurring beneath northeast China. Velocity-spectrum and beam-forming analyses reveal that this arrival has a lower slowness value than the direct P wave and a back azimuth slightly different from the great-circle direction. The measured slowness and arrival time indicate that it is a transmitted S to P conversion from structures below the sources. We employ the common-conversion-point (CCP) stacking and diffraction migration methods to determine the location and geometric features of the seismic structures. The CCP stacking image indicates that the structure is a localized discontinuity at ~1000. km with a dimension at ~200. km by ~50. km along the E-W and N-S directions, respectively. It is located at ~150. km northeast to the two events. The 2D migrated images, on the other hand, indicate that the sources structure are reflectors dipping northeastwards by ~17° at a slightly shallower depths. The reflectors have a length scale of ~100. km ant their centers are ~50. km away from the epicenters of the two earthquakes. Forward waveform modeling suggests that the dipping reflectors may be thin layers with a thickness of few kilometers. The layers have a lower shear velocity and a higher density than that of the surrounding mantle, which matches well with those predicted for mid-ocean-ridge basalt (MORB) at mid-mantle depths, according to a recent ab initio study. Combined with the results from previous studies, our observations here suggest that the former oceanic crust may be ubiquitously present in the lower mantle beneath subduction zones. © 2013 Elsevier B.V. Source

Levander A.,Rice University | Miller M.S.,University of Southern California
Geochemistry, Geophysics, Geosystems | Year: 2012

We have produced common conversion point (CCP) stacked Ps and Sp receiver function image volumes of the Moho and lithosphere-asthenosphere boundary (LAB) beneath the western United States using Transportable Array data. The large image volumes and the diversity of tectonic environments they encompass allow us to investigate evolution of these structural discontinuities. The Moho is a nearly continuous topographic surface, whereas the LAB is not and the seismic images show a more complex expression. The first order change in LAB depth in the western U.S. occurs along the Cordilleran hingeline, the former Laurasian passive margin along the southwestern Precambrian North American terranes. The LAB is about 50% deeper to the east of the hingeline than to the west, with most of the increase in LAB thickness being in the mantle lithosphere. We infer that the Moho and the LAB are Late Mesozoic or Cenozoic everywhere west of the hingeline, modified during Farallon subduction and its aftermath. Between the hingeline and the Rocky Mountain Front, the LAB, and to a lesser extent the Moho, have been partially reset during the Cenozoic by processes that continue today. Seismicity and recent volcanism in the interior of the western U.S. are concentrated along gradients in crustal and/or lithospheric thickness, for example the hingeline, and the eastern edge of the coastal volcanic-magmatic terranes. To us this suggests that lateral gradients in integrated lithospheric strength focus deformation. Similarly, areas conjectured to be the sites of convective downwellings and associated volcanism are located along gradients in regional lithosphere thickness. © 2012. American Geophysical Union. Source

Evolution by natural selection is the driving force behind the endless variation we see in nature, yet our understanding of how changes at the molecular level give rise to different phenotypes and altered fitness at the population level remains inadequate. The reproductive fitness of an organism is the most basic metric that describes the chance that an organism will succeed or fail in its environment and it depends upon a complex network of inter- and intramolecular interactions. A deeper understanding of the quantitative relationships relating molecular evolution to adaptation, and consequently fitness, can guide our understanding of important issues in biomedicine such as drug resistance and the engineering of new organisms with applications to biotechnology. We have developed the "weak link" approach to determine how changes in molecular structure and function can relate to fitness and evolutionary outcomes. By replacing adenylate kinase (AK), an essential gene, in a thermophile with a homologous AK from a mesophile we have created a maladapted weak link that produces a temperature-sensitive phenotype. The recombinant strain adapts to nonpermissive temperatures through point mutations to the weak link that increase both stability and activity of the enzyme AK at higher temperatures. Here, we propose a fitness function relating enzyme activity to growth rate and use it to create a dynamic model of a population of bacterial cells. Using metabolic control analysis we show that the growth rate exhibits thresholdlike behavior, saturating at high enzyme activity as other reactions in the energy metabolism pathway become rate limiting. The dynamic model accurately recapitulates observed evolutionary outcomes. These findings suggest that in vitro enzyme kinetic data, in combination with metabolic network analysis, can be used to create fitness functions and dynamic models of evolution within simple metabolic systems. (c) 2010 American Institute of Physics. Source

Ball Z.T.,Rice University
Accounts of Chemical Research | Year: 2013

Chemists have long been fascinated by metalloenzymes and their chemistry. Because enzymes are essential for biological processes and to life itself, they present a key to understanding the world around us. At the same time, if chemists could harness the reactivity and selectivity of enzymes in designed transition-metal catalysts, we would have access to a powerful practical advance in chemistry. But the design of enzyme-like catalysts from scratch presents enormous challenges. Simplified, designed systems often don't provide the opportunity to mimic the complex features of enzymes such as selectivity in polyfunctional environments and access to reactive intermediates incompatible with bulk aqueous solution.Extensive efforts by numerous groups have led to remarkable designed metalloproteins that contain complex folds, including well-defined secondary and tertiary structure surrounding complex polymetallic centers. These structural achievements, however, have not yet led to general approaches to useful catalysts; continued efforts and new insights are needed. Our efforts have combined the attributes of enzymatic and traditional catalysis, bringing the benefits of polypeptide ligands to bear on completely nonbiological transition-metal centers. With a focus on designing useful catalytic activity, we have examined rhodium(II) carboxylates, bound to peptide chains through carboxylate side chains. Among other advantages, these complexes are stable and catalytically active in water.Our efforts have centered on two main interests: (1) understanding how Nature's ligand of choice, polypeptides, can be used to control the chemistry of nonbiological metal centers, and (2) mimicking metalloenzyme characteristics in designed, nonbiological catalysts. This Account conveys our motivation and goals for these studies, outlines progress to date, and discusses the future of enzyme-like catalyst design.In particular, these studies have resulted in on-bead, high-throughput screens for asymmetric metallopeptide catalysts. In addition, peptide-based molecular recognition strategies have facilitated the site-specific modification of protein substrates. Molecular recognition enables site-specific, proximity-driven modification of a broad range of amino acids, and the concepts outlined here are compatible with natural protein substrates and with complex, cell-like environments. We have also explored rhodium metallopeptides as hybrid organic-inorganic inhibitor molecules that block protein-protein interactions. © 2012 American Chemical Society. Source

Tour J.M.,Rice University
ACS Nano | Year: 2012

As advances in nanoscience and nanotechnology are sought, what will be the source of the inspiration to open the doors for new developments? In my opinion, it most often resides in the ingenuity of students, and among those ingenious students, was there a formative spark or a progressive set of stimuli in their childhoods that gave rise to the most precious asset in scientific advance, namely, creativity? Here, I outline the work of three ofmy studentswho have propelled the field of nanotechnology, and then I glimpse into their childhood years to see if there lays the key © 2012 American Chemical Society. Source

Ecklund E.H.,Rice University | Lincoln A.E.,Southern Methodist University
PLoS ONE | Year: 2011

Scholars partly attribute the low number of women in academic science to the impact of the science career on family life. Yet, the picture of how men and women in science - at different points in the career trajectory - compare in their perceptions of this impact is incomplete. In particular, we know little about the perceptions and experiences of junior and senior scientists at top universities, institutions that have a disproportionate influence on science, science policy, and the next generation of scientists. Here we show that having fewer children than wished as a result of the science career affects the life satisfaction of science faculty and indirectly affects career satisfaction, and that young scientists (graduate students and postdoctoral fellows) who have had fewer children than wished are more likely to plan to exit science entirely. We also show that the impact of science on family life is not just a woman's problem; the effect on life satisfaction of having fewer children than desired is more pronounced for male than female faculty, with life satisfaction strongly related to career satisfaction. And, in contrast to other research, gender differences among graduate students and postdoctoral fellows disappear. Family factors impede talented young scientists of both sexes from persisting to research positions in academic science. In an era when the global competitiveness of US science is at risk, it is concerning that a significant proportion of men and women trained in the select few spots available at top US research universities are considering leaving science and that such desires to leave are related to the impact of the science career on family life. Results from our study may inform university family leave policies for science departments as well as mentoring programs in the sciences. © 2011 Ecklund, Lincoln. Source

Acosta S.,Rice University
Inverse Problems | Year: 2013

In this paper we develop a time reversal method for the radiative transport equation to solve two problems: an inverse problem for the recovery of an initial condition from boundary measurements, and the exact boundary controllability of the transport field with finite steering time. Absorbing and scattering effects, modeled by coefficients with low regularity, are incorporated in the formulation of these problems. This time reversal approach leads to a convergent iterative procedure to reconstruct the initial condition provided that the scattering coefficient is sufficiently small in the L ∞ norm. Then, using duality arguments, we show that the solvability of the inverse problem leads to exact controllability of the transport field with minimum-norm control obtained constructively. The solution approach to both of these problems may have applications in areas such as optical imaging and optimization of radiation delivery. © 2013 IOP Publishing Ltd. Source

Hyeon C.,Korea Institute for Advanced Study | Onuchic J.N.,Rice University
Biophysical Journal | Year: 2011

Despite significant fluctuation under thermal noise, biological machines in cells perform their tasks with exquisite precision. Using molecular simulation of a coarse-grained model and theoretical arguments, we envisaged how kinesin, a prototype of biological machines, generates force and regulates its dynamics to sustain persistent motor action. A structure-based model, which can be versatile in adapting its structure to external stresses while maintaining its native fold, was employed to account for several features of kinesin dynamics along the biochemical cycle. This analysis complements our current understandings of kinesin dynamics and connections to experiments. We propose a thermodynamic cycle for kinesin that emphasizes the mechanical and regulatory role of the neck linker and clarify issues related to the motor directionality, and the difference between the external stalling force and the internal tension responsible for the head-head coordination. The comparison between the thermodynamic cycle of kinesin and macroscopic heat engines highlights the importance of structural change as the source of work production in biomolecular machines. © 2011 Biophysical Society. Source

Wallach D.S.,Rice University
Communications of the ACM | Year: 2011

A proposal for a new cost-free open-access publication model for computer science papers is described. The top conferences, where publication can make or break a career, may publish 10% of the submitted papers. As submission rates have gone up, program committees must decide between huge workloads per reviewer, or adding PC members to the point where most members are completely disconnected from most papers' discussions. Many current academics bemoan the good old days when one could have a group working on an involved, complex project, and have only one or a small number of groundbreaking papers. CSPub is, at its core, a mashup of conference submission and review management software with technical report archiving services like arXiv and with bibliographic management and tracking and search services like DBLP and Google Scholar. Such annotations help when somebody is searching CSPub for a paper to cite on a particular topic, and they may also contribute directly to how a paper is ranked. Source

Kimbro R.T.,Rice University | Rigby E.,University of Houston
Health Affairs | Year: 2010

