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The Lawrence Berkeley National Laboratory , also known as the "Berkeley Lab", is a United States national laboratory located in the Berkeley Hills near Berkeley, California that conducts unclassified scientific research on behalf of the United States Department of Energy . It is managed and operated by the University of California, whose oldest campus, the University of California, Berkeley's main campus, it overlooks. Plans announced by the university in 2012 called for a second Berkeley Lab campus to be built on land it owns nearby at Richmond Field Station. Wikipedia.

Peled E.S.,University of California at Berkeley | Newman Z.L.,University of California at Berkeley | Isacoff E.Y.,University of California at Berkeley | Isacoff E.Y.,Lawrence Berkeley National Laboratory
Current Biology | Year: 2014

SummaryBackground Spontaneous "miniature" transmitter release takes place at low rates at all synapses. Long thought of as an unavoidable leak, spontaneous release has recently been suggested to be mediated by distinct pre- and postsynaptic molecular machineries and to have a specialized role in setting up and adjusting neuronal circuits. It remains unclear how spontaneous and evoked transmission are related at individual synapses, how they are distributed spatially when an axon makes multiple contacts with a target, and whether they are commonly regulated. Results Electrophysiological recordings in the Drosophila larval neuromuscular junction, in the presence of the use-dependent glutamate receptor (GluR) blocker philanthotoxin, indicated that spontaneous and evoked transmission employ distinct sets of GluRs. In vivo imaging of transmission using synaptically targeted GCaMP3 to detect Ca 2+ influx through the GluRs revealed little spatial overlap between synapses participating in spontaneous and evoked transmission. Spontaneous and evoked transmission were oppositely correlated with presynaptic levels of the protein Brp: synapses with high Brp favored evoked transmission, whereas synapses with low Brp were more active spontaneously. High-frequency stimulation did not increase the overlap between evoked and spontaneous transmission, and instead decreased the rate of spontaneous release from synapses that were highly active in evoked transmission. Conclusions Although individual synapses can participate in both evoked and spontaneous transmission, highly active synapses show a preference for one mode of transmission. The presynaptic protein Brp promotes evoked transmission and suppresses spontaneous release. These findings suggest the existence of presynaptic mechanisms that promote synaptic specialization to either evoked or spontaneous transmission. © 2014 Elsevier Ltd.

Anders A.,Lawrence Berkeley National Laboratory
Plasma Sources Science and Technology | Year: 2012

Cathodic vacuum arc plasmas are known to contain multiply charged ions. Twenty years after Pressure ionization: its role in metal vapour vacuum arc plasmas and ion sources appeared in volume 1 of Plasma Sources Science and Technology, this is a great opportunity to re-visit the issue of pressure ionization, a non-ideal plasma effect, and put it in perspective to the many other factors that influence observable charge state distributions, such as the role of the cathode material, the path in the densitytemperature phase diagram, the noise in vacuum arc plasma as described by a fractal model approach, the effects of external magnetic fields and charge exchange collisions with neutrals. A much more complex image of the vacuum arc plasma emerges, putting decades of experimentation and modeling in perspective. © 2012 IOP Publishing Ltd.

Wu Y.,Massachusetts Institute of Technology | Lazic P.,Massachusetts Institute of Technology | Hautier G.,Massachusetts Institute of Technology | Hautier G.,Catholic University of Louvain | And 2 more authors.
Energy and Environmental Science | Year: 2013

In this paper, we present a first principles high throughput screening system to search for new water-splitting photocatalysts. We use the approach to screen through nitrides and oxynitrides. Most of the known photocatalytic materials in the screened chemical space are reproduced. In addition, sixteen new materials are suggested by the screening approach as promising photocatalysts, including three binary nitrides, two ternary oxynitrides and eleven quaternary oxynitrides. © The Royal Society of Chemistry 2013.

Saito R.,Kyoto University | Shirai S.,University of California at Berkeley | Shirai S.,Lawrence Berkeley National Laboratory
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2012

A supersymmetric standard model with heavier scalar particles is very interesting from various viewpoints, especially Higgs properties. If the scalar mass scale is O(10-104) TeV, the standard model-like Higgs with mass around 125 GeV, which is implied by the recent LHC experiments, is predicted. However this scenario is difficult to be directly tested with collider experiments. In this Letter, we propose a test of this scenario by using observations of primordial gravitational waves (GWs). The future GW experiments such as DECIGO and BBO can probe the scalar mass around O(103-104) TeV, which is preferred from the Higgs mass about 125 GeV, if the primordial GWs have large amplitude. © 2012 Elsevier B.V.

Mohammed I.,University of Zurich | Seljak U.,Lawrence Berkeley National Laboratory
Monthly Notices of the Royal Astronomical Society | Year: 2014

We develop a model for the matter power spectrum as the sum of Zeldovich approximation and even powers of k, i.e. A0 - A2k2 + A4k4 - . . . , compensated at low k. With terms up to k4, the model can predict the true power spectrum to a few per cent accuracy up to k ~ 0.7 h Mpc-1, over a wide range of redshifts and models. The An coefficients contain information about cosmology, in particular amplitude of fluctuations. We write a simple form of the covariance matrix as a sum of Gaussian part and A0 variance, which reproduces the simulations remarkably well. In contrast, we show that one needs an N-body simulation volume of more than 1000 (Gpc h-1)3 to converge to 1 per cent accuracy on covariance matrix. We investigate the supersample variance effect and show it can be modelled as an additional parameter that can be determined from the data. This allows a determination of σ8 amplitude to about 0.2 per cent for a survey volume of 1(Gpc h-1)3, compared to 0.4 per cent otherwise.We explore the sensitivity of these coefficients to baryonic effects using hydrodynamic simulations of van Daalen et al. We find that because of baryons redistributing matter inside haloes all the coefficients A2n for n > 0 are strongly affected by baryonic effects, while A0 remains almost unchanged, a consequence of halo mass conservation. Our results suggest that observations such as weak lensing power spectrum can be effectively marginalized over the baryonic effects, while still preserving the bulk of the cosmological information contained in 0 and Zeldovich terms. © 2014 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

Liu Y.,University of California at Berkeley | Zentgraf T.,University of California at Berkeley | Bartal G.,University of California at Berkeley | Zhang X.,University of California at Berkeley | Zhang X.,Lawrence Berkeley National Laboratory
Nano Letters | Year: 2010

We propose and demonstrate efficiently molding surface plasmon polaritons (SPPs) based on transformation optics. SPPs are surface modes of electromagnetic waves tightly bound at metal-dielectric interfaces, which allow us to scale optics beyond the diffraction limit. Taking advantage of transformation optics, here we show that the propagation of SPPs can be manipulated in a prescribed manner by careful control of the dielectric material properties adjacent to a metal. Since the metal properties are completely unaltered, this methodology provides a practical way for routing light at very small scales. For instance, our approach enables SPPs to travel at uneven and curved surfaces over a broad wavelength range, where SPPs would normally suffer significant scattering losses. In addition, a plasmonic 180° waveguide bend and a plasmonic Luneburg lens with simple designs are presented. The unique design flexibility of the transformational plasmon optics introduced here may open a new door to nano optics and downscaling of photonic circuits. © 2010 American Chemical Society.

Berland K.,University of Oslo | Berland K.,Chalmers University of Technology | Cooper V.R.,Oak Ridge National Laboratory | Lee K.,Lawrence Berkeley National Laboratory | And 5 more authors.
Reports on Progress in Physics | Year: 2015

A density functional theory (DFT) that accounts for van der Waals (vdW) interactions in condensed matter, materials physics, chemistry, and biology is reviewed. The insights that led to the construction of the Rutgers-Chalmers van der Waals density functional (vdW-DF) are presented with the aim of giving a historical perspective, while also emphasizing more recent efforts which have sought to improve its accuracy. In addition to technical details, we discuss a range of recent applications that illustrate the necessity of including dispersion interactions in DFT. This review highlights the value of the vdW-DF method as a general-purpose method, not only for dispersion bound systems, but also in densely packed systems where these types of interactions are traditionally thought to be negligible. © 2015 IOP Publishing Ltd.

Kleiser I.K.W.,California Institute of Technology | Kasen D.,Lawrence Berkeley National Laboratory | Kasen D.,University of California at Berkeley
Monthly Notices of the Royal Astronomical Society | Year: 2014

Transient surveys have recently discovered a class of supernovae (SNe) with extremely rapidly declining light curves. These events are also often relatively faint, especially compared to Type Ia SNe. The common explanation for these events involves a weak explosion, producing a radioactive outflow with small ejected mass and kinetic energy (M ~ 0.1 M⊙ and E ~ 0.1 B, respectively), perhaps from the detonation of a helium shell on a white dwarf. We argue, in contrast, that these events may be Type Ib/c SNe with typical masses and energies (M ~ 3 M⊙, E ~ 1 B), but which ejected very little radioactive material. In our picture, the light curve is powered by the diffusion of thermal energy deposited by the explosion shock wave, and the rapid evolution is due to recombination, which reduces the opacity and results in an 'oxygen-plateau' light curve. Using a radiative transfer code and simple 1D ejecta profiles, we generate synthetic spectra and light curves and demonstrate that this model can reasonably fit the observations of one event, SN 2010X. Similar models may explain the features of other rapidly evolving SNe such as SN 2002bj and SN 2005ek. SNe such as these may require stripped-envelope progenitors with rather large radii (R ~ 20 R⊙), which may originate from a mass-loss episode occurring just prior to explosion. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

Dickel D.E.,Lawrence Berkeley National Laboratory
Philosophical transactions of the Royal Society of London. Series B, Biological sciences | Year: 2013

Transcriptional enhancers are a major class of functional element embedded in the vast non-coding portion of the human genome. Acting over large genomic distances, enhancers play critical roles in the tissue and cell type-specific regulation of genes, and there is mounting evidence that they contribute to the aetiology of many human diseases. Methods for genome-wide mapping of enhancer regions are now available, but the functional architecture contained within human enhancer elements remains unclear. Here, we review recent approaches aimed at understanding the functional anatomy of individual enhancer elements, using systematic qualitative and quantitative assessments of mammalian enhancer variants in cultured cells and in vivo. These studies provide direct insight into common architectural characteristics of enhancers including the presence of multiple transcription factor-binding sites and the mixture of both transcriptionally activating and repressing domains within the same enhancer. Despite such progress in understanding the functional composition of enhancers, the inherent complexities of enhancer anatomy continue to limit our ability to predict the impact of sequence changes on in vivo enhancer function. While providing an initial glimpse into the mutability of mammalian enhancers, these observations highlight the continued need for experimental enhancer assessment as genome sequencing becomes routine in the clinic.

Yun W.S.,Daegu Gyeongbuk Institute of Science and Technology | Yun W.S.,Lawrence Berkeley National Laboratory | Lee J.D.,Daegu Gyeongbuk Institute of Science and Technology
Physical Chemistry Chemical Physics | Year: 2014

The magnetism of the 3d transition-metal (TM) doped single-layer (1L) MoS2, where the Mo atom is partially replaced by the 3d TM atom, is investigated using the first-principles density functional calculations. In a series of 3d TM doped 1L-MoS2's, the induced spin polarizations are negligible for Sc, Ti, and Cr dopings, while the induced spin polarizations are confirmed for V, Mn, Fe, Co, Ni, Cu, and Zn dopings and the systems become magnetic. Especially, the Cu doped system shows unexpectedly strong magnetism although Cu is nonmagnetic in its bulk state. The driving force is found to be a strong hybridization between Cu 3d states and 3p states of neighboring S, which results in an extreme unbalanced spin-population in the spin-split impurity bands near the Fermi level. Finally, we also discuss further issues of the Cu induced magnetism of 1L-MoS2 such as investigation of additional charge states, the Cu doping at the S site instead of the Mo site, and the Cu adatom on the layer (i.e., 1L-MoS2). This journal is © the Partner Organisations 2014.