Amid growing concern about childhood obesity, the United States spends billions of dollars on food assistance: providing meals and subsidizing food purchases. We examine the relationship between food assistance and body mass index (BMI) for young, low-income children, who are a primary target population for federal food programs and for efforts to prevent childhood obesity. Our findings indicate that food assistance may unintentionally contribute to the childhood obesity problem in cities with high food prices. We also find that subsidized meals at school or day care are beneficial for children's weight status, and we argue that expanding access to subsidized meals may be the most effective tool to use in combating obesity in poor children. © 2010 Project HOPE-The People-to-People Health Foundation, Inc. Source

Bradshaw S.J.,Rice University | Klimchuk J.A.,NASA
Astrophysical Journal | Year: 2015

The million degree plasma of the solar corona must be supplied by the underlying layers of the atmosphere. The mechanism and location of energy release, and the precise source of coronal plasma, remain unresolved. In earlier work, we pursued the idea that warm plasma is supplied to the corona via direct heating of the chromosphere by nanoflares, contrary to the prevailing belief that the corona is heated in situ and the chromosphere is subsequently energized and ablated by thermal conduction. We found that single (low-frequency) chromospheric nanoflares could not explain the observed intensities, Doppler-shifts, and red/blue asymmetries in Fe xii and xiv emission lines. In the present work, we follow up on another suggestion that the corona could be powered by chromospheric nanoflares that repeat on a timescale substantially shorter than the cooling/draining timescale. That is, a single magnetic strand is re-supplied with coronal plasma before the existing plasma has time to cool and drain. We perform a series of hydrodynamic experiments and predict the Fe xii and xiv line intensities, Doppler-shifts, and red/blue asymmetries. We find that our predicted quantities disagree dramatically with observations and fully developed loop structures cannot be created by intermediate- or high-frequency chromospheric nanoflares. We conclude that the mechanism ultimately responsible for producing coronal plasma operates above the chromosphere, but this does not preclude the possibility of a similar mechanism powering the chromosphere, extreme examples of which may be responsible for heating chromospheric plasma to transition region temperatures (e.g., type II spicules). © 2015. The American Astronomical Society. All rights reserved. Source

Takizawa K.,Waseda University | Tezduyar T.E.,Rice University
Computational Mechanics | Year: 2011

We present the multiscale space-time techniques we have developed for fluid-structure interaction (FSI) computations. Some of these techniques are multiscale in the way the time integration is performed (i.e. temporally multiscale), some are multiscale in the way the spatial discretization is done (i.e. spatially multiscale), and some are in the context of the sequentially-coupled FSI (SCFSI) techniques developed by the Team for Advanced Flow Simulation and Modeling T AFSM . In the multiscale SCFSI technique, the FSI computational effort is reduced at the stage we do not need it and the accuracy of the fluid mechanics (or structural mechanics) computation is increased at the stage we need accurate, detailed flow (or structure) computation. As ways of increasing the computational accuracy when or where needed, and beyond just increasing the mesh refinement or decreasing the time-step size, we propose switching to more accurate versions of the Deforming-Spatial-Domain/Stabilized Space-Time (DSD/SST) formulation, using more polynomial power for the basis functions of the spatial discretization or time integration, and using an advanced turbulence model. Specifically, for more polynomial power in time integration, we propose to use NURBS, and as an advanced turbulence model to be used with the DSD/SST formulation, we introduce a space-time version of the residual-based variational multiscale method. We present a number of test computations showing the performance of the multiscale space-time techniques we are proposing. We also present a stability and accuracy analysis for the higher-accuracy versions of the DSD/SST formulation. © 2011 Springer-Verlag. Source

Kougioumtzoglou I.A.,University of Liverpool | Spanos P.D.,Rice University
Journal of Engineering Mechanics | Year: 2013

A numerical path integral solution approach is developed for determining the response and first-passage probability density functions (PDFs) of nonlinear oscillators subject to evolutionary broad-band stochastic excitations. Specifically, based on the concepts of statistical linearization and of stochastic averaging, the system response amplitude is modeled as a one-dimensional Markov diffusion process. Further, using a discrete version of the Chapman-Kolmogorov equation and the associated first-order stochastic differential equation, the response amplitude and first-passage PDFs are derived. The main concept of the approach relates to the evolution of the response PDF in short time steps, assuming a Gaussian form for the conditional response PDF. A number of nonlinear oscillators are considered in the numerical examples section including the versatile Preisach hysteretic oscillator. For this oscillator, first-passage PDFs are derived for the first time to the authors' best knowledge. Comparisons with pertinent Monte Carlo data demonstrate the reliability of the approach. © 2013 American Society of Civil Engineers. Source

Gravity is the one constant, ubiquitous force that has shaped life on Earth over its 4.8 billion years of evolution. But the sheer inescapability of Earth's gravitational pull has meant that its influence on Earth's organisms is difficult to study. Neutralization of the gravity vector (so-called simulated microgravity) by random movement in three-dimensional space is the best option for Earth-based experiments, with spaceflight alone offering the possibility to assess the effects of an extremely reduced gravitational field (microgravity). However, the technical constraints associated with spaceflight introduce complications that can compromise the interpretation of microgravity experiments. It can be unclear whether changes detected in these experiments reflect additional spaceflight-related stresses (temperature shifts, vibrational effects, radiation exposure, and so on) as opposed to the loss of gravitational force per se. In this issue, Herranz et al. (2010) report a careful study in which the effects of simulated and actual microgravity on gene expression in Drosophila melanogaster were compared and the effects of the flight-associated stresses on the microgravity responses were investigated. A striking finding emerged. The additional stresses associated with the spaceflight experiment altered the response to microgravity. Despite controlling for the effects of these stressesconstraints, the group found that responses to microgravity are much stronger in the stressedconstrained background than in its absence. This interaction of gravity with other environmental influences is a novel finding with important implications for microgravity research and other situations where multiple stress factors are combined. © 2010 Blackwell Publishing Ltd. Source

Llope W.J.,Rice University
Journal of Environmental Radioactivity | Year: 2011

The gamma radiation emitted from a variety of commercial decorative granites available for use in U.S. homes has been measured with portable survey meters as well as an NaI(Th) gamma spectrometer. The 40K, U-nat, and 232Th activity concentrations were determined using a full-spectrum analysis. The dose rates that would result from two different arrangements of decorative granite slabs as countertops were explored in simulations involving an adult anthropomorphic phantom. © 2011 Elsevier Ltd. Source

Nakhleh L.,Rice University
IEEE/ACM Transactions on Computational Biology and Bioinformatics | Year: 2010

Phylogenetic networks are leaf-labeled, rooted, acyclic, and directed graphs that are used to model reticulate evolutionary histories. Several measures for quantifying the topological dissimilarity between two phylogenetic networks have been devised, each of which was proven to be a metric on certain restricted classes of phylogenetic networks. A biologically motivated class of phylogenetic networks, namely, reduced phylogenetic networks, was recently introduced. None of the existing measures is a metric on the space of reduced phylogenetic networks. In this paper, we provide a metric on the space of reduced phylogenetic networks that is computable in time polynomial in the size of the networks. © 2006 IEEE. Source

Zhang S.,Pennsylvania State University | Gao H.,Brown University | Bao G.,Rice University
ACS Nano | Year: 2015

This review article focuses on the physiochemical mechanisms underlying nanoparticle uptake into cells. When nanoparticles are in close vicinity to a cell, the interactions between the nanoparticles and the cell membrane generate forces from different origins. This leads to the membrane wrapping of the nanoparticles followed by cellular uptake. This article discusses how the kinetics, energetics, and forces are related to these interactions and dependent on the size, shape, and stiffness of nanoparticles, the biomechanical properties of the cell membrane, as well as the local environment of the cells. The discussed fundamental principles of the physiochemical causes for nanoparticle-cell interaction may guide new studies of nanoparticle endocytosis and lead to better strategies to design nanoparticle-based approaches for biomedical applications. © 2015 American Chemical Society. Source

Chan E.P.,U.S. National Institute of Standards and Technology | Walish J.J.,Massachusetts Institute of Technology | Urbas A.M.,Air Force Research Lab | Thomas E.L.,Rice University
Advanced Materials | Year: 2013

Polymer gels are remarkable materials with physical structures that can adapt significantly and quite rapidly with changes in the local environment, such as temperature, light intensity, electrochemistry, and mechanical force. An interesting phenomenon observed in certain polymer gel systems is mechanochromism - a change in color due to a mechanical deformation. Mechanochromic photonic gels are periodically structured gels engineered with a photonic stopband that can be tuned by mechanical forces to reflect specific colors. These materials have potential as mechanochromic sensors because both the mechanical and optical properties are highly tailorable via incorporation of diluents, solvents, nanoparticles, or polymers, or the application of stimuli such as temperature, pH, or electric or strain fields. Recent advances in photonic gels that display strain-dependent optical properties are discussed. In particular, this discussion focuses primarily on polymer-based photonic gels that are directly or indirectly fabricated via self-assembly, as these materials are promising soft material platforms for scalable mechanochromic sensors. Mechanochromic photonic gels are polymer gels that display mechanical strain-responsive structural color. These gels are interesting materials for mechanochromic sensing applications due to their highly tunable mechanical and optical properties. In this progress report, recent advances in developing mechanochromic photonic gels that display strain-responsive optical properties for scalable sensors are highlighted. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Davidovich R.L.,RAS Institute of Chemistry | Stavila V.,Sandia National Laboratories | Whitmire K.H.,Rice University
Coordination Chemistry Reviews | Year: 2010

The stereochemistry of lead(II) complexes with S- and Se-donor atom ligands, including mixed ligand complexes is reviewed with respect to the geometry of the first coordination sphere of the Pb(II) atom in these compounds and rationalized in terms of the valence shell electron-pair repulsion (VSEPR) model. The most comprehensively structurally characterized classes of lead(II) thio and seleno complexes are discussed, including monothio-, dithio(seleno)-, trithio- and tetrathio-complexes, as well as Pb(II) dialkyldithio(seleno)carbamates, alkylxanthates and dialkyl(aryl) phosphorodithio(seleno)lates. Data about the polyhedral shape of the primary coordination sphere, coordination number (CN), bond lengths (primary and secondary) and bond angles of the Pb(II) atom in the compounds under investigation are systematized in comprehensive tables. The particularities of the stereochemistry of Pb(II) complexes with S(Se)-donor atom ligands are comparatively discussed with the stereochemistry of lead(II) complexes with oxygen donor ligands. © 2010 Elsevier B.V. Source

Schmidt J.E.,California Institute of Technology | Deem M.W.,Rice University | Davis M.E.,California Institute of Technology
Angewandte Chemie - International Edition | Year: 2014

Crystalline molecular sieves are used in numerous applications, where the properties exploited for each technology are the direct consequence of structural features. New materials are typically discovered by trial and error, and in many cases, organic structure-directing agents (OSDAs) are used to direct their formation. Here, we report the first successful synthesis of a specified molecular sieve through the use of an OSDA that was predicted from a recently developed computational method that constructs chemically synthesizable OSDAs. Pentamethylimidazolium is computationally predicted to have the largest stabilization energy in the STW framework, and is experimentally shown to strongly direct the synthesis of pure-silica STW. Other OSDAs with lower stabilization energies did not form STW. The general method demonstrated here to create STW may lead to new, simpler OSDAs for existing frameworks and provide a way to predict OSDAs for desired, theoretical frameworks. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Tate A.T.,Princeton University | Rudolf V.H.W.,Rice University
Oikos | Year: 2012

The immune response of a host can have important impacts on host-pathogen interactions, but investment in immunity often changes dynamically across the life history of a host. One form of investment involves the induction of a primed immune response against previously encountered pathogens that protects the host from re-infection. In addition to providing immediate protective effects, immune priming can also provide two types of 'delayed' protection against pathogens: priming across life stages (ontogenic priming) and priming across generations (trans-generational priming). Consequently both types of immune priming have the potential to mediate life history variability in host-pathogen interactions, which could have important consequences for disease prevalence and dynamics as well as for the demographic structure of the host population. Here we develop a stage-structured SIRS model for an invertebrate host to explore the relative and combined impact of ontogenic priming and trans-generational priming on infection prevalence, host population size, and population age structure. Our model predicts that both types of immune priming can dramatically reduce disease prevalence at equilibrium, but their individual and combined effects on population size and age structure depend on the magnitude of tradeoffs between immune protection and reproduction as well as on the symmetry of infection parameters between life stages. This model underscores the potential importance of life-history based immune investment patterns for disease dynamics and highlights the need for wide-spread empirical estimation of parameters that represent the maintenance of immune priming in insects. © 2011 The Authors. Oikos © 2011 Nordic Society Oikos. Source

Si Q.,Rice University
Physica Status Solidi (B) Basic Research | Year: 2010

Quantum criticality describes the collective fluctuations of matter undergoing a second-order phase transition at zero temperature. It is being discussed in a number of strongly correlated electron systems. A prototype case occurs in the heavy fermion metals, in which antiferromagnetic quantum critical points (QCPs) have been explicitly observed. Here, I address two types of antiferromagnetic QCPs. In addition to the standard description based on the fluctuations of the antiferromagnetic order, a local QCP is also considered. It contains inherently quantum modes that are associated with a critical breakdown of the Kondo effect. Across such a QCP, there is a sudden collapse of a large Fermi surface to a small one. I also consider the proximate antiferromagnetic and paramagnetic phases, and these considerations lead to a global phase diagram. Finally, I discuss the pertinent experiments and outline some directions for future studies. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Yazdani A.,Rice University | Jeffrey P.,Cranfield University
Water Resources Research | Year: 2012

The reliability and robustness against failures of networked water distribution systems are central tenets of water supply system design and operation. The ability of such networks to continue to supply water when components are damaged or fail is dependent on the connectivity of the network and the role and location of the individual components. This paper employs a set of advanced network analysis techniques to study the connectivity of water distribution systems, its relationship with system robustness, and susceptibility to damage. Water distribution systems are modeled as weighted and directed networks by using the physical and hydraulic attributes of system components. A selection of descriptive measurements is utilized to quantify the structural properties of benchmark systems at both local (component) and global (network) scales. Moreover, a novel measure of component criticality, the demand-adjusted entropic degree, is proposed to support identification of critical nodes and their ranking according to failure impacts. The application and value of this metric is demonstrated through two case study networks in the USA and UK. Discussion focuses on the potential for gradual evolution of abstract graph-based tools and techniques to more practical network analysis methods, where a theoretical framework for the analysis of robustness and vulnerability of water distribution networks to better support planning and management decisions is presented. © 2012. American Geophysical Union. All Rights Reserved. Source

Nicolaou K.C.,Rice University
Journal of the American Chemical Society | Year: 2016

The total synthesis of the spliceosome inhibitor thailanstatin A has been achieved in a longest linear sequence of nine steps from readily available starting materials. A key feature of the developed synthetic strategy is the implementation of a unique, biomimetic asymmetric intramolecular oxa-Michael reaction/hydrogenation sequence that allows diastereodivergent access to highly functionalized tetrahydropyrans, which can be used for the synthesis of designed analogues of this bioactive molecule. © 2016 American Chemical Society. Source

Johnson D.H.,Rice University
2013 IEEE Digital Signal Processing and Signal Processing Education Meeting, DSP/SPE 2013 - Proceedings | Year: 2013

The course Fundamentals of Electrical Engineering was recast for an massively open online course (MOOC) environment and taught beginning in January 2013 using the Coursera platform. Enrollment grew throughout the course's twelve week duration, ending up at over 34,000 registrants. Of these about 4,000 were watching videos at the course's end and 500 were working the problem sets. Recasting the course for the MOOC teaching scenario is estimated to have taken about 500 man-hours and supporting the course while it was active is estimated to have consumed another 400 hours. While preparing video lectures took most of this time, the aspect of the course requiring the most inventiveness was composing problems for the homework because of issues related to computerized grading, necessary because of the massive number of students. © 2013 IEEE. Source

Duarte M.,Ecole Polytechnique Federale de Lausanne | Dick C.,Xilinx Inc. | Sabharwal A.,Rice University
IEEE Transactions on Wireless Communications | Year: 2012

We present an experiment-based characterization of passive suppression and active self-interference cancellation mechanisms in full-duplex wireless communication systems. In particular, we consider passive suppression due to antenna separation at the same node, and active cancellation in analog and/or digital domain. First, we show that the average amount of cancellation increases for active cancellation techniques as the received self-interference power increases. Our characterization of the average cancellation as a function of the self-interference power allows us to show that for a constant signal-to-interference ratio at the receiver antenna (before any active cancellation is applied), the rate of a full-duplex link increases as the self-interference power increases. Second, we show that applying digital cancellation after analog cancellation can sometimes increase the self-interference, and thus digital cancellation is more effective when applied selectively based on measured suppression values. Third, we complete our study of the impact of self-interference cancellation mechanisms by characterizing the probability distribution of the self-interference channel before and after cancellation. © 2002-2012 IEEE. Source

Trigeminal sensory innervation of the cornea is critical for protection and synthesis of neuropeptides required for normal vision. Little is known about axon guidance during mammalian corneal innervation. In contrast to the chick where a pericorneal nerve ring forms via Npn/Sema signaling, mouse corneal axons project directly into the presumptive cornea without initial formation of an analogous nerve ring. Here we show that during development of the mouse cornea, Npn1 is strongly expressed by the trigeminal ganglion whereas Npn2 is expressed at low levels. At the same time Sema3A and Sema3F are expressed in distinct patterns in the ocular tissues. Npn1(sema-/-) mutant corneas become precociously and aberrantly innervated by nerve bundles that project further into the corneal stroma. In contrast, stromal innervation was not affected in Npn2(-/-) mutants. The corneal epithelium was prematurely innervated in both Npn1(sema-/-) and Npn2(-/-) mutants. These defects were exacerbated in Npn1(sema-/-);Npn2(-/-) double mutants, which in addition showed ectopic innervation of the region between the optic cup and lens vesicle. Collectively, our data show that Sema3A/Npn1 and Sema3F/Npn2 signaling play distinct roles and both are required for proper innervation of the mouse cornea. Source

Medlock K.B.,Rice University
Energy Strategy Reviews | Year: 2012

Conventional thinking just ten years ago was that the United States would become a major importer of liquefied natural gas. Yet, today the discussion has shifted to one of export potential, largely driven by the rapid development of shale gas resources. This has had dramatic implications not only for the US, but also for the rest of the world. In particular, the outlook for several gas exporting countries has been substantially altered. Namely, while the US has certainly from an energy security standpoint, Russia, Iran, Venezuela and Qatar have seen their projected fortunes reduced. Development of shale gas has effectively increased the global elasticity of supply and could substantially reduce overall dependence on exports from these critical countries. © 2011 Elsevier Ltd. Source

Fischer-Baum S.,Rice University | Benjamin A.S.,University of Illinois at Urbana - Champaign
Psychonomic Bulletin and Review | Year: 2014

Information about the order of items in a sequence can be conveyed either spatially or temporally. In the present investigation, we examined whether these different modes of presentation map onto compatible mental representations of serial order. We examined this issue in three immediate serial-recall experiments, in which participants recalled lists of letters in the temporal order in which they had appeared. Each letter in a to-be-remembered sequence was presented in a unique spatial position, with the order of these spatial positions progressing from either left to right or right to left. In this way, the visually presented lists contained both temporal and spatial order information. Recall of the temporal order information was more accurate with congruent spatial order information—that is, when the letters progressed from left to right, following the typical reading direction of English—than when the spatial order information was incongruent. These results suggest compatible representations of serial order when sequences are conveyed spatially and temporally. © 2014, Psychonomic Society, Inc. Source

Weisman R.B.,Rice University
Analytical and Bioanalytical Chemistry | Year: 2010

Single-walled carbon nanotubes (SWCNTs) are a family of structurally related artificial nanomaterials with unusual properties and many potential applications. Most SWCNTs can emit spectrally narrow near-IR fluorescence at wavelengths that are characteristic of their precise diameter and chiral angle. Near-IR fluorimetry therefore offers a powerful approach for identifying the structural species present in SWCNT samples. Such characterization is increasingly important for nanotube production, study, separation, and applications. General-purpose and specialized instruments suitable for SWCNT fluorimetric analysis are described, and methods for interpreting fluorimetric data to deduce the presence and relative abundances of different SWCNT species are presented. Fluorescence methods are highly effective for detecting SWCNTs in challenging samples such as complex environmental or biological specimens because of the methods' high sensitivity and selectivity and the near absence of interfering background emission at near-IR wavelengths. Current limitations and future prospects for fluorimetric characterization of SWCNTs are discussed. © 2009 Springer-Verlag. Source

Rocha J.D.,Rice University
Analytical chemistry | Year: 2011

A new method and instrumentation are described for rapid compositional analysis of single-walled carbon nanotube (SWCNT) samples. The customized optical system uses multiple fixed-wavelength lasers to excite NIR fluorescence from SWCNTs individualized in aqueous suspensions. The emission spectra are efficiently captured by a NIR spectrometer with InGaAs multichannel detector and then analyzed by a computer program that consults a database of SWCNT spectral parameters. The identities and relative abundances of semiconducting SWCNTs species are quickly deduced and displayed in graphs and tables. Results are found to be consistent with those based on manual interpretation of full excitation-emission scans from a conventional spectrofluorometer. The new instrument also measures absorption spectra using a broadband lamp and multichannel spectrometers, allowing samples to be automatically characterized by their emission efficiencies. The system provides rapid data acquisition and is sensitive enough to detect the fluorescence of a few picograms of SWCNTs in ~50 μL sample volumes. Source