Wilson D.N.,Center for Integrated Protein Science Munich | Wilson D.N.,Ludwig Maximilians University of Munich | Cate J.H.D.,University of California at Berkeley | Cate J.H.D.,Lawrence Berkeley National Laboratory
Cold Spring Harbor Perspectives in Biology | Year: 2012

Structures of the bacterial ribosome have provided a framework for understanding universal mechanisms of protein synthesis. However, the eukaryotic ribosome is much larger than it is in bacteria, and its activity is fundamentally different in many keyways. Recent cryo-electron microscopy reconstructions and X-ray crystal structures of eukaryotic ribosomes and ribosomal subunits now provide an unprecedented opportunity to explore mechanisms of eukaryotic translation and its regulation in atomic detail. This review describes the X-ray crystal structures of the Tetrahymena thermophila 40S and 60S subunits and the Saccharomyces cerevisiae 80S ribosome, as well as cryo-electron microscopy reconstructions of translating yeast and plant 80S ribosomes. Mechanistic questions about translation in eukaryotes that will require additional structural insights to be resolved are also presented. © 2012 Cold Spring Harbor Laboratory Press; all rights reserved.

Xu N.,Lawrence Berkeley National Laboratory | Xu N.,Central China Normal University
Nuclear Physics A | Year: 2014

With large acceptance and excellent particle identification, STAR is one of the best mid-rapidity collider experiments for studying high-energy nuclear collisions. The STAR experiment provides full information on initial conditions, properties of the hot and dense medium as well as the properties at freeze-out. In Au+Au collisions at sNN=200 GeV, STAR's focus is on the nature of the sQGP produced at RHIC. In order to explore the properties of the QCD phase diagram, since 2010, the experiment has collected sizable data sets of Au+Au collisions at the lower collision energy region where the net-baryon density is large. At the 2014 Quark Matter Conference, the STAR experiment made 16 presentations that cover physics topics including collective dynamics, electromagnetic probes, heavy-flavor, initial state physics, jets, QCD phase diagram, thermodynamics and hadron chemistry, and future experimental facilities, upgrades, and instrumentation [1]. In this overview we will highlight a few results from the STAR experiment, especially those from the recent measurements of the RHIC beam energy scan program. At the end, instead of a summary, we will discuss STAR's near future physics programs at RHIC. © 2014 Elsevier B.V.

Clark M.D.,Columbia University | Kumar S.K.,Columbia University | Owen J.S.,Columbia University | Chan E.M.,Lawrence Berkeley National Laboratory
Nano Letters | Year: 2011

We present a theoretical description of how continuous monomer production affects the focusing of nanocrystal size distributions in solution. We show that sufficiently high monomer production rates can drive a decrease in the polydispersity even as the average nanocrystal size increases. This is in sharp contrast to Ostwald ripening, where polydispersity increases with mean crystal size. We interpret several experimental nanocrystal studies through our model and show how production-controlled growth promises exquisite control over the size and polydispersity of functional nanocrystals. © 2011 American Chemical Society.

Williams P.T.,Lawrence Berkeley National Laboratory
Medicine and Science in Sports and Exercise | Year: 2012

Purpose: Physical activity recommendations are defined in terms of time spent being physically active (e.g., 30 min of brisk walking, 5 d•wk -1). However, walking volume may be more naturally assessed by distance than by time. Analyses were therefore performed to test whether time or distance provides the best metric for relating walking volume to estimated total and regional adiposity. Methods: Linear and logistic regression analyses were used to relate exercise dose to body mass index (BMI), body circumferences, and obesity in a cross-sectional sample of 12,384 female and 3434 male walkers who reported both usual distance walked and time spent walking per week on survey questionnaires. Metabolic equivalent hours per day (MET•h• d-1, 1 MET = 3.5 mL O2•kg-1•min-1) were calculated from the time and pace, or distance and pace, using published compendium values. Results: Average MET-hours per day walked was 37% greater when calculated from time spent walking versus usual distance in women and was 32% greater in men. Per MET-hours per day, declines in BMI and circumferences (slope ± SE) were nearly twice as great, or greater, for distance-versus time-derived estimates for kilograms per squared meter of BMI (females =-0.58 ± 0.03 vs-0.31 ± 0.02, males =-0.35 ± 0.04 vs-0.15 ± 0.02), centimeter of waist circumference (females =-1.42 ± 0.07 vs-0.72 ± 0.04, males =-0.96 ± 0.10 vs-0.45 ± 0.07), and reductions in the odds for total obesity (odds ratio: females = 0.72 vs 0.84, males = 0.84 vs 0.92) and abdominal obesity (females = 0.74 vs 0.85, males = 0.79 vs 0.91, all comparisons significant). Conclusions: Distance walked may provide a better metric of walking volume for epidemiologic obesity research, and better public health targets for weight control, than walking duration. Additional research is required to determine whether these results, derived in a sample that regularly walks for exercise, apply more generally. © 2012 by the American College of Sports Medicine.

Firestone R.B.,Lawrence Berkeley National Laboratory
Astrophysical Journal | Year: 2014

Four supernovae (SNe), exploding ≤300 pc from Earth, were recorded 44, 37, 32, and 22 kyr ago in the radiocarbon (14C) record during the past 50 kyr. Each SN left a nearly identical signature in the record, beginning with an initial sudden increase in atmospheric radiocarbon, when the SN exploded, followed by a hiatus of 1500 yr, and concluding with a sustained 2000 yr increase in global radiocarbon due to γ-rays produced by diffusive shock in the SN remnant (SNR). For the past 18 kyr excess radiocarbon has decayed with the 14C half-life. SN22kyrBP, is identified as the Vela SN that exploded 250 ± 30 pc from Earth. These SN are confirmed in the 10Be, 26Al, 36Cl, and NO geologic records. The rate of near-Earth SNe is consistent with the observed rate of historical SNe giving a galactic rate of 14 ± 3 kyr-1 assuming the Chandra Galactic Catalog SNR distribution. The Earth has been used as a calorimeter to determine that 2 × 1049 erg were released as γ-rays at the time of each SN explosion and 1050 erg in γ-rays following each SN. The background rate of 14C production by cosmic rays has been determined as 1.61 atoms cm-2 s-1. Approximately 1/3 of the cosmic ray energy produced by diffusive shock in the SNR was observed to be emitted as high-energy γ-rays. Analysis of the 10Be/ 9Be ratio in marine sediment identified 19 additional near-Earth SNe that exploded 50-300 kyr ago. Comparison of the radiocarbon record with global temperature variations indicated that each SN explosion is correlated with a concurrent global warming of ≈3°C-4°C. © 2014. The American Astronomical Society. All rights reserved.

Whitelam S.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2010

We use computer simulation to study crystal-forming model proteins equipped with interactions that are both orientationally specific and nonspecific. Distinct dynamical pathways of crystal formation can be selected by tuning the strengths of these interactions. When the nonspecific interaction is strong, liquidlike clustering can precede crystallization; when it is weak, growth can proceed via ordered nuclei. Crystal yields are in certain parameter regimes enhanced by the nonspecific interaction, even though it promotes association without local crystalline order. Our results suggest that equipping nanoscale components with weak nonspecific interactions (such as depletion attractions) can alter both their dynamical pathway of assembly and optimize the yield of the resulting material. © 2010 The American Physical Society.

Zhou Q.,University of California at Berkeley | Zettl A.,University of California at Berkeley | Zettl A.,Lawrence Berkeley National Laboratory
Applied Physics Letters | Year: 2013

Graphene has extremely low mass density and high mechanical strength, and key qualities for efficient wide-frequency-response electrostatic audio speaker design. Low mass ensures good high frequency response, while high strength allows for relatively large free-standing diaphragms necessary for effective low frequency response. Here, we report on construction and testing of a miniaturized graphene-based electrostatic audio transducer. The speaker/earphone is straightforward in design and operation and has excellent frequency response across the entire audio frequency range (20 Hz-20 kHz), with performance matching or surpassing commercially available audio earphones. © 2013 AIP Publishing LLC.

Pruess K.,Lawrence Berkeley National Laboratory | Nordbotten J.,University of Bergen
Transport in Porous Media | Year: 2011

We have used the TOUGH2-MP/ECO2N code to perform numerical simulation studies of the long-term behavior of CO2 stored in an aquifer with a sloping caprock. This problem is of great practical interest, and is very challenging due to the importance of multi-scale processes. We find that the mechanism of plume advance is different from what is seen in a forced immiscible displacement, such as gas injection into a water-saturated medium. Instead of pushing the water forward, the plume advances because the vertical pressure gradients within the plume are smaller than hydrostatic, causing the groundwater column to collapse ahead of the plume tip. Increased resistance to vertical flow of aqueous phase in anisotropic media leads to reduced speed of up-dip plume advancement. Vertical equilibrium models that ignore effects of vertical flow will overpredict the speed of plume advancement. The CO2 plume becomes thinner as it advances, but the speed of advancement remains constant over the entire simulation period of up to 400 years, with migration distances of more than 80 km. Our simulations include dissolution of CO2 into the aqueous phase and associated density increase, and molecular diffusion. However, no convection develops in the aqueous phase because it is suppressed by the relatively coarse (sub-) horizontal gridding required in a regional-scale model. A first crude sub-grid-scale model was developed to represent convective enhancement of CO2 dissolution. This process is found to greatly reduce the thickness of the CO2 plume, but, for the parameters used in our simulations, does not affect the speed of plume advancement. © 2011 The Author(s).

Cordeiro P.J.,University of California at Berkeley | Tilley T.D.,University of California at Berkeley | Tilley T.D.,Lawrence Berkeley National Laboratory
ACS Catalysis | Year: 2011

Site-isolated Ti(IV) centers were introduced onto the surface of a mesoporous SBA-15 support via the thermolytic molecular precursor method. Prior to thermal treatment to generate Ti-OH sites, residual silanol groups were capped via reaction with Me2N-SiMe3 to give TiMe capSBA15. After low temperature treatment in oxygen, the resulting Ti-OH sites of TiMecapSBA15-O2 were modified by reaction with a series of protic reagents: phenol, pentafluorophenol, acetic acid, and trifluoroacetic acid. The structure of the resulting TiSBA15 catalysts and the Ti(IV) epoxidation intermediates (formed upon treatment of Ti(IV) materials with TBHP or H2O2) were probed using diffuse-reflectance UV-visible spectroscopy and infrared spectroscopy. A titanium-hydroperoxo species similar to that found in TS-1 is proposed for all catalysts. Samples modified with phenol and pentafluorophenol exhibited conversions of 1-octene that are 20 to 50% higher than those for TiMecapSBA15-O2, without a significant drop in selectivity for the epoxide product, 1,2-epoxyoctane, when TBHP was used as the oxidant. With aqueous H 2O2 as the oxidant, the phenol-treated materials exhibited 1-octene conversions that are 15 to 50% greater than those observed for TiMecapSBA15-O2, and an increased selectivity for 1,2-epoxyoctane of 10 to 30%. Additionally, the efficiency of H 2O2 usage, as monitored via 1H NMR spectroscopy, increased by a factor of 2 to three for catalysts modified with phenol and pentafluorophenol, with respect to the efficiency observed over TiMecapSBA15-O2. Catalysts modified with acetic acid and trifluoroacetic acid displayed decreased catalytic turnover numbers and epoxide selectivities when TBHP was used as the oxidant, but exhibited catalytic turnover numbers and epoxide selectivities similar to TiMecapSBA15- O2 when H2O2 was used as the oxidant. After treatment of TiMecapSBA15-O2 with acetic acid, the H 2O2 efficiency decreased by a factor of 2 for the epoxidation of 1-octene with H2O2. © 2011 American Chemical Society.

Jiang F.,University of California at Berkeley | Doudna J.A.,University of California at Berkeley | Doudna J.A.,Lawrence Berkeley National Laboratory | Doudna J.A.,Howard Hughes Medical Institute
Current Opinion in Structural Biology | Year: 2015

Prokaryotic CRISPR-Cas genomic loci encode RNA-mediated adaptive immune systems that bear some functional similarities with eukaryotic RNA interference. Acquired and heritable immunity against bacteriophage and plasmids begins with integration of ~30 base pair foreign DNA sequences into the host genome. CRISPR-derived transcripts assemble with CRISPR-associated (Cas) proteins to target complementary nucleic acids for degradation. Here we review recent advances in the structural biology of these targeting complexes, with a focus on structural studies of the multisubunit Type I CRISPR RNA-guided surveillance and the Cas9 DNA endonuclease found in Type II CRISPR-Cas systems. These complexes have distinct structures that are each capable of site-specific double-stranded DNA binding and local helix unwinding. © 2015 Elsevier Ltd.

Stapp H.P.,Lawrence Berkeley National Laboratory
NeuroQuantology | Year: 2012

The original Copenhagen interpretation of quantum mechanics was offered as a pragmatic methodology for making predictions about future experiences on the basis of knowledge gleaned from past experiences. It was, therefore, fundamentally about mental realities, and refrained from speaking about a more inclusive reality. Von Neumann created, later, what is called the orthodox formulation of quantum mechanics. It incorporates all of the Copenhagen-based predictions about connections between experiences into a rationally coherent conception of a dynamically integrated psychophysical reality. Von Neumann's formulation allows the same laws and concepts that are used to make predictions about atomic phenomena to account for the capacity of our mental intentions to influence our bodily actions. Danko Georgiev claims to have found logical flaws in my use of von Neumann's theory to explain this causal effectiveness of our mental intentions. The bulk of Georgiev's paper gives a detailed discussion of a system with just two base states, up and down. This is not an adequate model of the pertinent physical system, a human brain. Georgiev's attempt to relate his two-state work to the case at hand is flawed by statements such as "...in von Neumann's formulation there are no such things as minds, spirits, ghosts, or souls, ..." Von Neumann's formulation certainly does involve minds. Georgiev's choice of words seems designed to suggest that I am introducing mental qualities and assumptions that go beyond what are already parts of von Neumann's theory. I explain here why these allegations, and all his other allegations of errors, are incorrect.

Ko D.-K.,University of Pennsylvania | Urban J.J.,Lawrence Berkeley National Laboratory | Murray C.B.,University of Pennsylvania
Nano Letters | Year: 2010

Single component and multicomponent nanocrystal (NC) solids represent an exciting new form of condensed matter, as they can potentially capture not only the quantum features of the individual building blocks but also novel collective properties through coupling of NC components. Unlike bulk semiconductors, however, there is no current theory for how introduction of dopants will impact the electronic structure and transport properties of NC solids. Empirically, it is known that in semiconductor NC systems, mixing two different materials of NCs electronically dopes the film. However, it has been challenging to connect the macroscopic measurements of doping effects on transport behavior to a microscopic understanding of how the identity, placement, and abundance of dopants impact these measurements. In this Letter, we report the first temperature-dependent thermopower measurements in doped and undoped NC solids. In combination with temperature-dependent electrical conductivity measurements, how the doping affects the carrier concentration as well as mobility is explored exclusively. These complementary measurements serve as a unique electronic spectroscopy tool to quantitatively reveal the energetics of carriers and electronic states in NC solids. © 2010 American Chemical Society.

Noy A.,University of California at Merced | Noy A.,Lawrence Berkeley National Laboratory
Advanced Materials | Year: 2011

Every cell in a living organisms performs a complex array of functions using a vast arsenal of proteins, ion channels, pumps, motors, signaling molecules, and cargo carriers. With all the progress that humankind has made to date in the development of sophisticated machinery and computing capabilities, understanding and communicating with living systems on that level of complexity lags behind. A breakthrough in these capabilities could only come if a way is found to integrate biological components into artificial devices. The central obstacle for this vision of bionanoelectronics is the absence of a versatile interface that facilitates two-way communication between biological and electronic structures. 1D nanomaterials, such as nanotubes and nanowires, open up the possibility of constructing tight interfaces that could enable such bidirectional flow of information. This report discusses the overall progress in building such interfaces on the level of individual proteins and whole cells and focuses on the latest efforts to create device platforms that integrate membrane proteins, channels, and pumps with nanowire bioelectronics. Bionanoelectronic devices that combine biological and electronic components in nanoscale architectures could enable bidirectional communication between biological organisms and artificial objects. These devices may produce a new generation of diagnostic tools, smart prosthetics, and sophisticated neural interfaces and also reveal the inner workings of the biological systems in unprecedented detail. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rutqvist J.,Lawrence Berkeley National Laboratory
Computers and Geosciences | Year: 2011

This paper presents recent advancement in and applications of TOUGH-FLAC, a simulator for multiphase fluid flow and geomechanics. The TOUGH-FLAC simulator links the TOUGH family multiphase fluid and heat transport codes with the commercial FLAC3D geomechanical simulator. The most significant new TOUGH-FLAC development in the past few years is a revised architecture, enabling a more rigorous and tight coupling procedure with improved computational efficiency. The applications presented in this paper are related to modeling of crustal deformations caused by deep underground fluid movements and pressure changes as a result of both industrial activities (the In Salah CO2 Storage Project and the Geysers Geothermal Field) and natural events (the 1960s Matsushiro Earthquake Swarm). Finally, the paper provides some perspectives on the future of TOUGH-FLAC in light of its applicability to practical problems and the need for high-performance computing capabilities for field-scale problems, such as industrial-scale CO2 storage and enhanced geothermal systems. It is concluded that despite some limitations to fully adapting a commercial code such as FLAC3D for some specialized research and computational needs, TOUGH-FLAC is likely to remain a pragmatic simulation approach, with an increasing number of users in both academia and industry. © 2010 Elsevier Ltd.

Mehrbod M.,University of California at Berkeley | Mofrad M.R.K.,University of California at Berkeley | Mofrad M.R.K.,Lawrence Berkeley National Laboratory
PLoS Computational Biology | Year: 2013

Integrin clustering plays a pivotal role in a host of cell functions. Hetero-dimeric integrin adhesion receptors regulate cell migration, survival, and differentiation by communicating signals bidirectionally across the plasma membrane. Thus far, crystallographic structures of integrin components are solved only separately, and for some integrin types. Also, the sequence of interactions that leads to signal transduction remains ambiguous. Particularly, it remains controversial whether the homo-dimerization of integrin transmembrane domains occurs following the integrin activation (i.e. when integrin ectodomain is stretched out) or if it regulates integrin clustering. This study employs molecular dynamics modeling approaches to address these questions in molecular details and sheds light on the crucial effect of the plasma membrane. Conducting a normal mode analysis of the intact αllbβ3 integrin, it is demonstrated that the ectodomain and transmembrane-cytoplasmic domains are connected via a membrane-proximal hinge region, thus merely transmembrane-cytoplasmic domains are modeled. By measuring the free energy change and force required to form integrin homo-oligomers, this study suggests that the β-subunit homo-oligomerization potentially regulates integrin clustering, as opposed to α-subunit, which appears to be a poor regulator for the clustering process. If α-subunits are to regulate the clustering they should overcome a high-energy barrier formed by a stable lipid pack around them. Finally, an outside-in activation-clustering scenario is speculated, explaining how further loading the already-active integrin affects its homo-oligomerization so that focal adhesions grow in size. © 2013 Mehrbod, Mofrad.

Riley W.J.,Lawrence Berkeley National Laboratory | Shen C.,Pennsylvania State University
Hydrology and Earth System Sciences | Year: 2014

Watershed-scale hydrological and biogeochemical models are usually discretized at resolutions coarser than where significant heterogeneities in topography, abiotic factors (e.g., soil properties), and biotic (e.g., vegetation) factors exist. Here we report on a method to use fine-scale (220 m grid cells) hydrological model predictions to build reduced-order models of the statistical properties of near-surface soil moisture at coarse resolution (25 times coarser, ∼7 km). We applied a watershed-scale hydrological model (PAWS-CLM4) that has been previously tested in several watersheds. Using these simulations, we developed simple, relatively accurate (R2 ∼0.7-0.8), reduced-order models for the relationship between mean and higher-order moments of near-surface soil moisture during the nonfrozen periods over five years. When applied to transient predictions, soil moisture variance and skewness were relatively accurately predicted (R2 0.7-0.8), while the kurtosis was less accurately predicted (R2 ∼0.5). We also tested 16 system attributes hypothesized to explain the negative relationship between soil moisture mean and variance toward the wetter end of the distribution and found that, in the model, 59% of the variance of this relationship can be explained by the elevation gradient convolved with mean evapotranspiration. We did not find significant relationships between the time rate of change of soil moisture variance and covariances between mean moisture and evapotranspiration, drainage, or soil properties, as has been reported in other modeling studies. As seen in previous observational studies, the predicted soil moisture skewness was predominantly positive and negative in drier and wetter regions, respectively. In individual coarse-resolution grid cells, the transition between positive and negative skewness occurred at a mean soil moisture of ∼0.25-0.3. The type of numerical modeling experiments presented here can improve understanding of the causes of soil moisture heterogeneity across scales, and inform the types of observations required to more accurately represent what is often unresolved spatial heterogeneity in regional and global hydrological models. © Author(s) 2014. CC Attribution 3.0 License.

Baglin C.M.,Lawrence Berkeley National Laboratory
Nuclear Data Sheets | Year: 2013

Experimental nuclear structure and decay data for all known A=91 nuclides (As, Se, Br, Kr, Rb, Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd) have been evaluated. This evaluation, covering data received by 1 September 2013, supersedes the 1998 evaluation by C. M. Baglin published in Nuclear Data Sheets 86, 1 (1999) (15 December 1998 literature cutoff), and subsequent evaluations by C. M. Baglin added to the ENSDF database for Kr, Sr and Zr (29 December 2000 literature cutoff) and by B. Singh for 91Tc (6 November 2000 literature cutoff). © 2013 Elsevier Inc.

Shamsuzzoha Basunia M.,Lawrence Berkeley National Laboratory
Nuclear Data Sheets | Year: 2013

Evaluated spectroscopic data and level schemes from radioactive decay and nuclear reaction studies are presented for 28F, 28Ne, 28Na, 28Mg, 28Al, 28Si, 28P, and 28S. This evaluation for A=28 supersedes the earlier evaluations by P.M. Endt (1998En04 and 1990En08). However, additional/detailed data for these nuclides can be found in earlier evaluations 1978En02 and 1973EnVA also by P.M. Endt. © 2013.