Natelson D.,Rice University
ACS Nano | Year: 2012

Mechanical break junctions, particularly those in which a metal tip is repeatedly moved in and out of contact with a metal film, have provided many insights into electronic conduction at the atomic and molecular scale, most often by averaging over many possible junction configurations. This averaging throws away a great deal of information, and Makk et al. in this issue of ACS Nano demonstrate that, with both simulated and real experimental data, more sophisticated two-dimensional analysis methods can reveal information otherwise obscured in simple histograms. As additional measured quantities come into play in break junction experiments, including thermopower, noise, and optical response, these more sophisticated analytic approaches are likely to become even more powerful. While break junctions are not directly practical for useful electronic devices, they are incredibly valuable tools for unraveling the electronic transport physics relevant for ultrascaled nanoelectronics. © 2012 American Chemical Society. Source

Liang E.,Rice University
High Energy Density Physics | Year: 2010

We summarize recent results on pair creation using ultra-intense lasers and their potential applications to astrophysics and positronium physics. © 2010 Elsevier B.V. All rights reserved. Source

Wen Z.,Shanghai JiaoTong University | Yin W.,Rice University
Mathematical Programming | Year: 2013

Minimization with orthogonality constraints (e.g.; XT X = I) and/or spherical constraints (e.g.; ||x||2 = 1) has wide applications in polynomial optimization, combinatorial optimization, eigenvalue problems, sparse PCA, p-harmonic flows, 1-bit compressive sensing, matrix rank minimization, etc. These problems are difficult because the constraints are not only non-convex but numerically expensive to preserve during iterations. To deal with these difficulties, we apply the Cayley transform - a Crank-Nicolson-like update scheme - to preserve the constraints and based on it, develop curvilinear search algorithms with lower flops compared to those based on projections and geodesics. The efficiency of the proposed algorithms is demonstrated on a variety of test problems. In particular, for the maxcut problem, it exactly solves a decomposition formulation for the SDP relaxation. For polynomial optimization, nearest correlation matrix estimation and extreme eigenvalue problems, the proposed algorithms run very fast and return solutions no worse than those from their state-of-the-art algorithms. For the quadratic assignment problem, a gap 0.842 % to the best known solution on the largest problem "tai256c" in QAPLIB can be reached in 5 min on a typical laptop. © 2012 Springer and Mathematical Optimization Society. Source

Niemeier D.,University of California at Davis | Gombachika H.,University of Malawi | Richards-Kortum R.,Rice University
Science | Year: 2014

More of the world's population has access to cell phones than to basic sanitation facilities, a gap that can only be closed if the engineering and international aid communities adopt new approaches to design for scarcity and scalability. Source

Sluijs A.,University Utrecht | Dickens G.R.,University Utrecht | Dickens G.R.,Rice University
Global Biogeochemical Cycles | Year: 2012

Negative stable carbon isotope excursions (CIEs) across the Paleocene-Eocene thermal maximum (PETM; ∼56Ma) range between 2‰ and 7‰, even after discounting sections with truncated records. Individual carbon isotope records differ in shape and magnitude from variations in the global exogenic carbon cycle through changes in (1) the relative abundance of mixed components with different δ13C within a measured substrate, (2) isotope fractionation through physiological change, and (3) the isotope composition of the carbon source. All three factors likely influence many early Paleogene δ13C records, especially across the PETM and other hyperthermal events. We apply these concepts to late Paleocene-early Eocene (∼58-52Ma) records from Lomonosov Ridge, Arctic Ocean. Linear regression analyses show correlations between the δ13C of total organic carbon (TOC) and two proxies for the relative contribution of terrestrial organic components to sediment TOC: the branched and isoprenoid tetraether index and palynomorphs. We use these correlations to subtract the terrestrial component from δ13CTOC and calculate marine organic matter δ13C. The results show that the magnitude of the CIE in δ13CTOC across the PETM is exaggerated relative to the magnitude of the CIE in δ13C MOM by ∼3‰ due to increased contributions of terrestrial organic carbon during the event. Collectively, all carbon isotope records across the PETM and other major climate-carbon cycle perturbations in Earth's history are potentially biased through one or more of the above factors. Indeed, it is highly unlikely that any δ13C record shows the true shape and magnitude of the CIE for the global exogenic carbon cycle. For the PETM, we conclude that CIE in the exogenic carbon cycle is likely <4‰, but it will take additional analyses and modeling to obtain an accurate value for this CIE. © 2012. American Geophysical Union. All Rights Reserved. Source

Reimer J.,Baylor College of Medicine | Froudarakis E.,Baylor College of Medicine | Cadwell C.R.,Baylor College of Medicine | Yatsenko D.,Baylor College of Medicine | And 3 more authors.
Neuron | Year: 2014

Neural responses are modulated by brain state, which varies with arousal, attention, and behavior. In mice, running and whisking desynchronize the cortex and enhance sensory responses, but the quiescent periods between bouts of exploratory behaviors have not been well studied. We found that these periods of "quiet wakefulness" were characterized by state fluctuations on a timescale of 1-2 s. Small fluctuations in pupil diameter tracked these state transitions in multiple cortical areas. During dilation, the intracellular membrane potential was desynchronized, sensory responses were enhanced, and population activity was less correlated. In contrast, constriction was characterized by increased low-frequency oscillations and higher ensemble correlations. Specific subtypes of cortical interneurons were differentially activated during dilation and constriction, consistent with their participation in the observed state changes. Pupillometry has been used to index attention and mental effort in humans, but the intracellular dynamics and differences in population activity underlying this phenomenon were previously unknown. © 2014 Elsevier Inc. Source

Yeung L.Y.,University of California at Los Angeles | Yeung L.Y.,Rice University | Ash J.L.,University of California at Los Angeles | Young E.D.,University of California at Los Angeles
Science | Year: 2015

The abundances of molecules containing more than one rare isotope have been applied broadly to determine formation temperatures of natural materials. These applications of "clumped" isotopes rely on the assumption that isotope-exchange equilibrium is reached, or at least approached, during the formation of those materials. In a closed-system terrarium experiment, we demonstrate that biological oxygen (O2) cycling drives the clumped-isotope composition of O2 away from isotopic equilibrium. Our model of the system suggests that unique biological signatures are present in clumped isotopes of O2 - and not formation temperatures. Photosynthetic O2 is depleted in 18O18O and 17O18O relative to a stochastic distribution of isotopes, unlike at equilibrium, where heavy-isotope pairs are enriched. Similar signatures may be widespread in nature, offering new tracers of biological and geochemical cycling. © 2015, American Association for the Advancement of Science. All rights reserved. Source

Liang E.,Rice University
High Energy Density Physics | Year: 2013

Ultra-intense laser irradiating high-Z solid targets has become a new, powerful and efficient tool to create electron-positron pairs and intense gamma-ray beams. This paper reviews the recent developments in this field, both in theory and experiments. We will also discuss potential astrophysical applications of such laboratory experiments using ultra-intense lasers. © 2013 Elsevier B.V. Source

Chen S.X.,University of Washington | Zhang D.Y.,Rice University | Seelig G.,University of Washington
Nature Chemistry | Year: 2013

Small variations in nucleic acid sequences can have far-reaching phenotypic consequences. Reliably distinguishing closely related sequences is therefore important for research and clinical applications. Here, we demonstrate that conditionally fluorescent DNA probes are capable of distinguishing variations of a single base in a stretch of target DNA. These probes use a novel programmable mechanism in which each single nucleotide polymorphism generates two thermodynamically destabilizing mismatch bubbles rather than the single mismatch formed during typical hybridization-based assays. Up to a 12,000-fold excess of a target that contains a single nucleotide polymorphism is required to generate the same fluorescence as one equivalent of the intended target, and detection works reliably over a wide range of conditions. Using these probes we detected point mutations in a 198 base-pair subsequence of the Escherichia coli rpoB gene. That our probes are constructed from multiple oligonucleotides circumvents synthesis limitations and enables long continuous DNA sequences to be probed. © 2013 Macmillan Publishers Limited. All rights reserved. Source

Blumenthal-Barby J.S.,Baylor College of Medicine | Burroughs H.,Rice University
American Journal of Bioethics | Year: 2012

Policymakers, employers, insurance companies, researchers, and health care providers have developed an increasing interest in using principles from behavioral economics and psychology to persuade people to change their health-related behaviors, lifestyles, and habits. In this article, we examine how principles from behavioral economics and psychology are being used to nudge people (the public, patients, or health care providers) toward particular decisions or behaviors related to health or health care, and we identify the ethically relevant dimensions that should be considered for the utilization of each principle. © 2012 Copyright Taylor and Francis Group, LLC. Source

Thiolate-protected Au nanoclusters with core diameters smaller than 2 nm have captured considerable attention in recent years due to their diverse applications ranging from biological labeling to photovoltaics and catalysis. This new class of nanomaterials exhibits discrete electronic structure and molecular-like properties, such as HOMO-LUMO electronic transition, intrinsic magnetism, chiroptical properties, and enhanced catalytic properties. This review focuses on the research into thiolate-protected Au38(SR) 24-one of the most representative nanoclusters, including its identification, size-focusing synthesis, structure determination, and intrinsic chirality. The properties of two size-adjacent Au nanoclusters [Au 40(SR)24 and Au36(SR)24] are also discussed. The experimental and theoretical methodologies developed in studies of the Au38(SR)24 model nanocluster open up new opportunities in the synthesis and properties investigation of other atomically precise Aun(SR)m nanoclusters. © 2014 IUPAC and De Gruyter Berlin Boston. Source

Jacques L.,Catholic University of Louvain | Laska J.N.,Dropcam Inc. | Boufounos P.T.,MItsubishi Electric | Baraniuk R.G.,Rice University
IEEE Transactions on Information Theory | Year: 2013

The compressive sensing (CS) framework aims to ease the burden on analog-to-digital converters (ADCs) by reducing the sampling rate required to acquire and stably recover sparse signals. Practical ADCs not only sample but also quantize each measurement to a finite number of bits; moreover, there is an inverse relationship between the achievable sampling rate and the bit depth. In this paper, we investigate an alternative CS approach that shifts the emphasis from the sampling rate to the number of bits per measurement. In particular, we explore the extreme case of 1-bit CS measurements, which capture just their sign. Our results come in two flavors. First, we consider ideal reconstruction from noiseless 1-bit measurements and provide a lower bound on the best achievable reconstruction error.We also demonstrate that i.i.d. random Gaussian matrices provide measurement mappings that, with overwhelming probability, achieve nearly optimal error decay. Next, we consider reconstruction robustness to measurement errors and noise and introduce the binary -stable embedding property, which characterizes the robustness of the measurement process to sign changes. We show that the same class of matrices that provide almost optimal noiseless performance also enable such a robustmapping.On the practical side, we introduce the binary iterative hard thresholding algorithm for signal reconstruction from 1-bit measurements that offers state-of-the-art performance.© 2013 IEEE. Source