Sternberg S.H.,University of California at Berkeley | Haurwitz R.E.,University of California at Berkeley | Doudna J.A.,University of California at Berkeley | Doudna J.A.,Howard Hughes Medical Institute | Doudna J.A.,Lawrence Berkeley National Laboratory
RNA | Year: 2012

Bacteria and archaea possess adaptive immune systems that rely on small RNAs for defense against invasive genetic elements. CRISPR (clustered regularly interspaced short palindromic repeats) genomic loci are transcribed as long precursor RNAs, which must be enzymatically cleaved to generate mature CRISPR-derived RNAs (crRNAs) that serve as guides for foreign nucleic acid targeting and degradation. This processing occurs within the repetitive sequence and is catalyzed by a dedicated Cas6 family member in many CRISPR systems. In Pseudomonas aeruginosa, crRNA biogenesis requires the endoribonuclease Csy4 (Cas6f), which binds and cleaves at the 3′ side of a stable RNA stem-loop structure encoded by the CRISPR repeat. We show here that Csy4 recognizes its RNA substrate with an ∼50 pM equilibrium dissociation constant, making it one of the highest-affinity protein:RNA interactions of this size reported to date. Tight binding is mediated exclusively by interactions upstream of the scissile phosphate that allow Csy4 to remain bound to its product and thereby sequester the crRNA for downstream targeting. Substrate specificity is achieved by RNA major groove contacts that are highly sensitive to helical geometry, as well as a strict preference for guanosine adjacent to the scissile phosphate in the active site. Collectively, our data highlight diverse modes of substrate recognition employed by Csy4 to enable accurate selection of CRISPR transcripts while avoiding spurious, off-target RNA binding and cleavage. Published by Cold Spring Harbor Laboratory Press. Copyright © 2012 RNA Society.

Mills E.,Lawrence Berkeley National Laboratory
Energy for Sustainable Development | Year: 2016

The inequity of costly and low-quality fuel-based lighting is compounded by adverse health and safety risks including burns, indoor air pollution, poisoning due to accidental ingestion of kerosene fuel by children, compromised visual health, maternal health issues, and reduced service in health facilities illuminated solely or sporadically with fuel-based lighting. This article compiles and synthesizes information on the health and safety impacts of fuel-based lighting from 135 reports spanning 33 countries. Energy efficient, off-grid lighting solutions offer the most promising and scalable means to eliminate adverse health outcomes, while lowering lighting costs and reducing greenhouse-gas emissions. Deployments seeking the greatest possible health benefit should target the most impacted geographical and demographic user groups. Because women and children are disproportionately impacted, improved lighting technologies for use by these groups will yield particularly significant health benefits. © 2015 International Energy Initiative.

Cappa C.D.,University of California at Davis | Wilson K.R.,Lawrence Berkeley National Laboratory
Atmospheric Chemistry and Physics | Year: 2011

Vacuum Ultraviolet (VUV) photoionization mass spectrometry has been used to measure the evolution of chemical composition for two distinct organic aerosol types as they are passed through a thermodenuder at different temperatures. The two organic aerosol types considered are primary lubricating oil (LO) aerosol and secondary aerosol from the α-pinene + O3 reaction (αP). The evolution of the VUV mass spectra for the two aerosol types with temperature are observed to differ dramatically. For LO particles, the spectra exhibit distinct changes with temperature in which the lower peaks, corresponding to compounds with higher vapor pressures, disappear more rapidly than the high peaks. In contrast, the αP aerosol spectrum is essentially unchanged by temperature even though the particles experience significant mass loss due to evaporation. The variations in the LO spectra are found to be quantitatively in agreement with expectations from absorptive partitioning theory whereas the αP spectra suggest that the evaporation of αP derived aerosol appears to not be governed by partitioning theory. We postulate that this difference arises from diffusivity within the ±P particles being sufficiently slow that they do not exhibit the expected liquid-like behavior and perhaps exist in a glassy state. To reconcile these observations with decades of aerosol growth measurements, which indicate that OA formation is described by equilibrium partitioning, we present a conceptual model wherein the secondary OA is formed and then rapidly converted from an absorbing form to a non-absorbing form. The results suggest that, although OA growth may be describable by equilibrium partitioning theory, the properties of organic aerosol once formed may differ significantly from the properties determined in the equilibrium framework. © 2011 Author(s).

White M.,University of California at Berkeley | White M.,Lawrence Berkeley National Laboratory
Monthly Notices of the Royal Astronomical Society | Year: 2014

This year marks the 100th anniversary of the birth of Yakov Zel'dovich. Amongst his many legacies is the Zel'dovich approximation for the growth of large-scale structure, which remains one of the most successful and insightful analytic models of structure formation. We use the Zel'dovich approximation to compute the two-point function of the matter and biased tracers, and compare to the results of N-body simulations and other Lagrangian perturbation theories.We show that Lagrangian perturbation theories converge well and that the Zel'dovich approximation provides a good fit to the N-body results except for the quadrupole moment of the halo correlation function. We extend the calculation of halo bias to third order and also consider non-local biasing schemes, none of which remove the discrepancy. We argue that a part of the discrepancy owes to an incorrect prediction of inter-halo velocity correlations. We use the Zel'dovich approximation to compute the ingredients of the Gaussian streaming model and show that this hybrid method provides a good fit to clustering of haloes in redshift space down to scales of tens of Mpc. © 2014 The Author Published by Oxford University Press on behalf of the Royal Astronomical Society.

Parameswaran S.A.,University of California at Berkeley | Turner A.M.,University of Amsterdam | Arovas D.P.,University of California at San Diego | Vishwanath A.,University of California at Berkeley | Vishwanath A.,Lawrence Berkeley National Laboratory
Nature Physics | Year: 2013

Band insulators appear in a crystalline system only when the filling - the number of electrons per unit cell and spin projection - is an integer. At fractional filling, an insulating phase that preserves all symmetries is a Mott insulator; that is, it is either gapless or, if gapped, exhibits fractionalized excitations and topological order. We raise the inverse question - at an integer filling is a band insulator always possible? Here we show that lattice symmetries may forbid a band insulator even at certain integer fillings, if the crystal is non-symmorphic - a property shared by most three-dimensional crystal structures. In these cases, one may infer the existence of topological order if the ground state is gapped and fully symmetric. This is demonstrated using a non-perturbative flux-threading argument, which has immediate applications to quantum spin systems and bosonic insulators in addition to electronic band structures in the absence of spin-orbit interactions. © 2013 Macmillan Publishers Limited. All rights reserved.

Johnson L.R.,Lawrence Berkeley National Laboratory
Geophysical Journal International | Year: 2010

A model is presented that treats an earthquake as the failure of asperities in a manner consistent with modern concepts of sliding friction. The mathematical description of the model includes results for elliptical and circular asperities, oblique tectonic slip, static and dynamic solutions for slip on the fault, stress intensity factors, strain energy and second-order moment tensor. The equations that control interaction of asperities are derived and solved both in a quasi-static tectonic mode when none of the asperities are in the process of failing and a dynamic failure mode when asperities are failing and sending out slip pulses that can trigger failure of additional asperities. The model produces moment rate functions for each asperity failure so that, given an appropriate Green function, the radiation of elastic waves is a straightforward calculation. The model explains an observed scaling relationship between repeat time and seismic moment for repeating seismic events and is consistent with the properties of pseudo-tachylites treated as fossil asperities. Properties of the model are explored with simulations of seismic activity that results when a section of the fault containing a spatial distribution of asperities is subjected to tectonic slip. The simulations show that the failure of a group of strongly interacting asperities satisfies the same scaling relationship as the failure of individual asperities, and that realistic distributions of asperities on a fault plane lead to seismic activity consistent with probability estimates for the interaction of asperities and predicted values of the Gutenberg-Richter a and b values. General features of the model are the exterior crack solution as a theoretical foundation, a heterogeneous state of stress and strength on the fault, dynamic effects controlled by propagating slip pulses and radiated elastic waves with a broad frequency band. No claim to original US government works Journal compilation © 2010 RAS.

Golji J.,University of California at Berkeley | Mofrad M.R.K.,University of California at Berkeley | Mofrad M.R.K.,Lawrence Berkeley National Laboratory
PLoS Computational Biology | Year: 2013

Vinculin can interact with F-actin both in recruitment of actin filaments to the growing focal adhesions and also in capping of actin filaments to regulate actin dynamics. Using molecular dynamics, both interactions are simulated using different vinculin conformations. Vinculin is simulated either with only its vinculin tail domain (Vt), with all residues in its closed conformation, with all residues in an open I conformation, and with all residues in an open II conformation. The open I conformation results from movement of domain 1 away from Vt; the open II conformation results from complete dissociation of Vt from the vinculin head domains. Simulation of vinculin binding along the actin filament showed that Vt alone can bind along the actin filaments, that vinculin in its closed conformation cannot bind along the actin filaments, and that vinculin in its open I conformation can bind along the actin filaments. The simulations confirm that movement of domain 1 away from Vt in formation of vinculin 1 is sufficient for allowing Vt to bind along the actin filament. Simulation of Vt capping actin filaments probe six possible bound structures and suggest that vinculin would cap actin filaments by interacting with both S1 and S3 of the barbed-end, using the surface of Vt normally occluded by D4 and nearby vinculin head domain residues. Simulation of D4 separation from Vt after D1 separation formed the open II conformation. Binding of open II vinculin to the barbed-end suggests this conformation allows for vinculin capping. Three binding sites on F-actin are suggested as regions that could link to vinculin. Vinculin is suggested to function as a variable switch at the focal adhesions. The conformation of vinculin and the precise F-actin binding conformation is dependent on the level of mechanical load on the focal adhesion. © 2013 Golji and Mofrad.

Vay J.-L.,Lawrence Berkeley National Laboratory | Haber I.,University of Maryland University College | Godfrey B.B.,University of Maryland University College
Journal of Computational Physics | Year: 2013

Pseudo-spectral electromagnetic solvers (i.e. representing the fields in Fourier space) have extraordinary precision. In particular, Haber et al. presented in 1973 a pseudo-spectral solver that integrates analytically the solution over a finite time step, under the usual assumption that the source is constant over that time step. Yet, pseudo-spectral solvers have not been widely used, due in part to the difficulty for efficient parallelization owing to global communications associated with global FFTs on the entire computational domains.A method for the parallelization of electromagnetic pseudo-spectral solvers is proposed and tested on single electromagnetic pulses, and on Particle-In-Cell simulations of the wakefield formation in a laser plasma accelerator.The method takes advantage of the properties of the Discrete Fourier Transform, the linearity of Maxwell's equations and the finite speed of light for limiting the communications of data within guard regions between neighboring computational domains.Although this requires a small approximation, test results show that no significant error is made on the test cases that have been presented.The proposed method opens the way to solvers combining the favorable parallel scaling of standard finite-difference methods with the accuracy advantages of pseudo-spectral methods. © 2013 Elsevier Inc.

Godfrey B.B.,University of Maryland University College | Vay J.-L.,Lawrence Berkeley National Laboratory
Journal of Computational Physics | Year: 2013

Rapidly growing numerical instabilities routinely occur in multidimensional particle-in-cell computer simulations of plasma-based particle accelerators, astrophysical phenomena, and relativistic charged particle beams. Reducing instability growth to acceptable levels has necessitated higher resolution grids, high-order field solvers, current filtering, etc. except for certain ratios of the time step to the axial cell size, for which numerical growth rates and saturation levels are reduced substantially. This paper derives and solves the cold beam dispersion relation for numerical instabilities in multidimensional, relativistic, electromagnetic particle-in-cell programs employing either the standard or the Cole-Karkkainnen finite difference field solver on a staggered mesh and the common Esirkepov current-gathering algorithm. Good overall agreement is achieved with previously reported results of the WARP code. In particular, the existence of select time steps for which instabilities are minimized is explained. Additionally, an alternative field interpolation algorithm is proposed for which instabilities are almost completely eliminated for a particular time step in ultra-relativistic simulations. © 2013 Elsevier Inc..

Mardirossian N.,University of California at Berkeley | Head-Gordon M.,Lawrence Berkeley National Laboratory
Journal of Chemical Theory and Computation | Year: 2013

For a set of eight equilibrium intermolecular complexes, it is discovered that the basis set limit (BSL) cannot be reached by aug-cc-pV5Z for three of the Minnesota density functionals: M06-L, M06-HF, and M11-L. In addition, the M06 and M11 functionals exhibit substantial, but less severe, difficulties in reaching the BSL. By using successively finer grids, it is demonstrated that this issue is not related to the numerical integration of the exchange-correlation functional. In addition, it is shown that the difficulty in reaching the BSL is not a direct consequence of the structure of the augmented functions in Dunning's basis sets, since modified augmentation yields similar results. By using a very large custom basis set, the BSL appears to be reached for the HF dimer for all of the functionals. As a result, it is concluded that the difficulties faced by several of the Minnesota density functionals are related to an interplay between the form of these functionals and the structure of standard basis sets. It is speculated that the difficulty in reaching the basis set limit is related to the magnitude of the inhomogeneity correction factor (ICF) of the exchange functional. A simple modification of the M06-L exchange functional that systematically reduces the basis set superposition error (BSSE) for the HF dimer in the aug-cc-pVQZ basis set is presented, further supporting the speculation that the difficulty in reaching the BSL is caused by the magnitude of the exchange functional ICF. Finally, the BSSE is plotted with respect to the internuclear distance of the neon dimer for two of the examined functionals. © 2013 American Chemical Society.

Hosur P.,University of California at Berkeley | Parameswaran S.A.,University of California at Berkeley | Vishwanath A.,University of California at Berkeley | Vishwanath A.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2012

We study transport in Weyl semimetals with N isotropic Weyl nodes in the presence of Coulomb interactions or disorder at temperature T. In the interacting clean limit, we determine the conductivity σ(ω,T) by solving a quantum Boltzmann equation within a "leading log" approximation and find it to be proportional to T, up to logarithmic factors arising from the flow of couplings. In the noninteracting disordered case, we compute the Kubo conductivity and show that it behaves differently for ωT and ωT: in the former regime we recover a previous result, of a finite dc conductivity and a Drude width vanishing as NT2; in the latter, we find that σ(ω,T) vanishes linearly with ω with a leading term as T→0 equal to the clean, free-fermion result: σ0(N)(ω,T=0)= Ne212hωv F. We compare our results to transport data on Y 2Ir 2O 7 and comment on the possible relevance to recent experiments on Eu 2Ir 2O 7. © 2012 American Physical Society.

Wang L.-W.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2012

There are materials that exist in unusual solid-liquid hybrid phases, for example, the superionics at high temperatures of 700°C. Using ab initio molecular dynamics, we show that the intensely studied Cu 2S high chalcocite phase is actually a solid-liquid hybrid phase which exists in relatively low temperature (>105°C). Its formation mechanism is different from the superionics. We also show that the previously proposed atomic structure for high chalcocite is incorrect, and the low chalcocite to high chalcocite transition should be described as a sublattice solid to liquid transition. © 2012 American Physical Society.

Hohlfeld E.,Lawrence Berkeley National Laboratory | Mahadevan L.,Harvard University
Physical Review Letters | Year: 2012

Sulci are surface folds commonly seen in strained soft elastomers and form via a strongly subcritical, yet scale-free, instability. Treating the threshold for nonlinear instability as a nonlinear critical point, we explain the nature of sulcus patterns in terms of the scale and translation symmetries which are broken by the formation of an isolated, small sulcus. Our perturbative theory and simulations show that sulcus formation in a thick, compressed slab can arise either as a supercritical or as a weakly subcritical bifurcation relative to this nonlinear critical point, depending on the boundary conditions. An infinite number of competing, equilibrium patterns simultaneously emerge at this critical point, but the one selected has the lowest energy. We give a simple, physical explanation for the formation of these sulcification patterns using an analogy to a solid-solid phase transition with a finite energy of transformation. © 2012 American Physical Society.

Persson K.A.,Lawrence Berkeley National Laboratory | Waldwick B.,Massachusetts Institute of Technology | Lazic P.,Massachusetts Institute of Technology | Ceder G.,Massachusetts Institute of Technology
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

We present an efficient scheme for combining ab initio calculated solid states with experimental aqueous states through a framework of consistent reference energies. Our work enables accurate prediction of phase stability and dissolution in equilibrium with water, which has many important application areas. We formally outline the thermodynamic principles of the scheme and show examples of successful applications of the proposed framework on (1) the evaluation of the water-splitting photocatalyst material Ta 3N 5 for aqueous stability, (2) the stability of small nanoparticle Pt in acid water, and (3) the prediction of particle morphology and facet stabilization of olivine LiFePO 4 as a function of aqueous conditions. ©2012 American Physical Society.

Wang D.,Lawrence Berkeley National Laboratory
Molecular & cellular proteomics : MCP | Year: 2012

RNA helicase DDX5 (also p68) is involved in all aspects of RNA metabolism and serves as a transcriptional coregulator, but its functional role in breast cancer remains elusive. Here, we report an integrative biology study of DDX5 in breast cancer, encompassing quantitative proteomics, global MicroRNA profiling, and detailed biochemical characterization of cell lines and human tissues. We showed that protein expression of DDX5 increased progressively from the luminal to basal breast cancer cell lines, and correlated positively with that of CD44 in the basal subtypes. Through immunohistochemistry analyses of tissue microarrays containing over 200 invasive human ductal carcinomas, we observed that DDX5 was up-regulated in the majority of malignant tissues, and its expression correlated strongly with those of Ki67 and EGFR in the triple-negative tumors. We demonstrated that DDX5 regulated a subset of MicroRNAs including miR-21 and miR-182 in basal breast cancer cells. Knockdown of DDX5 resulted in reorganization of actin cytoskeleton and reduction of cellular proliferation. The effects were accompanied by up-regulation of tumor suppressor PDCD4 (a known miR-21 target); as well as up-regulation of cofilin and profilin, two key proteins involved in actin polymerization and cytoskeleton maintenance, as a consequence of miR-182 down-regulation. Treatment with miR-182 inhibitors resulted in morphologic phenotypes resembling those induced by DDX5 knockdown. Using bioinformatics tools for pathway and network analyses, we confirmed that the network for regulation of actin cytoskeleton was predominantly enriched for the predicted downstream targets of miR-182. Our results reveal a new functional role of DDX5 in breast cancer via the DDX5→miR-182→actin cytoskeleton pathway, and suggest the potential clinical utility of DDX5 and its downstream MicroRNAs in the theranostics of breast cancer.

Noland C.L.,University of California at Berkeley | Doudna J.A.,University of California at Berkeley | Doudna J.A.,Howard Hughes Medical Institute | Doudna J.A.,Lawrence Berkeley National Laboratory
RNA | Year: 2013

Small RNAs guide RNA-induced silencing complexes (RISCs) to bind to cognate mRNA transcripts and trigger silencing of protein expression during RNA interference (RNAi) in eukaryotes. A fundamental aspect of this process is the asymmetric loading of one strand of a short interfering RNA (siRNA) or microRNA (miRNA) duplex onto RISCs for correct target recognition. Here, we use a reconstituted system to determine the extent to which the core components of the human RNAi machinery contribute to RNA guide strand selection. We show that Argonaute2 (Ago2), the endonuclease that binds directly to siRNAs and miRNAs within RISC, has intrinsic but substrate-dependent RNA strand selection capability. This activity can be enhanced substantially when Ago2 is in complex with the endonuclease Dicer and the double-stranded RNA-binding proteins (dsRBPs).trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). The extent to which human Dicer/dsRBP complexes contribute to strand selection is dictated by specific duplex parameters such as thermodynamics, 5' nucleotide identity, and structure. Surprisingly, our results also suggest that strand selection for some miRNAs is enhanced by PACTcontaining complexes but not by those containing TRBP. Furthermore, overall mRNA targeting by miRNAs is disfavored for complexes containing TRBP but not PACT. These findings demonstrate that multiple proteins collaborate to ensure optimal strand selection in humans and reveal the possibility of delineating RNAi pathways based on the presence of TRBP or PACT. Copyright © 2013 RNA Society.

Ryu S.,University of California at Berkeley | Moore J.E.,University of California at Berkeley | Moore J.E.,Lawrence Berkeley National Laboratory | Ludwig A.W.W.,University of California at Santa Barbara
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

One of the defining properties of the conventional three-dimensional ("Z 2" or "spin-orbit") topological insulator is its characteristic magnetoelectric effect, as described by axion electrodynamics. In this paper, we discuss an analog of such a magnetoelectric effect in the thermal (or gravitational) and magnetic dipole responses in all symmetry classes that admit topologically nontrivial insulators or superconductors to exist in three dimensions. In particular, for topological superconductors (or superfluids) with time-reversal symmetry, which lack SU(2) spin rotation symmetry (e.g., due to spin-orbit interactions), such as the B phase of 3He, the thermal response is the only probe that can detect the nontrivial topological character through transport. We show that, for such topological superconductors, applying a temperature gradient produces a thermal- (or mass-) surface current perpendicular to the thermal gradient. Such charge, thermal, or magnetic dipole responses provide a definition of topological insulators and superconductors beyond the single-particle picture. Moreover, we find, for a significant part of the "tenfold" list of topological insulators found in previous work in the absence of interactions, that in general dimensions, the effective field theory describing the space-time responses is governed by a field theory anomaly. Since anomalies are known to be insensitive to whether the underlying fermions are interacting, this shows that the classification of these topological insulators is robust to adiabatic deformations by interparticle interactions in general dimensionality. In particular, this applies to symmetry classes DIII, CI, and AIII in three spatial dimensions, and to symmetry classes D and C in two spatial dimensions. © 2012 American Physical Society.

Miniati F.,ETH Zurich | Martin D.F.,Lawrence Berkeley National Laboratory
Astrophysical Journal, Supplement Series | Year: 2011

We present the implementation of a three-dimensional, second-order accurate Godunov-type algorithm for magnetohydrodynamics (MHD) in the adaptive-mesh-refinement (AMR) cosmological code CHARM. The algorithm is based on the full 12-solve spatially unsplit corner-transport-upwind (CTU) scheme. The fluid quantities are cell-centered and are updated using the piecewise-parabolic method (PPM), while the magnetic field variables are face-centered and are evolved through application of the Stokes theorem on cell edges via a constrained-transport (CT) method. The so-called multidimensional MHD source terms required in the predictor step for high-order accuracy are applied in a simplified form which reduces their complexity in three dimensions without loss of accuracy or robustness. The algorithm is implemented on an AMR framework which requires specific synchronization steps across refinement levels. These include face-centered restriction and prolongation operations and a reflux-curl operation, which maintains a solenoidal magnetic field across refinement boundaries. The code is tested against a large suite of test problems, including convergence tests in smooth flows, shock-tube tests, classical two- and three-dimensional MHD tests, a three-dimensional shock-cloud interaction problem, and the formation of a cluster of galaxies in a fully cosmological context. The magnetic field divergence is shown to remain negligible throughout. © 2011. The American Astronomical Society. All rights reserved.

Xiang D.,SLAC | Wan W.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2010

A technique is proposed to generate ultrashort coherent soft x-ray radiation in storage rings using angular-modulated electron beams. In the scheme a laser operating in the TEM01 mode is first used to modulate the angular distribution of the electron beam in an undulator. After passing through a special beam line with nonzero transfer matrix element R54, the angular modulation is converted to density modulation which contains considerable high harmonic components of the laser. It is found that the harmonic number can be 1 or 2 orders of magnitude higher than the standard coherent harmonic generation method which relies on beam energy modulation. The technique has the potential of generating femtosecond coherent soft x-ray radiation directly from an infrared seed laser and may open new research opportunities for ultrafast sciences in storage rings. © 2010 The American Physical Society.