Gonnermann H.M.,Rice University
Annual Review of Earth and Planetary Sciences | Year: 2015

Magma fragmentation is the breakup of a continuous volume of molten rock into discrete pieces, called pyroclasts. Because magma contains bubbles of compressible magmatic volatiles, decompression of low-viscosity magma leads to rapid expansion. The magma is torn into fragments, as it is stretched into hydrodynamically unstable sheets and filaments. If the magma is highly viscous, resistance to bubble growth will instead lead to excess gas pressure and the magma will deform viscoelastically by fracturing like a glassy solid, resulting in the formation of a violently expanding gas-pyroclast mixture. In either case, fragmentation represents the conversion of potential energy into the surface energy of the newly created fragments and the kinetic energy of the expanding gas-pyroclast mixture. If magma comes into contact with external water, the conversion of thermal energy will vaporize water and quench magma at the melt-water interface, thus creating dynamic stresses that cause fragmentation and the release of kinetic energy. Lastly, shear deformation of highly viscous magma may cause brittle fractures and release seismic energy. Copyright © 2015 by Annual Reviews. All rights reserved. Source

Wang J.,Rice University | Henkin T.M.,Ohio State University
Nucleic Acids Research | Year: 2010

Gram-positive bacteria utilize a tRNA-responsive transcription antitermination mechanism, designated the T box system, to regulate expression of many amino acid biosynthetic and aminoacyl-tRNA synthetase genes. The RNA transcripts of genes controlled by this mechanism contain 5′ untranslated regions, or leader RNAs, that specifically bind cognate tRNA molecules through pairing of nucleotides in the tRNA anticodon loop with nucleotides in the Specifier Loop domain of the leader RNA. We have determined the solution structure of the Specifier Loop domain of the tyrS leader RNA from Bacillus subtilis. Fifty percent of the nucleotides in the Specifier Loop domain adopt a loop E motif. The Specifier Sequence nucleotides, which pair with the tRNA anticodon, stack with their Watson-Crick edges rotated toward the minor groove and exhibit only modest flexibility. We also show that a Specifier Loop domain mutation that impairs the function of the B. subtilis glyQS T box RNA disrupts the tyrS loop E motif. Our results suggest a mechanism for tRNA-Specifier Loop binding in which the phosphate backbone kink created by the loop E motif causes the Specifier Sequence bases to rotate toward the minor groove, which increases accessibility for pairing with bases in the anticodon loop of tRNA. © The Author(s) 2010. Published by Oxford University Press. Source

Thapar R.,Rice University
ACS Chemical Biology | Year: 2015

Ribonucleoprotein complexes involved in pre-mRNA splicing and mRNA decay are often regulated by phosphorylation of RNA-binding proteins. Cells use phosphorylation-dependent signaling pathways to turn on and off gene expression. Not much is known about how phosphorylation-dependent signals transmitted by exogenous factors or cell cycle checkpoints regulate RNA-mediated gene expression at the atomic level. Several human diseases are linked to an altered phosphorylation state of an RNA binding protein. Understanding the structural response to the phosphorylation signal and its effect on ribonucleoprotein assembly provides mechanistic understanding, as well as new information for the design of novel drugs. In this review, I highlight recent structural studies that reveal the mechanisms by which phosphorylation can regulate protein-protein and protein-RNA interactions in ribonucleoprotein complexes. © 2014 American Chemical Society. Source

Brewster J.L.,Pepperdine University | Gustin M.C.,Rice University
Science Signaling | Year: 2014

The protein kinase Hog1 (high osmolarity glycerol 1) was discovered 20 years ago, being revealed as a central signaling mediator during osmoregulation in the budding yeast Saccharomyces cerevisiae. Homologs of Hog1 exist in all evaluated eukaryotic organisms, and this kinase plays a central role in cellular responses to external stresses and stimuli. Here, we highlight the mechanism by which cells sense changes in extracellular osmolarity, the method by which Hog1 regulates cellular adaptation, and the impacts of the Hog1 pathway upon cellular growth and morphology. Studies that have addressed these issues reveal the influence of the Hog1 signaling pathway on diverse cellular processes. Copyright 2014 by the American Association for the Advancement of Science; all rights reserved. Source

Nicolaou K.C.,Rice University
Angewandte Chemie - International Edition | Year: 2014

The current state of affairs in the drug discovery and development process is briefly summarized and then ways to take advantage of the ever-increasing fundamental knowledge and technical knowhow in chemistry and biology and related disciplines are discussed. The primary motivation of this Essay is to celebrate the great achievements of chemistry, biology, and medicine and to inform and inspire students and academics to enter the field of drug discovery and development while, at the same time, continue to advance the fundamentals of their disciplines. It is also meant to encourage and catalyze multidisciplinary partnerships between academia and industry as scientists attempt to merge their often complementary interests and expertise to achieve new improvements and breakthroughs in their respective fields, and the common goal of applying them to the discovery and invention of new and better medicines, especially in areas of unmet needs. Concerted effort: What is the current state of the art and science of drug design and discovery? How can the cooperation between academic investigators and industry be improved? This Essay is meant to inspire and motivate, especially those in academia, to think about how to use their expertise to contribute to the drug discovery and development process. Photograph: Fotolia. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Maleki A.,Columbia University | Anitori L.,TNO | Yang Z.,Nanyang Technological University | Baraniuk R.G.,Rice University
IEEE Transactions on Information Theory | Year: 2013

Recovering a sparse signal from an undersampled set of random linear measurements is the main problem of interest in compressed sensing. In this paper, we consider the case where both the signal and the measurements are complex-valued. We study the popular recovery method of l1- regularized least squares or LASSO.While several studies have shown that LASSO provides desirable solutions under certain conditions, the precise asymptotic performance of this algorithm in the complex setting is not yet known. In this paper, we extend the approximate message passing (AMP) algorithm to solve the complex-valued LASSO problem and obtain the complex approximate message passing algorithm (CAMP). We then generalize the state evolution framework recently introduced for the analysis of AMP to the complex setting. Using the state evolution, we derive accurate formulas for the phase transition and noise sensitivity of both LASSO and CAMP. Our theoretical results are concerned with the case of i.i.d. Gaussian sensing matrices. Simulations confirm that our results hold for a larger class of random matrices. © 2013 IEEE. Source

Miller T.E.X.,Rice University | Inouye B.D.,Florida State University
Ecology | Year: 2011

Most population dynamics models explicitly track the density of a single sex. When the operational sex ratio can vary, two-sex models may be needed to understand and predict population trajectories. Various functions have been proposed to describe the relative contributions of females and males to recruitment, and these functions can differ qualitatively in the patterns that they generate. Which mating function best describes the dynamics of real populations is not known, since alternative two-sex models have not been confronted with experimental data. We conducted the first such comparison, using laboratory populations of the bean beetle Callosobruchus maculatus. Manipulations of the operational sex ratio and total density provided strong support for a demographic model in which the birth rate was proportional to the harmonic mean of female and male densities, and females, males, and their offspring made unique contributions to density dependence. We offer guidelines for transferring this approach to other, less tractable systems in which possibilities for sex ratio manipulations are more limited. We show that informative experimental designs require strong perturbations of the operational sex ratio. The functional form of density dependence (saturating vs. over-compensatory) and the relative contributions of each sex to density dependence can both determine in which direction and at which population densities such perturbations would be most informative. Our experimental results and guidelines for design strategies promote synthesis of two-sex population dynamics theory with empirical data. © 2011 by the Ecological Society of America. Source

Davis T.J.,CSIRO | Hentschel M.,University of Stuttgart | Hentschel M.,Max Planck Institute for Solid State Research | Liu N.,Rice University | Giessen H.,University of Stuttgart
ACS Nano | Year: 2012

An electrostatic eigenmode method that describes the coupling between plasmonic nanoparticles is used to model the optical resonances of the 3D plasmonic ruler. The model provides a mathematical description of the ruler that enables us to identify the key resonance in the scattering spectrum that encodes the location of the central nanorod. The model demonstrates excellent agreement with experimentally measured spectra. We show that the spectra can uniquely encode the horizontal and vertical displacements of the central nanorod. From an understanding of the spatial dependence of the plasmonic coupling between the nanorods, we devise a method for estimating the position of the central nanorod and apply this to experimental data. Our method paves the way toward the use of high-resolution spectra from 3D plasmonic oligomers for structural analysis of single entities such as complex macromolecules, DNA scaffolds, proteins, and peptides. © 2012 American Chemical Society. Source

Kanschat G.,Texas A&M University | Riviere B.,Rice University
Journal of Computational Physics | Year: 2010

We consider a model of coupled free and porous media flow governed by Stokes and Darcy equations with the Beavers-Joseph-Saffman interface condition. This model is discretized using divergence-conforming finite elements for the velocities in the whole domain. Discontinuous Galerkin techniques and mixed methods are used in the Stokes and Darcy subdomains, respectively. This discretization is strongly conservative in Hdiv(Ω) and we show convergence. Numerical results validate our findings and indicate optimal convergence orders. © 2010 Elsevier Inc. Source

The most fundamental approach to an understanding of electronic, optical, and transport phenomena which the condensed matter physics (of conventional as well as nonconventional systems) offers is generally founded on two experiments: the inelastic electron scattering and the inelastic light scattering. This work embarks on providing a systematic framework for the theory of inelastic electron scattering and of inelastic light scattering from the electronic excitations in GaAs/Ga1-xAlxAs quantum wells. To this end, we start with the Kubo's correlation function to derive the generalized nonlocal, dynamic dielectric function, and the inverse dielectric function within the framework of Bohm-Pines' random-phase approximation. This is followed by a thorough development of the theory of inelastic electron scattering and of inelastic light scattering. The methodological part is then subjected to the analytical diagnoses which allow us to sense the subtlety of the analytical results and the importance of their applications. The general analytical results, which know no bounds regarding, e.g., the subband occupancy, are then specified so as to make them applicable to practicality. After trying and testing the eigenfunctions, we compute the density of states, the Fermi energy, the full excitation spectrum made up of intrasubband and intersubband - single-particle and collective (plasmon) - excitations, the loss functions for all the principal geometries envisioned for the inelastic electron scattering, and the Raman intensity, which provides a measure of the real transitions induced by the (laser) probe, for the inelastic light scattering. It is found that the dominant contribution to both the loss peaks and the Raman peaks comes from the collective (plasmon) excitations. As to the single-particle peaks, the analysis indicates a long-lasting lack of quantitative comparison between theory and experiments. It is inferred that the inelastic electron scattering can be a potential alternative of the inelastic light scattering for investigating elementary electronic excitations in quantum wells. Copyright 2012 Author(s). Source

Imambekov A.,Rice University | Schmidt T.L.,Yale University | Glazman L.I.,Yale University
Reviews of Modern Physics | Year: 2012