Horava P.,University of California at Berkeley | Horava P.,Lawrence Berkeley National Laboratory
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2010

We present a family of nonrelativistic Yang-Mills gauge theories in D+1 dimensions whose free-field limit exhibits quantum critical behavior with gapless excitations and dynamical critical exponent z=2. The ground state wavefunction is intimately related to the partition function of relativistic Yang-Mills in D dimensions. The gauge couplings exhibit logarithmic scaling and asymptotic freedom in the upper critical spacetime dimension, equal to 4+1. The theories can be deformed in the infrared by a relevant operator that restores Poincaré invariance as an accidental symmetry. In the large-N limit, our nonrelativistic gauge theories can be expected to have weakly curved gravity duals. © 2010 Elsevier B.V.

Lu Y.-M.,University of California at Berkeley | Lu Y.-M.,Lawrence Berkeley National Laboratory | Vishwanath A.,University of California at Berkeley
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

We study topological phases of interacting systems in two spatial dimensions in the absence of topological order (i.e., with a unique ground state on closed manifolds and no fractional excitations). These are the closest interacting analogs of integer quantum Hall states, topological insulators, and superconductors. We adapt the well-known Chern-Simons K-matrix description of quantum Hall states to classify such "integer" topological phases. Our main result is a general formalism that incorporates symmetries into the K-matrix description. Remarkably, this simple analysis yields the same list of topological phases as a recent group cohomology classification, and in addition provides field theories and explicit edge theories for all these phases. The bosonic topological phases, which only appear in the presence of interactions and which remain well defined in the presence of disorder, include (i) bosonic insulators with a Hall conductance quantized to even integers, (ii) a bosonic analog of quantum spin Hall insulators, and (iii) a bosonic analog of a chiral topological superconductor, whose K matrix is the Cartan matrix of Lie group E 8. We also discuss interacting fermion systems where symmetries are realized in a projective fashion, where we find the present formalism can handle a wider range of symmetries than a recent group super-cohomology classification. Lastly, we construct microscopic models of these phases from coupled one-dimensional systems. © 2012 American Physical Society.

Wang F.,Massachusetts Institute of Technology | Lee D.-H.,University of California at Berkeley | Lee D.-H.,Lawrence Berkeley National Laboratory
Physical Review B - Condensed Matter and Materials Physics | Year: 2012

In the past few years materials with protected gapless surface (edge) states have risen to the central stage of condensed matter physics. Almost all discussions centered around topological insulators and superconductors, which possess full quasiparticle gaps in the bulk. In this paper we argue that systems with topological stable bulk nodes offer another class of materials with robust gapless surface states. Moreover the location of the bulk nodes determines the Miller index of the surfaces that show (or do not show) such states. Measuring the spectroscopic signature of these zero modes allows a phase-sensitive determination of the nodal structures of unconventional superconductors when other phase-sensitive techniques are not applicable. We apply this idea to gapless iron-based superconductors and show how to distinguish accidental from symmetry-dictated nodes. We shall argue that the same idea leads to a method for detecting a class of the elusive spin liquids. © 2012 American Physical Society.

Kim A.G.,Lawrence Berkeley National Laboratory
Publications of the Astronomical Society of the Pacific | Year: 2011

I present an analysis for fitting cosmological parameters from a Hubble diagram of a standard candle with unknown intrinsic magnitude dispersion. The dispersion is determined from the data, simultaneously with the cosmological parameters. This contrasts with the strategies used to date. The advantages of the presented analysis are that it is done in a single fit (it is not iterative), it provides a statistically founded and unbiased estimate of the intrinsic dispersion, and its cosmological-parameter uncertainties account for the intrinsic-dispersion uncertainty. Applied to Type Ia supernovae, my strategy provides a statistical measure to test for subtypes and assess the significance of any magnitude corrections applied to the calibrated candle. Parameter bias and differences between likelihood distributions produced by the presented and currently used fitters are negligibly small for existing and projected supernova data sets. © 2011. The Astronomical Society of the Pacific.

Tokunaga T.K.,Lawrence Berkeley National Laboratory
Water Resources Research | Year: 2011

Adsorbed water films commonly coat mineral surfaces in unsaturated soils and rocks, reducing flow and transport rates. Therefore, it is important to understand how adsorbed film thickness depends on matric potential, surface chemistry, and solution chemistry. Here the problem of adsorbed water film thickness is examined by combining capillary scaling with the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. Novel aspects of this analysis include determining capillary influences on film thicknesses and incorporating solution chemistry-dependent electrostatic potential at air-water interfaces. Capillary analysis of monodisperse packings of spherical grains provided estimated ranges of matric potentials where adsorbed films are stable and showed that pendular rings within drained porous media retain most of the "residual" water except under very low matric potentials. Within drained pores, capillary contributions to thinning of adsorbed films on spherical grains are shown to be small, such that DLVO calculations for flat surfaces are suitable approximations. Hamaker constants of common soil minerals were obtained to determine ranges of the dispersion component to matric potential-dependent film thickness. The pressure component associated with electrical double-layer forces was estimated using the compression and linear superposition approximations. The pH-dependent electrical double-layer pressure component is the dominant contribution to film thicknesses at intermediate values of matric potential, especially in lower ionic strength solutions (<10 mol m -3) on surfaces with higher-magnitude electrostatic potentials (more negative than ≈-50 mV). Adsorbed water films are predicted to usually range in thickness from ≈1 to 20 nm in drained pores and fractures of unsaturated environments. Copyright 2011 by the American Geophysical Union.

Haxton T.K.,Lawrence Berkeley National Laboratory
Journal of Chemical Theory and Computation | Year: 2015

We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent three-dimensional orientation to each site, we preferentially integrate out stiff degrees of freedom (bond lengths and angles, as well as dihedral angles in rings) that are accurately approximated by their average values, while retaining soft degrees of freedom (unconstrained dihedral angles) mostly responsible for conformational variability. We demonstrate that our scheme retains nearly atomistic resolution by mapping all experimental protein configurations in the Protein Data Bank onto coarse-grained configurations and then analytically backmapping those configurations back to all-atom configurations. This roundtrip mapping throws away all information associated with the eliminated (stiff) degrees of freedom except for their average values, which we use to construct optimal backmapping functions. Despite the 4:1 reduction in the number of degrees of freedom, we find that heavy atoms move only 0.051 Å on average during the roundtrip mapping, while hydrogens move 0.179 Å on average, an unprecedented combination of efficiency and accuracy among coarse-grained protein models. We discuss the advantages of such a high-resolution model for parametrizing effective interactions and accurately calculating observables through direct or multiscale simulations. © 2015 American Chemical Society.

Park J.Y.,Korea Basic Science Institute | Park J.Y.,KAIST | Baker L.R.,Ohio State University | Somorjai G.A.,University of California at Berkeley | Somorjai G.A.,Lawrence Berkeley National Laboratory
Chemical Reviews | Year: 2015

Recent findings on fundamental mechanisms of energy dissipation and conversion occurring on the surface and at interfaces is reviewed. The various energy dissipation mechanisms and detection schemes for hot electrons were also studied. Hot electron flows generated with a catalytic nanodiode provide insights into the role of electron excitation leading to energy conversion processes. It was found that hot electron flux is well correlated with the turnover rates of catalytic reactions, which suggests possible applications for chemical sensors and novel energy conversion. Together, these findings demonstrate the prevalence of surface ion chemistry across a wide range of heterogeneous reactions and catalyst systems and show that charge transfer and ion chemistry represent one of the fundamental mechanisms of chemical activation on surfaces. In real catalyst systems, tandem reactions occur between the products of covalent and ionic activation pathways.

Williams P.T.,Lawrence Berkeley National Laboratory
PLoS ONE | Year: 2013

Objective: Test whether inadequate exercise is related to sepsis mortality. Research Design and Methods: Mortality surveillance of an epidemiological cohort of 155,484 National Walkers' and Runners' Health Study participants residing in the United States. Deaths were monitored for an average of 11.6-years using the National Death index through December 31, 2008. Cox proportional hazard analyses were used to compare sepsis mortality (ICD-10 A40-41) to inadequate exercise (<1.07 METh/d run or walked) as measured on their baseline questionnaires. Deaths occurring within one year of the baseline survey were excluded. Results: Sepsis was the underlying cause in 54 deaths (sepsisunderlying) and a contributing cause in 184 deaths (sepsiscontributing), or 238 total sepsis-related deaths (sepsis total). Inadequate exercise was associated with 2.24-fold increased risk for sepsis underlying (95%CI: 1.21 to 4.07-fold, P = 0.01), 2.11-fold increased risk for sepsiscontributing (95%CI: 1.51- to 2.92-fold, P<10 -4), and 2.13-fold increased risk for sepsistotal (95%CI: 1.59- to 2.84-fold, P<10-6) when adjusted for age, sex, race, and cohort. The risk increase did not differ significantly between runners and walkers, by sex, or by age. Sepsistotal risk was greater in diabetics (P = 10-5), cancer survivors (P = 0.0001), and heart attack survivors (P = 0.003) and increased with waist circumference (P = 0.0004). The sepsis total risk associated with inadequate exercise persisted when further adjusted for diabetes, prior cancer, prior heart attack and waist circumference, and when excluding deaths with cancer, or cardiovascular, respiratory, or genitourinary disease as the underlying cause. Inadequate exercise also increased sepsistotal risk in 2163 baseline diabetics (4.78-fold, 95%CI: 2.1- to 13.8-fold, P = 0.0001) when adjusted, which was significantly greater (P = 0.03) than the adjusted risk increase in non-diabetics (1.80-fold, 95%CI: 1.30- to 2.46-fold, P = 0.0006). Conclusion: Inadequate exercise is a risk factor for sepsis mortality, particular in diabetics.

Williams P.T.,Lawrence Berkeley National Laboratory
Medicine and Science in Sports and Exercise | Year: 2013

Purpose: This study aimed to test whether equivalent changes in moderate (walking) and vigorous exercise (running) produce equivalent weight loss under free-living, nonexperimental conditions. Methods: Regression analyses of changes (Δ) in body mass index (BMI) versus exercise energy expenditure (ΔMET-hours per day, 1 MET = 3.5 mL O2·kg -1·min-1) from survey questionnaires completed at baseline and 6.2 yr thereafter in 15,237 walkers and 32,216 runners were used in this study. Results: At baseline, walkers spent less energy walking than runners spent running (mean ± SD; males = 2.22 ± 1.65 vs 5.31 ± 3.12 MET·h·d-1, females = 2.15 ± 1.63 vs 4.76 ± 3.03 MET·h·d-1), and walkers were significantly heavier than runners (males = 26.63 ± 4.04 vs 24.09 ± 2.58 kg·m-2, females = 25.44 ± 5.14 vs 21.61 ± 2.49 kg·m-2). During follow-up, energy expenditure declined less for walking in walkers than for running in runners (males = -0.19 ± 1.92 vs -1.27 ± 2.87 MET·h·d-1, females = -0.30 ± 1.93 vs -1.28 ± 2.85 MET·h·d -1). ΔBMI was inversely related to both ΔMET-hours per day run and ΔMET-hours per day walked, but more strongly to ΔMET-hours per day run than walked in men and in heavier women. Specifically, the regression coefficient for ΔBMI versus ΔMET-hours per day was significantly more negative for running than walking in men in the first quartile (differences in slope ± SE: -0.06 ± 0.03, P = 0.01), second quartile (-0.10 ± 0.03, P = 0.001), third quartile (-0.17 ± 0.03, P < 10-8), and fourth quartile of BMI (-0.14 ± 0.03, P < 10-4) and in the fourth BMI quartile of women (-0.32 ± 0.04 kg·m-2 per MET-hours per day, P < 10-17). This represented 90% greater weight loss per MET-hours per day run than walked in the fourth BMI quartile for both sexes. Agerelated weight gain was attenuated by running in both sexes (P < 10-6) and by walking in women (P = 0.005). Conclusion: Although ΔBMI was significantly associated with both ΔMET-hours per day run and walked, the ΔBMI was significantly greater for Δrunning than Δwalking. Copyright © 2013 by the American College of Sports Medicine.