For many years, the Luttinger liquid theory has served as a useful paradigm for the description of one-dimensional (1D) quantum fluids in the limit of low energies. This theory is based on a linearization of the dispersion relation of the particles constituting the fluid. Recent progress in understanding 1D quantum fluids beyond the low-energy limit is reviewed, where the nonlinearity of the dispersion relation becomes essential. The novel methods which have been developed to tackle such systems combine phenomenology built on the ideas of the Fermi-edge singularity and the Fermi-liquid theory, perturbation theory in the interaction strength, and new ways of treating finite-size properties of integrable models. These methods can be applied to a wide variety of 1D fluids, from 1D spin liquids to electrons in quantum wires to cold atoms confined by 1D traps. Existing results for various dynamic correlation functions are reviewed, in particular, the dynamic structure factor and the spectral function. Moreover, it is shown how a dispersion nonlinearity leads to finite particle lifetimes and its impact on the transport properties of 1D systems at finite temperatures is discussed. The conventional Luttinger liquid theory is a special limit of the new theory, and the relation between the two is explained. © 2012 American Physical Society. Source

Dunham A.E.,Rice University | Erhart E.M.,Texas State University | Wright P.C.,State University of New York at Stony Brook
Global Change Biology | Year: 2011

Most studies that examine the influence of climatic change on flora and fauna have focused on northern latitudes; however, there is increasing recognition that tropical regions are also being affected. Despite this, regions such as Madagascar, which are rich in endemic biodiversity but may have low adaptive capacity to climatic change, are poorly represented in studies examining the effects of climate variability on biota. We investigated how El Niño Southern Oscillations (ENSO) influence precipitation patterns in the rainforest region of southeastern Madagascar (1962-2006) and then constructed models to assess the potential contribution of climatic variables on the reproductive parameters of the Milne Edward's sifaka, a threatened lemur species (Propithecus edwardsi), over a 20-year period. The Southern Oscillation Index of sea surface temperature (SST) anomalies in the tropical Pacific was associated with precipitation patterns including wetter wet seasons during warmer phases and drier dry seasons following cooler phases. The best-supported models of lemur fecundity (female offspring per female that survive to 1 year of age per year) included cyclone presence during gestation and ENSO phase before conception and during the first 6 months of life. Models also suggested that heavy rains during gestation may limit birth rates and that prolonged drought during female lactation may limit first year offspring survival; although these variables were given little importance for predicting overall fecundity relative to ENSO phases and cyclone presence. Our results linking lemur reproduction with climatic variability suggest that climatic changes may be an additional threat to Madagascar's unique and already endangered flora and fauna. The association between precipitation in southeastern Madagascar and SST anomalies in the tropical Pacific suggests that dynamics of wildlife populations even in tropical areas such as Madagascar can be affected by global climate cycles making them potentially vulnerable to global climate change. © 2010 Blackwell Publishing Ltd. Source

Aggarwal V.,Princeton University | Sabharwal A.,Rice University
IEEE Transactions on Information Theory | Year: 2010

Most communication systems use some form of feedback, often related to channel state information. The common models used in analyses either assume perfect channel state information at the receiver and/or noiseless state feedback links. However, in practical systems, neither is the channel estimate known perfectly at the receiver and nor is the feedback link perfect. In this paper, we study the achievable diversity multiplexing tradeoff using i.i.d. Gaussian codebooks, considering the errors in training the receiver and the errors in the feedback link for frequency division duplex (FDD) systems, where the forward and the feedback are independent multiple input multiple output (MIMO) channels. Our key result is that the maximum diversity order with one-bit of feedback information is identical to systems with more feedback bits. Thus, asymptotically in ${\ssr SNR}$, more than one bit of feedback does not improve the system performance at constant rates. Furthermore, the one-bit diversity-multiplexing performance is identical to the system which has perfect channel state information at the receiver along with noiseless feedback link. This achievability uses novel concepts of power controlled feedback and training, which naturally surface when we consider imperfect channel estimation and noisy feedback links. In the process of evaluating the proposed training and feedback protocols, we find an asymptotic expression for the joint probability of the $ {\ssr SNR}$ exponents of eigenvalues of the actual channel and the estimated channel which may be of independent interest. © 2006 IEEE. Source

Carpiano R.M.,University of British Columbia | Kimbro R.T.,Rice University
Journal of Health and Social Behavior | Year: 2012

Neighborhood social capital-resources inherent within community networks-has been identified as a potential facilitator of personal well-being. We test hypotheses concerning how neighborhood social capital moderates the influence of parenting strain on mastery (individuals' understanding of their ability to control personal life circumstances) for female primary caregivers of children. First, we test how different forms of neighborhood social capital-social support, social leverage (information exchange), informal social control, and neighborhood organization participation-modify the association between parenting strain and mastery. Second, we test whether such moderation depends on one's access to these forms via neighbor ties. Analyses of Los Angeles Family and Neighborhood Survey data (N = 765) indicate that the negative relationship between parenting strain and mastery worsens as informal social control increases. Social support and informal social control, however, buffer this parenting strain-mastery relationship when caregivers have stronger ties to neighbors. Our findings implicate mechanisms of "negative social capital" and warrant more nuanced considerations of neighborhood social capital's health-promoting potential. © American Sociological Association 2012. Source

Raghu S.,Stanford University | Raghu S.,Rice University | Kivelson S.A.,Stanford University
Physical Review B - Condensed Matter and Materials Physics | Year: 2011

We present a well-controlled perturbative renormalization-group treatment of superconductivity from short-ranged repulsive interactions in a variety of model two-dimensional electronic systems. Our analysis applies in the limit where the repulsive interactions between the electrons are small compared to their kinetic energy. © 2011 American Physical Society. Source

Bradshaw S.J.,Rice University | Cargill P.J.,Imperial College London | Cargill P.J.,University of St. Andrews
Astrophysical Journal | Year: 2013

The effect of the numerical spatial resolution in models of the solar corona and corona/chromosphere interface is examined for impulsive heating over a range of magnitudes using one-dimensional hydrodynamic simulations. It is demonstrated that the principal effect of inadequate resolution is on the coronal density. An underresolved loop typically has a peak density of at least a factor of two lower than a resolved loop subject to the same heating, with larger discrepancies in the decay phase. The temperature for underresolved loops is also lower indicating that lack of resolution does not "bottle up" the heat flux in the corona. Energy is conserved in the models to under 1% in all cases, indicating that this is not responsible for the low density. Instead, we argue that in underresolved loops the heat flux "jumps across" the transition region to the dense chromosphere from which it is radiated rather than heating and ablating transition region plasma. This emphasizes the point that the interaction between corona and chromosphere occurs only through the medium of the transition region. Implications for three-dimensional magnetohydrodynamic coronal models are discussed. © 2013. The American Astronomical Society. All rights reserved. Source

Tittl A.,University of Stuttgart | Mai P.,University of Stuttgart | Taubert R.,University of Stuttgart | Dregely D.,University of Stuttgart | And 2 more authors.
Nano Letters | Year: 2011

We report on the experimental realization of a palladium-based plasmonic perfect absorber at visible wavelengths and its application to hydrogen sensing. Our design exhibits a reflectance <0.5% and zero transmittance at 650 nm and the operation wavelength of the absorber can be tuned by varying its structural parameters. Exposure to hydrogen gas causes a rapid and reversible increase in reflectance on a time scale of seconds. This pronounced response introduces a novel optical hydrogen detection scheme with very high values of the relative intensity response. © 2011 American Chemical Society. Source

Kruger H.,Rice University
Communications in Mathematical Physics | Year: 2010

I study the Lyapunov exponent and the integrated density of states for general Jacobi operators. The main result is that questions about these can be reduced to questions about ergodic Jacobi operators. I use this to show that for finite gap Jacobi operators, regularity implies that they are in the Cesàro-Nevai class, proving a conjecture of Barry Simon. Furthermore, I use this to study Jacobi operators with coefficients a(n) = 1 and b(n) = f(nρ (mod 1)) for ρ > 0 not an integer. © Springer-Verlag 2010. Source

Agency: NSF | Branch: Standard Grant | Program: | Phase: RES ON GENDER IN SCI & ENGINE | Award Amount: 396.64K | Year: 2015

This proposal was submitted in response to EHR Core Research (ECR) program announcement NSF 15-509. As part of ECR, this project is funded by the Research on Gender in Science and Engineering (GSE) program. GSE seeks to understand and address gender-based differences in science, technology, engineering and mathematics (STEM) education and workforce participation through education and implementation research that will lead to a larger and more diverse domestic STEM workforce. Over the past two decades, social science research has found that girls and women encounter barriers in STEM education and then face additional obstacles entering and advancing in STEM careers. Yet, the effects of motherhood and fatherhood on the careers of STEM professionals are not well studied. This research will explore whether parenting--especially motherhood--incurs penalties in STEM employment in terms of retention, advancement, and salary. Using a sociological theoretical perspective that socially structured life courses move through gendered institutions, the study will examine how parenthood shapes career trajectories, retention, and salaries for women and men in STEM fields. The proposed empirical research project will use representative, longitudinal data to analyze these parenthood effects among STEM professionals. The researchers will also investigate how these parenthood effects differ by race/ethnicity, education level, sector, and STEM field. The findings will inform theory about gender differences in retention across all career stages and efforts to develop interventions that improve womens long-term persistence and success in STEM.

This project will use nationally representative, longitudinal, restricted-use data of STEM professionals from the Nation Center for Science and Engineerings (NCSES) Science and Engineering Statistical Data System (SESTAT) to examine the effects of parenthood on career paths and pay. The sample (N=17,599) includes STEM professionals employed full-time in 2003 and followed through 2010. Through a series of bi- and multivariate statistical analyses, the researchers will address the following research questions: Who leaves full-time STEM employment after becoming a parent? Where do they go? How do these parenthood effects vary by gender, race/ethnicity, education level, sector, and STEM field? Is the cost in lost income of making a career change higher if respondents made the change for family reasons compared to other reasons? Among workers who remain in full-time STEM careers, how do gender, parenthood, education level, and race/ethnicity affect salary? Since a large majority of workers become parents at some point during their careers, understanding the gendered effects of parenthood on the careers of STEM practitioners is central to understanding the retention of talented women and men in these fields. The researchers will also look for systematic variation by race/ethnicity, education level, sector and STEM field.

Agency: NSF | Branch: Standard Grant | Program: | Phase: ATMOSPHERIC CHEMISTRY | Award Amount: 238.54K | Year: 2016

This project focuses on increasing the understanding of how human-produced emissions combine with biogenic emissions from forests to influence the formation of small particles in the atmosphere. A mobile laboratory will be deployed to two different types of forests (urban and remote) in order to compare and contrast the impact of long-range and short-range transport of nitrogen species to forests. The results will lead to improved control strategies that minimize the health, visibility and climate effects of anthropogenic emissions.

The primary objectives of the science campaign are to: (1) Characterize the ambient aerosol, radiation, and trace gases at two forest sites, both above and below the canopy, and along a north-south transect in the central United States; (2) Quantify the level of oxidation found in SOA using atomic ratios (such as the oxygen to carbon ratio, O:C) and determine the impact the presence of particulate organic nitrate (PON) has on the observed oxidation state of the submicron particulate matter (PM); (3) Investigate how in-canopy gradients and through-canopy transport impact submicron PM, PON, and oxidants; (4) Determine the impact nitrogen oxides (NOx) have on volatile organic carbon (VOC) oxidation and SOA formation in all locations; (5) Compare and contrast the chemistry of remote, on-road, and urban forested areas; (6) Identify the factors contributing to SOA using positive matrix factorization (PMF) to identify important components of SOA under different levels of anthropogenic influence both above and below canopy; and (7) Investigate the fate of NOx in all locations.

Agency: NSF | Branch: Standard Grant | Program: | Phase: CONDENSED MATTER PHYSICS | Award Amount: 395.84K | Year: 2015

Nontechnical description:
Electrical insulators are commonly recognized as materials that prevent the flow of electricity. However, recent research demonstrates a type of topological insulators which has novel properties. Although electricity cannot flow through them, it can flow around their narrow outer edges. The material, called a quantum spin Hall topological insulator, acts as an electron superhighway. It is one of the building blocks needed to create future electronics and computers. In this project the principle investigator will perform experiments on the newly discovered topological insulators made of compound semiconductors indium arsenide and gallium antimonide, addressing important issues relate to materials science and quantum physics. Understanding of materials science of this class of material and their topological properties is directly relevant to spintronics and quantum information technology.

Technical descripton:
The two-dimensional topological insulator, which supports quantized helical edge modes, is created by band-gap engineering using molecular beam epitaxy and electrostatic gates. The project is exploring interesting physics at the messoscopic length scale, with the focus on the helical edge modes and their interface with superconductors, where proximity effect and Andreev reflection are being systematically studied. Major focus of the study is searching for Majorana bound states in hybrid topological insulator-superconductor Josephson junctions. The experimental research work addresses fundamental phenomenon and its physics in a very clean model system. The project supports the education of two Ph.D. students, where they receive a combination of advanced training in semiconductor materials, nanotechnology, and ultra-low temperature measurements.

Ouyang M.,Huazhong University of Science and Technology | Duenas-Osorio L.,Rice University
Chaos | Year: 2012

This paper introduces an approach to assess and improve the time-dependent resilience of urban infrastructure systems, where resilience is defined as the systems' ability to resist various possible hazards, absorb the initial damage from hazards, and recover to normal operation one or multiple times during a time period T. For different values of T and its position relative to current time, there are three forms of resilience: previous resilience, current potential resilience, and future potential resilience. This paper mainly discusses the third form that takes into account the systems' future evolving processes. Taking the power transmission grid in Harris County, Texas, USA as an example, the time-dependent features of resilience and the effectiveness of some resilience-inspired strategies, including enhancement of situational awareness, management of consumer demand, and integration of distributed generators, are all simulated and discussed. Results show a nonlinear nature of resilience as a function of T, which may exhibit a transition from an increasing function to a decreasing function at either a threshold of post-blackout improvement rate, a threshold of load profile with consumer demand management, or a threshold number of integrated distributed generators. These results are further confirmed by studying a typical benchmark system such as the IEEE RTS-96. Such common trends indicate that some resilience strategies may enhance infrastructure system resilience in the short term, but if not managed well, they may compromise practical utility system resilience in the long run. © 2012 American Institute of Physics. Source

Agency: NSF | Branch: Standard Grant | Program: | Phase: | Award Amount: 240.00K | Year: 2014

This DMREF project aims to make breakthroughs in understanding and designing novel superconductors, magnetic semiconductors, and other magnetic materials. The research can lead to development of materials with higher transition temperatures suitable for applications to electronic devices with novel functionalities. To achieve this goal, collaborative research will be performed by five Principal Investigators (PIs) specializing in a variety of techniques and methods, including neutron scattering (Dai) and muon spin relaxation (Uemura) as advanced magnetic probes, synthesis and charge transport of nano-scale systems (Ni and Kim), and theory and computational material design (Kotliar). The team members will unite their forces and expertise to characterize high-quality specimens with multiple experimental probes, to explore electric field-effect doping of charge carriers using nano-scale devices, to interpret the results using advanced computational models, and to design and synthesize new materials. As demonstrated in recent discoveries of ferromagnetic semiconductors that have crystal structures identical to those of Fe-based high-Tc superconductors, encounters and coherent collaboration between experts from different research communities will lead to unanticipated breakthroughs. Since 2011, the PIs from Columbia and Rice have organized live/video lecture courses for entry-level graduate students Frontiers of Condensed Matter Physics seeking broader impact, and have accumulated about 100 video lectures of leading scientists describing modern studies of solid state physics. The present project will allow adding a new series to this course involving faculty members from Columbia, Rice, Harvard, Rutgers, and UCLA and connecting their classrooms with a web-based technology for simultaneous broadcast.

Condensation and pairing mechanisms of high-Tc cuprate and iron-based superconductors have not yet been established. However, there are growing signatures pointing toward the important role played by magnetic interactions. With multi-probe experimental researchers using neutrons, muons, transport, and scanning tunneling microscopy (STM), supplemented by quantitative comparison to advanced computation, the present DMREF project will shed new light on the quest for understanding unconventional superconductors. In conjunction with the predictive powers of advanced computational methods, a better understanding of the physical mechanisms at work will contribute to the ability to design materials with higher transition temperatures. Carrier doping using electric field effects will provide a new route to search for novel superconductors, less sensitive to disorder effects associated with conventional doping with chemical substitutions. Transport results on Fermi-level tuning via electrolyte gate voltage will be directly compared to advanced theoretical computations on electronic structures. Additionally, the formation of interfaces of unconventional superconductors and their magnetic derivatives, and engineering of phase changes via charge-doping with field-effect gating, will result in devices with novel functionality, leading to an as yet unexplored interdisciplinary research front. This project will provide a unique collaborative experience involving leading researchers, graduate students, and postdocs with multiple research fields and techniques that will make important contributions to the development of the future leaders of modern physics research.

Agency: NSF | Branch: Continuing grant | Program: | Phase: | Award Amount: 310.00K | Year: 2014

With this award, Drs. Edward Nikonowicz (Rice University) and Shuxing Zhang (M. D. Anderson Cancer Center) will identify and characterize small molecules that selectively bind to unique RNA structure motifs. This award is being made through the Chemistry of Life Processes (CLP) Program of the Chemistry Division, the Genetic Mechanisms Cluster of the Division of Molecular and Cellular Biosciences, and the Computational and Data-Enabled Science and Engineering (CDS&E) Program at NSF. The central role of ribonucleic acids (RNAs) in biology has long been recognized, but the large number of non-coding RNA molecules, which are not translated into a protein, and the diverse functions of these RNAs have only come to light in the last decade. The goal of this project is to identify a collection of chemical compounds that bind with high selectivity and affinity to small elements of unusual structure found in non-coding RNA molecules. These compounds could be used as new tools for biotechnological and biochemical research and for applications in medicine. In addition to supporting the training through research of graduate students, this project will support training of high-school and undergraduate students in the use of modern chemical, biophysical, and computational tools to address fundamental problems in RNA and chemical biology. Students present their work at local scientific meetings, giving them exposure to the scientific community and the opportunity to communicate their results to a scientifically literate, yet broad audience.

Non-coding RNAs (nc-RNA), including rRNAs, riboswitches, and pre-microRNAs, often have an architecture that includes a variety of non-canonical features important for the molecules structures and function. Therefore, the detailed structure provides an important backdrop to interpret functional and mechanistic studies. Small molecules that bind to specific RNA structure motifs can become powerful tools for probing RNA conformation and folding and to facilitate the study of specific RNA activities in vitro and in vivo. NMR spectroscopy will be used to define the breadth of conformational space accessed by a set of frequently occurring non-canonical RNA elements. A computational workflow that integrates the NMR-defined structure information and the in silico screening of virtual chemical libraries will be developed to identify chemical compounds that selectively bind to specific non-canonical elements. The interactions of these small molecules with RNAs will be characterized using biophysical and high-resolution structure methods including NMR spectroscopy and X-ray crystallography.

Agency: NSF | Branch: Standard Grant | Program: | Phase: | Award Amount: 40.00K | Year: 2014

The award supports the attendance of fifty US-based students to attend the sixth Federated Logic Conference (FLoC 14) which will be held in Vienna, Austria, in July 2014, as part of the Vienna Summer of Logic (VSL 14). The federated logic conference is an event which brings together ten major international conferences in the area of Formal Methods, and around 75 satellite workshops. While the participating conferences are normally held individually by their local conference organization on an annual basis, they all agree to this joint and federated event to be held every three-four years.

Enhancing the security, privacy, usability, and reliability of computing systems is widely accepted as one the grand challenges facing the computing-research community. Formal Methods have emerged as one of the primary approaches towards that goal. A federated conference provides an opportunity for accelerating research via synergy between the different strands of research in Formal Methods. It is also an outstanding training opportunity for young researchers, as it offers them a grand view of the whole area.

Agency: NSF | Branch: Standard Grant | Program: | Phase: POP & COMMUNITY ECOL PROG | Award Amount: 20.10K | Year: 2016

Parasites regulate the dynamics of almost all populations, and the vast majority of hosts (including humans) are infected by multiple parasite species at the same time. Do infections by multiple parasite species increase the risk of epidemics in host populations? This research will establish a general framework that predicts how co-infections affect epidemics in host populations. Results will help predict the consequences of concurrent emerging parasites and will inform strategies to help curb epidemics that threaten wildlife, animal stocks, agricultural crops, and human populations. The project will extend the research and training of a doctoral student by supporting two new experiments that will improve existing mathematical models. The researchers will engage a diverse range of students in the Houston Public Schools through lectures on infectious disease and participation in the design of experiments and analysis of resulting data.

When multiple parasites infect hosts, the order of infection likely plays an important role because it can determine transmission rates and host mortality. The effects of arrival order - or priority effects - are well documented within single hosts but rarely incorporated in classical models to predict and understand multi-parasite epidemics. The goal of this project is to determine (1) how the relative timing of infections alters epidemics in multi-parasite systems and whether multiple infections increase variation in outcome of epidemics, and (2) test whether this variation can be predicted with mechanistic models that incorporate the consequences of co-infection from single-host data. These goals will be accomplished using a combination of experiments and models. The first experiment will examine multi-parasite epidemics with multiple arrival orders of parasites and doubly infected and singly infected populations. This will determine how priority effects alter epidemic patterns at the host population level. A series of single host infection experiments will be conducted to parameterize a predictive epidemic model that accounts for the infection history of hosts and how this history influences interactions among co-infecting parasites and hosts. Comparing model predictions to empirical epidemics will test whether variation in epidemics patterns in natural populations can be predicted from individual host data when accounting for the infection history of hosts. The predictive power of this model will be compared to traditional models that do not include priority effects.