The Michaelis-Menten kinetics and the reverse Michaelis-Menten kinetics are two popular mathematical formulations used in many land biogeochemical models to describe how microbes and plants would respond to changes in substrate abundance. However, the criteria of when to use either of the two are often ambiguous. Here I show that these two kinetics are special approximations to the equilibrium chemistry approximation (ECA) kinetics, which is the first-order approximation to the quadratic kinetics that solves the equation of an enzyme-substrate complex exactly for a single-enzyme and single-substrate biogeochemical reaction with the law of mass action and the assumption of a quasi-steady state for the enzyme-substrate complex and that the product genesis from enzyme-substrate complex is much slower than the equilibration between enzyme-substrate complexes, substrates, and enzymes. In particular, I show that the derivation of the Michaelis-Menten kinetics does not consider the mass balance constraint of the substrate, and the reverse Michaelis-Menten kinetics does not consider the mass balance constraint of the enzyme, whereas both of these constraints are taken into account in deriving the equilibrium chemistry approximation kinetics. By benchmarking against predictions from the quadratic kinetics for a wide range of substrate and enzyme concentrations, the Michaelis-Menten kinetics was found to persistently underpredict the normalized sensitivity ∂ ln v / ∂ ln k2+ of the reaction velocity v with respect to the maximum product genesis rate k2+, persistently overpredict the normalized sensitivity ∂ ln v / ∂ ln k1+ of v with respect to the intrinsic substrate affinity k1+, persistently overpredict the normalized sensitivity ∂ ln v / ∂ ln [E]T of v with respect the total enzyme concentration [E]T, and persistently underpredict the normalized sensitivity ∂ ln v / ∂ ln [S]T of v with respect to the total substrate concentration [S]T. Meanwhile, the reverse Michaelis-Menten kinetics persistently underpredicts ∂ ln v / ∂ ln k2+ and ∂ ln v / ∂ ln [E]T, and persistently overpredicts ∂ ln v / ∂ ln k1+ and ∂ ln v / ∂ ln [S]T. In contrast, the equilibrium chemistry approximation kinetics always gives consistent predictions of ∂ ln v / ∂ ln k2+, ∂ ln v / ∂ ln k1+, ∂ ln v / ∂ ln [E]T, and ∂ ln v / ∂ ln [S]T, indicating that ECA-based models will be more calibratable if the modeled processes do obey the law of mass action. Since the equilibrium chemistry approximation kinetics includes advantages from both the Michaelis-Menten kinetics and the reverse Michaelis-Menten kinetics and it is applicable for almost the whole range of substrate and enzyme abundances, land biogeochemical modelers therefore no longer need to choose when to use the Michaelis-Menten kinetics or the reverse Michaelis-Menten kinetics. I expect that removing this choice ambiguity will make it easier to formulate more robust and consistent land biogeochemical models. © Author(s) 2015.

Berryman J.G.,Lawrence Berkeley National Laboratory
Transport in Porous Media | Year: 2012

An algorithm is presented for inverting either laboratory or field poroelastic data for all the drained constants of an anisotropic (specifically orthotropic) fractured poroelastic system. While fractures normally weaken the system by increasing the mechanical compliance, any liquids present in these fractures are expected to increase the stiffness somewhat, thus negating to some extent the mechanical weakening influence of the fractures themselves. The analysis presented in this article quantifies these effects and shows that the key physical variable needed to account for the pore-fluid effects is a factor of (1 - B), where B is Skempton's second coefficient and satisfies 0 ≤ B < 1. This scalar factor uniformly reduces the increase in compliance due to the presence of communicating fractures, thereby stiffening the fractured composite medium by a predictable amount. One further aim of the discussion is to determine the number of the poroelastic constants that needs to be known by other means to determine the rest from remote measurements, such as seismic wave propagation data in the field. Quantitative examples arising in the analysis show that, if the fracture aspect ratio a f≃0.1 and the pore fluid is liquid water, then for several cases considered, Skempton's B≃0.9, and so the stiffening effect of the pore-liquid reduces the change in compliance due to the fractures by a factor 1-B≃0.1, in these examples. The results do, however, depend on the actual moduli of the unfractured elastic material, as well as on the pore-liquid bulk modulus, so these quantitative predictions are just examples, and should not be treated as universal results. Attention is also given to two previously unremarked poroelastic identities, both being useful variants of Gassmann's equations for homogeneous-but anisotropic-poroelasticity. Relationships to Skempton's analysis of saturated soils are also noted. The article concludes with a discussion of alternative methods of analyzing and quantifying fluid-substitution behavior in poroelastic systems, especially for those systems having heterogeneous constitution. © 2011 Springer Science+Business Media B.V.

The separations of small molecules using columns containing porous polymer monoliths invented two decades ago went a long way from the very modest beginnings to the current capillary columns with efficiencies approaching those featured by their silica-based counterparts. This review article presents a variety of techniques that have been used to form capillary formats of monolithic columns with enhanced separation performance in isocratic elutions. The following text first describes the traditional approaches used for the preparation of efficient monoliths comprising variations in polymerization conditions including temperature as well as composition of monomers and porogenic solvents. Encouraging results of these experiments fueled research of completely new preparation methods such as polymerization to an incomplete conversion, use of single crosslinker, hypercrosslinking, and incorporation of carbon nanotubes that are described in the second part of the text. © 2011 Elsevier B.V.

Wangweerawong A.,Yale University | Bergman R.G.,Lawrence Berkeley National Laboratory | Ellman J.A.,Yale University
Journal of the American Chemical Society | Year: 2014

The first asymmetric intermolecular addition of non-acidic C-H bonds to imines is reported. The use of the activating N-perfluorobutanesulfinyl imine substituent is essential for achieving sufficient reactivity and provides outstanding diastereoselectivity (>98:2 dr). Straightforward removal of the sulfinyl group with HCl yields the highly enantiomerically enriched amine hydrochlorides. © 2014 American Chemical Society.

Vaughey J.T.,Argonne National Laboratory | Liu G.,Lawrence Berkeley National Laboratory | Zhang J.-G.,Pacific Northwest National Laboratory
MRS Bulletin | Year: 2014

The success of high capacity energy storage systems based on lithium (Li) batteries relies on the realization of the promise of Li-metal anodes. Li metal has many advantageous properties, including an extremely high theoretical specific capacity (3860 mAh g-1), the lowest electrochemical potential (-3.040 V versus standard hydrogen electrode), and low density (0.59 g cm-3), which, all together, make it a very desirable electrode for energy storage devices. However, while primary Li batteries are used for numerous commercial applications, rechargeable Li-metal batteries that utilize Li-metal anodes have not been as successful. This article discusses the properties of Li metal in the absence of surface stabilization, as well as three different approaches currently under investigation for stabilizing the surface of Li metal to control its reactivity within the electrochemical environment of a Li-based battery. © 2014 Materials Research Society.

Parkhill J.A.,Lawrence Berkeley National Laboratory | Head-Gordon M.,Chemical Science Division
Journal of Chemical Physics | Year: 2010

Paired, active-space treatments of static correlation are augmented with additional amplitudes to produce a hierarchy of parsimonious and efficient cluster truncations that approximate the total energy. The number of parameters introduced in these models grow with system size in a tractable way: two powers larger than the static correlation model it is built upon: for instance cubic for the models built on perfect pairing, fourth order for a perfect quadruples (PQ) reference, and fifth order for the models built on perfect hextuples. These methods are called singles+doubles (SD) corrections to perfect pairing, PQ, perfect hextuples, and two variants are explored. An implementation of the SD methods is compared to benchmark results for F2 and H2 O dissociation problems, the H4 and H8 model systems, and the insertion of beryllium into hydrogen. In the cases examined even the quartic number of parameters associated with PQSD is able to provide results which meaningfully improve on coupled-cluster singles doubles (CCSD) (which also has quartic amplitudes) and compete with existing multi-reference alternatives. © 2010 American Institute of Physics.

Whitelam S.,Lawrence Berkeley National Laboratory
Journal of Chemical Physics | Year: 2010

Advances in synthetic methods have spawned an array of nanoparticles and bio-inspired molecules of diverse shapes and interaction geometries. Recent experiments indicate that such anisotropic particles exhibit a variety of nonclassical self-assembly pathways, forming ordered assemblies via intermediates that do not share the architecture of the bulk material. Here we apply mean field theory to a prototypical model of interacting anisotropic particles, and find a clear thermodynamic impetus for nonclassical ordering in certain regimes of parameter space. In other parameter regimes, by contrast, assembly pathways are selected by dynamics. This approach suggests a means of predicting when anisotropic particles might assemble in a manner more complicated than that assumed by classical nucleation theory. © 2010 American Institute of Physics.

Parkhill J.A.,Lawrence Berkeley National Laboratory
Journal of Chemical Physics | Year: 2010

We present the next stage in a hierarchy of local approximations to complete active space self-consistent field (CASSCF) model in an active space of one active orbital per active electron based on the valence orbital-optimized coupled-cluster (VOO-CC) formalism. Following the perfect pairing (PP) model, which is exact for a single electron pair and extensive, and the perfect quadruples (PQ) model, which is exact for two pairs, we introduce the perfect hextuples (PH) model, which is exact for three pairs. PH is an approximation to the VOO-CC method truncated at hextuples containing all correlations between three electron pairs. While VOO-CCDTQ56 requires computational effort scaling with the 14th power of molecular size, PH requires only sixth power effort. Our implementation also introduces some techniques which reduce the scaling to fifth order and has been applied to active spaces roughly twice the size of the CASSCF limit without any symmetry. Because PH explicitly correlates up to six electrons at a time, it can faithfully model the static correlations of molecules with up to triple bonds in a size-consistent fashion and for organic reactions usually reproduces CASSCF with chemical accuracy. The convergence of the PP, PQ, and PH hierarchy is demonstrated on a variety of examples including symmetry breaking in benzene, the Cope rearrangement, the Bergman reaction, and the dissociation of fluorine. © 2010 American Institute of Physics.

Bluhm H.,Lawrence Berkeley National Laboratory
Journal of Electron Spectroscopy and Related Phenomena | Year: 2010

The interaction of water with surfaces plays a major role in many processes in the environment, atmosphere and technology. Weathering of rocks, adhesion between surfaces, and ionic conductance along surfaces are among many phenomena that are governed by the adsorption of molecularly thin water layers under ambient humidities. The properties of these thin water films, in particular their thickness, structure and hydrogen-bonding to the substrate as well as within the water film are up to now not very well understood. Ambient pressure photoelectron spectroscopy (APXPS) is a promising technique for the investigation of the properties of thin water films. In this article we will discuss the basics of APXPS as well as the particular challenges that are posed by investigations in water vapor at Torr pressures. We will also show examples of the application of APXPS to the study of water films on metals and oxides.