Agency: NSF | Branch: Standard Grant | Program: | Phase: CROSS-EF ACTIVITIES | Award Amount: 300.00K | Year: 2015

Memories of facts and experiences take time to be stored robustly in the brain. Understanding of the underlying mechanisms would not only yield insight into a fundamental ability found in all animals, but also allow for the optimization of learning and memory in healthy individuals as well as interventions in humans with compromised memory. Many current hypotheses of memory posit the importance of replay within ensembles of neurons in the brain. The idea is that in periods of quiescence or sleep, neurons in the hippocampus, a key brain structure for memory, re-excite the patterns of activity that occurred during the original learning/experience. This neural replay of the original activity patterns enables distributed cortical regions to form robust, lasting interconnections and thereby support memory. In rats learning to navigate mazes, the signals of dozens of individual hippocampal neurons can be accessed simultaneously. In this project, neural recording, computational, and statistical tools are developed and tested to observe neuronal activity in the hippocampus of rats over long periods of time-- periods that include repeated active learning and quiescence/sleep episodes-- and address fundamental questions about replay and how individual neurons participate in replay/learning over time. The algorithms developed in this project are shared widely through on-line media. The data collected contribute to instructional material used in interdisciplinary graduate training programs and courses focused on neural signal processing.

In this project, new neural recording technology and novel and computational analysis techniques are used to acquire and interpret week-long continuous recordings of hippocampal activity while an animal learns a novel task. The result is the first ever qualitative and quantitative assessment of replay over a period of this length. The resulting data have the potential to yield great insight into how changes in patterns of neural activity at the scales of milliseconds (replay) interact with changes at the scales of hours (circadian) and days (learning). The algorithms developed, which are shared through a public on-line site, may be foundational to a new experimental paradigm where neurons are recorded continuously over time. A particularly valuable outcome of the project are novel algorithms for automatically isolating the signals of individual neurons from each other, and tracking slow changes to their signatures over time. Additionally, a new latent-variable model technique for quantifying how individual replay events compare with the patterns exhibited during learning enables the statistics of replay variability to be assessed. The impacts of this work have the potential to be broad, from techniques that revolutionize systems neuroscience to data that underpins new models of learning and memory.

Agency: NSF | Branch: Standard Grant | Program: | Phase: | Award Amount: 1.00 | Year: 2015

There is a critical need to solve problems of societal and technical importance faster and at larger scales than is currently possible. This project will support several new applications to utilize the Blue Waters Supercomputer at scales that are scientifically needed but simply not possible otherwise or elsewhere. These include applications ranging from protein conformations to polar sciences. If successful, this research will engender a significant step up in capabilities towards extreme scale computing and data-intensive science.

The computational resources made available as part of this project will enable the design, development and testing of multiple new algorithms, middleware and methods. In the first track, the researchers propose a new approach to characterize the conformational landscape of the NMDAr LBD in its different forms, by using novel sampling methodologies and workload management tools. Leveraging sophisticated sampling methods, simulations will provide an unprecedented atomically detailed picture of the different states the protein can adopt as a function of the ligands it interacts with, and will also provide predictions of the kinetic pathways that link these states together. The result will be a conceptual framework to understand the sometimes perplexing experimental results and a springboard for the rational design of further experiments.

This study will open the way to a conceptually different approach to studying large conformational changes in complex macromolecules, as the same methodology and computational infrastructure can in principle be applied to a large number of biomedically relevant systems. The second track of this project is concerned with development, scaling and optimization of SPIDAL (Scalable Parallel Interoperable Data Intensive Libraries) and MIDAS (Middleware for Data-intensive Analysis and Science) that will be used to enhance the scalability of a range of data-intensive applications.

Agency: NSF | Branch: Standard Grant | Program: | Phase: COMMS, CIRCUITS & SENS SYS | Award Amount: 500.00K | Year: 2016

The PI will build a research program to develop novel integrated circuits and antennas that can generate high-power pulses with frequencies up to one terahertz (THz), several hundred times higher than the frequency of todays cellular networks. By exploiting the advantages of THz radiation, the proposed research program can transform wireless communications, imaging, and spectroscopic systems. THz communications systems will offer greater bandwidth and will also track mobile receivers with better fault tolerance than competing technologies with similar range and bandwidth, such as free space optical communication. THz imaging systems can not only bolster homelands security by accurate detection of hidden objects and explosives, but also can prevent tens of thousands of lives lost in car accidents every year by increasing the accuracy of collision avoidance automotive radars. THz spectroscopy systems can identify the species of gas molecules with high specificity and detect trace quantities of those molecules with high sensitivity. The PIs long-term educational goal is to inspire students at all levels to pursue careers in STEM disciplines. Working with the Rice University Office of STEM Engagement to provide research experience and internship opportunities for high-school teachers from Houston Independent School District, the PI will assist teachers with the development of their physics curriculum. The PI will work with the Rice Center for Excellence & Equity to engage underrepresented minority students in research and to provide summer internship opportunities for them.

The objective of the proposed research program is to develop novel integrated circuits and antennas that can generate, radiate, detect, and steer coherent high-power pulses with frequencies up to 1THz. With todays silicon processes, it is possible to build a complex integrated circuit with on-chip antennas operating in frequencies up to 500GHz. However, most of the existing solutions are narrow-band and based on continuous-wave signal generation. To push the performance limits of high-speed wireless communications, three-dimensional radar imaging, and THz spectroscopy, broadband sources and detectors are required. The basic research carried out under this program is expected to advance the state-of-the-art in broadband time-domain signal generation and detection. The PI will demonstrate the intellectual merit of the proposed program through the following contributions: (1) demonstrating picosecond impulse radiating arrays, (2) demonstrating picosecond impulse sampling arrays, (3) developing accurate and reliable measurement systems to characterize picosecond sources and detectors, (4) producing high-resolution three-dimensional radar images

Agency: NSF | Branch: Standard Grant | Program: | Phase: COMPUTATIONAL MATHEMATICS | Award Amount: 149.98K | Year: 2015

With the ability to reduce the cost of testing theories and ideas, numerical simulations will continue to play a growing role in scientific discovery and device development. Frequently, these simulations involve the solution of problems that are prescribed by physics. In many cases, the speed and accuracy with which such problems can be solved is a key limiting factor to what can and cannot be modeled numerically. Fast direct solvers have recently shown great promise for solving a large number of problems involving the same geometry by reusing the most expensive part of the solution technique. This situation happens often in settings such as product development where each problem involving the geometry corresponds to a different physical situation. When a large number of problems are under consideration, the fast direct solvers can show hundreds of times speed up over other techniques. While this speed up is great, many engineering situations involve a large number of problems with slightly different geometries. Each different geometry requires the most expensive part of the solver to be recomputed. This project will focus on the development and application of fast direct solvers to problems with evolving geometries. The new technique will recycle information obtained in the construction of the fast direct solver for one geometry to build solvers for the evolved geometries. As a result, the cost of the most expensive step in the fast direct solution technique will be substantially reduced while retaining the benefit of being able to solve multiple problems for each geometry quickly. This work should accelerate many numerical simulations and will have a technological impact on society through applications such as solar cell design, meta-material design, sonar, radar and simulations of blood flow.

The numerical simulations under consideration in the proposed work will involve the solution of linear boundary value problems. Many linear boundary value problems can be recast as integral equations. Solution techniques based on integral equations come with the cost of having to solve a dense linear system upon discretization. Fast direct solvers invert a dense system by exploiting structure in the matrix with a cost that grows linearly (or nearly linearly) with the problem size. The proposed work will adapt the fast linear algebra framework to create efficient direct solvers for a family of problems with similar geometries. The new technique will be the first to reuse the structural information obtained in the construction of a fast direct solver for a single geometry to build new direct solvers for evolved geometries. This recycling of structural information reduces the cost of the most expensive step in constructing fast direct solvers. The new technique should accelerate time-stepping for evolution equations, Stokes flow, optimal design algorithms, model reduction methods and periodic boundary value problem simulations. The solution technique will be applied to microfluids, inverse scattering, and periodic scattering.

Agency: NSF | Branch: Standard Grant | Program: | Phase: DISCOVERY RESEARCH K-12 | Award Amount: 24.24K | Year: 2014

The William Marsh Rice University project will work with middle school science teachers to design, field-test, refine, and evaluate a set of data management tools that will be embedded in a web-based science curriculum. The project helps middle school science teachers monitor their students progress, plan lessons, and reflect on their lessons. The project consists of three primary phases: first, the researchers will work with teachers to develop an initial set of data tools; second, teachers will test these tools in their classroom to verify that they are feasible and usable; and third, a pilot study will be conducted to examine how the tools are implemented in the classroom and an external evaluation will determine the early impact of the tools. As part of this study, the research team will work with 125 middle school science teachers across three different school districts. Ultimately, the findings from this project will identify characteristics of data management tools that are more likely to be used effectively by teachers and have a positive impact on science teaching and learning.

The project is employing a mixed methods design. Through design-based research, this project will help fill the need for research-based and teacher-driven design of online student management systems. During the first two years of the study, work will alternate between design/development and data collection, allowing the research team to collect and then incorporate teacher feedback into the tools design. During these first two years, data will be collected through teacher surveys, interviews, and observations. The culmination of the project will be a one-year pilot, which will allow the research team to study the implementation of the final tools, and an independent evaluator from the University of Houston to evaluate the early impact of the tools on teaching practices and student achievement. The development and research proposed in this project will benefit teachers and students throughout the United States by improving what data teachers see about their students progress in science and their own use of the curriculum.

Agency: NSF | Branch: Standard Grant | Program: | Phase: I-Corps | Award Amount: 50.00K | Year: 2014

Age-related macular degeneration (AMD) is a disease of the eye that is the leading cause of central vision loss in people over 50 in the US. The progress of the disease can often be unpredictable and rapid. Existing technologies (bolted to tables, bulky, operated by clinician) can evaluate AMD during clinic visits, but such visits are scheduled only once every few months. Existing clinical practices fail to detect degeneration in-between clinic visits and leave clinicians and patients guessing. This I-Corps team proposes to take advantage of the ever-growing ubiquity of camera-enabled smartphones coupled with the rapid development of computational imaging to solve the between-visit AMD progression problem and usher in a new generation of portable, low-cost, computational eye-imaging devices. The development of the mobileVision AMD imager will increase understanding of how AMD progresses and how well treatments are performing by capturing retinal images at a time scale of days rather than months. These images, coupled with their review by doctors, will enable new research directions for automatic AMD diagnosis, and may lead to the development of new, more effective clinical practices.

The proposed innovation is a take-home retinal imaging system. The physician shows the patient how to use the device during a scheduled visit, and then sends the patient home with the device. The patient then uses the device to take images of his or her own retina(s). The