Seol Y.,U.S. National Energy Technology Laboratory | Kneafsey T.J.,Lawrence Berkeley National Laboratory
Journal of Geophysical Research: Solid Earth | Year: 2011

An experimental study was performed using X-ray computed tomography (CT) scanning to capture three-dimensional (3-D) methane hydrate distributions and potential discrete flow pathways in a sand pack sample. A numerical study was also performed to develop and analyze empirical relations that describe the impacts of hydrate accumulation habits within pore space (e.g., pore filling or grain cementing) on multiphase fluid migration. In the experimental study, water was injected into a hydrate-bearing sand sample that was monitored using an X-ray CT scanner. The CT images were converted into numerical grid elements, providing intrinsic sample data including porosity and phase saturations. The impacts of hydrate accumulation were examined by adapting empirical relations into the flow simulations as additional relations governing the evolution of absolute permeability of hydrate bearing sediment with hydrate deposition. The impacts of pore space hydrate accumulation habits on fluid migration were examined by comparing numerical predictions with experimentally measured water saturation distributions and breakthrough curves. A model case with 3-D heterogeneous initial conditions (hydrate saturation, porosity, and water saturation) and pore body-preferred hydrate accumulations best captured water migration behavior through the hydrate-bearing sample observed in the experiment. In the best matching model, absolute permeability in the hydrate bearing sample does not decrease significantly with increasing hydrate saturation until hydrate saturation reaches about 40%, after which it drops rapidly, and complete blockage of flow through the sample can occur as hydrate accumulations approach 70%. The result highlights the importance of permeability modification due to hydrate accumulation habits when predicting multiphase flow through high-saturation, reservoir quality hydrate-bearing sediments. Copyright 2011 by the American Geophysical Union.

Niewoehner O.,University of California at Berkeley | Jinek M.,University of California at Berkeley | Jinek M.,Howard Hughes Medical Institute | Doudna J.A.,University of California at Berkeley | And 2 more authors.
Nucleic Acids Research | Year: 2014

In many bacteria and archaea, small RNAs derived from clustered regularly interspaced short palindromic repeats (CRISPRs) associate with CRISPR-associated (Cas) proteins to target foreign DNA for destruction. In Type I and III CRISPR/Cas systems, the Cas6 family of endoribonucleases generates functional CRISPR-derived RNAs by site-specific cleavage of repeat sequences in precursor transcripts. CRISPR repeats differ widely in both sequence and structure, with varying propensity to form hairpin folds immediately preceding the cleavage site. To investigate the evolution of distinct mechanisms for the recognition of diverse CRISPR repeats by Cas6 enzymes, we determined crystal structures of two Thermus thermophilus Cas6 enzymes both alone and bound to substrate and product RNAs. These structures show how the scaffold common to all Cas6 endonucleases has evolved two binding sites with distinct modes of RNA recognition: one specific for a hairpin fold and the other for a single-stranded 5′-terminal segment preceding the hairpin. These findings explain how divergent Cas6 enzymes have emerged to mediate highly selective pre-CRISPR-derived RNA processing across diverse CRISPR systems. © 2013 The Author(s).

Liu H.-H.,Lawrence Berkeley National Laboratory
Vadose Zone Journal | Year: 2011

Optimality principles have been used to investigate physical processes in different areas. This work applied an optimal principle (that water flow resistance is minimized for the entire flow domain) to steady-state unsaturated flow processes. Based on the calculus of variations, under optimal conditions, hydraulic conductivity for steady-state, gravity-dominated unsaturated flow is proportional to a power function of the magnitude of water flux. This relationship is consistent with an intuitive expectation that for an optimal water flow system, locations where relatively large water fluxes occur should correspond to relatively small resistance (or large conductance). This theoretical result was also consistent with observed fingering-flow behavior in unsaturated soils and an existing model. © Soil Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA. All rights reserved.

Shamsuzzoha Basunia M.,Lawrence Berkeley National Laboratory
Nuclear Data Sheets | Year: 2014

Evaluated spectroscopic data for 210Au, 210Hg, 210Tl, 210Pb, 210Bi, 210Po, 210At, 210Rn, 210Fr, 210Ra, 210Ac, and 210Th and corresponding level schemes from radioactive decay and reaction studies are presented. This evaluation supersedes the previous evaluation by E. Browne (2003Br13). Highlights of this publication are the identification of new μs isomers of 210Hg by 2013Go10 and measurement of an excited level energy at 1709 keV 30 of 210Rn from 214Rn α decay: 68.6 μs by 2006Ku26 denoted as x+1664.6 in the Adopted Levels. Earlier experimental limits for x≤50 keV was proposed in 1979Po19 and 1982Po03 - (HI,xnγ). © 2014.

Budnitz R.J.,Lawrence Berkeley National Laboratory
Energy Policy | Year: 2016

This article reviews the current status and future prospects of commercial nuclear electric power, with emphasis on issues of safety, physical security, proliferation, and economics. Discussions of these issues are presented separately for the current operating fleet, for new reactor designs similar in size to the current fleet, and for prospective new reactors of substantially smaller size. This article also discusses the issue of expansion of commercial nuclear power into new countries. The article concludes with recommendations, related both to technical issues and policy considerations. The major implications for policy are that although the level of safety and security achieved in today's operating reactor fleet worldwide is considered broadly acceptable, some advanced designs now under development potentially offer demonstrably safer performance, and may offer improved financial performance also. Management and safety culture are vital attributes for achieving adequate safety and security, as are a strong political culture that includes an absence of corruption, an independent regulatory authority, and a separation of nuclear operation from day-to-day politics. In some countries that are now considering a nuclear-power program for the first time, careful attention to these attributes will be essential for success. © 2016 Elsevier Ltd.

Burke J.R.,University of California at Santa Cruz | Hura G.L.,Lawrence Berkeley National Laboratory | Rubin S.M.,University of California at Santa Cruz
Genes and Development | Year: 2012

Cyclin-dependent kinase (Cdk) phosphorylation of the Retinoblastoma protein (Rb) drives cell proliferation through inhibition of Rb complexes with E2F transcription factors and other regulatory proteins. We present the first structures of phosphorylated Rb that reveal the mechanism of its inactivation. S608 phosphorylation orders a flexible "'pocket" domain loop such that it mimics and directly blocks E2F transactivation domain (E2FTD) binding. T373 phosphorylation induces a global conformational change that associates the pocket and N-terminal domains (RbN). This first multidomain Rb structure demonstrates a novel role for RbN in allosterically inhibiting the E2FTD-pocket association and protein binding to the pocket "LxCxE" site. Together, these structures detail the regulatory mechanism for a canonical growth-repressive complex and provide a novel example of how multisite Cdk phosphorylation induces diverse structural changes to influence cell cycle signaling. © 2012 by Cold Spring Harbor Laboratory Press.

Rajagopalan S.,Methodist Hospital Research Institute | Teter S.J.,University of Wisconsin - Madison | Zwart P.H.,Lawrence Berkeley National Laboratory | Brennan R.G.,Duke University | And 3 more authors.
Nature Structural and Molecular Biology | Year: 2013

IscR from Escherichia coli is an unusual metalloregulator in that both apo and iron sulfur (Fe-S)-IscR regulate transcription and exhibit different DNA binding specificities. Here, we report structural and biochemical studies of IscR suggesting that remodeling of the protein-DNA interface upon Fe-S ligation broadens the DNA binding specificity of IscR from binding the type 2 motif only to both type 1 and type 2 motifs. Analysis of an apo-IscR variant with relaxed target-site discrimination identified a key residue in wild-type apo-IscR that, we propose, makes unfavorable interactions with a type 1 motif. Upon Fe-S binding, these interactions are apparently removed, thereby allowing holo-IscR to bind both type 1 and type 2 motifs. These data suggest a unique mechanism of ligand-mediated DNA site recognition, whereby metallocluster ligation relocates a protein-specificity determinant to expand DNA target-site selection, allowing a broader transcriptomic response by holo-IscR. © 2013 Nature America, Inc. All rights reserved.

Fadley C.S.,University of California at Davis | Fadley C.S.,Lawrence Berkeley National Laboratory
Journal of Electron Spectroscopy and Related Phenomena | Year: 2010

In this overview, I will briefly explore some of the basic concepts and observable effects in X-ray photoelectron spectroscopy, including references to some key first publications, as well as other papers in this issue that explore many of them in more detail. I will then turn to some examples of several present and promising future applications of this diverse technique. Some of the future areas explored will be the use chemical shifts, multiplet splittings, and hard X-ray excitation in the study of strongly correlated materials; photoelectron diffraction and holography for atomic structure determinations; standing wave and hard X-ray excited photoemission for probing buried interfaces and more bulk-like properties of complex materials; valence-band mapping with soft and hard X-ray excitation; and time-resolved measurements with the sample at high ambient pressures in the multi-torr regime. © 2010 Elsevier B.V. All rights reserved.

Anders A.,Lawrence Berkeley National Laboratory
Surface and Coatings Technology | Year: 2010

High power impulse magnetron sputtering (HIPIMS) and related self-sputtering techniques are reviewed from a viewpoint of plasma-based ion implantation and deposition (PBII&D). HIPIMS combines the classical, scalable sputtering technology with pulsed power, which is an elegant way of ionizing the sputtered atoms. Related approaches, such as sustained self-sputtering, are also considered. The resulting intense flux of ions to the substrate consists of a mixture of metal and gas ions when using a process gas, or of metal ions only when using 'gasless' or pure self-sputtering. In many respects, processing with HIPIMS plasmas is similar to processing with filtered cathodic arc plasmas, though the former is easier to scale to large areas. Both ion implantation and etching (high bias voltage and without deposition) and thin film deposition (low bias, or bias of low duty cycle) have been demonstrated. © 2010 Elsevier B.V.

Bizarri G.,Lawrence Berkeley National Laboratory
Journal of Crystal Growth | Year: 2010

Finding new inorganic scintillator crystals with better performance for demanding applications, such as high-energy physics, medical imaging, and radiation detection, has been a long-standing challenge. Thanks to an intensive interdisciplinary effort between theoreticians, experimentalists and crystal growers, current scintillator performances are reaching the intrinsic limits imposed by the crystal. However, demand continues for more efficient scintillators with higher light output, better energy resolution and lower cost of production. This article discusses the basic concepts of scintillation in inorganic materials, focusing on how physics can provide pathways to assist in scintillator discovery.

Berryman J.G.,Lawrence Berkeley National Laboratory
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2011

Methods for computing Hashin-Shtrikman bounds and related self-consistent estimates of elastic constants for polycrystals composed of crystals having orthorhombic symmetry have been known for about three decades. However, these methods are underutilized, perhaps because of some perceived difficulties with implementing the necessary computational procedures. Several simplifications of these techniques are introduced, thereby reducing the overall computational burden, as well as the complications inherent in mapping out the Hashin-Shtrikman bounding curves. The self-consistent estimates of the effective elastic constants are very robust, involving a quickly converging iteration procedure. Once these self-consistent values are known, they may then be used to speed up the computations of the Hashin-Shtrikman bounds themselves. It is shown furthermore that the resulting orthorhombic polycrystal code can be used as well to compute both bounds and self-consistent estimates for polycrystals of higher-symmetry tetragonal, hexagonal, and cubic (but not trigonal) materials. The self-consistent results found this way are shown to be the same as those obtained using the earlier methods, specifically those methods designed specially for each individual symmetry type. But the Hashin-Shtrikman bounds found using the orthorhombic code are either the same or (more typically) tighter than those found previously for these special cases (i.e., tetragonal, hexagonal, and cubic). The improvement in the Hashin-Shtrikman bounds is presumably due to the additional degrees of freedom introduced into the available search space. © 2011 American Physical Society.

Zhu Z.-J.,Scripps Research Institute | Schultz A.W.,Scripps Research Institute | Wang J.,Scripps Research Institute | Johnson C.H.,Scripps Research Institute | And 3 more authors.
Nature Protocols | Year: 2013

Untargeted metabolomics provides a comprehensive platform for identifying metabolites whose levels are altered between two or more populations. By using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS), hundreds to thousands of peaks with a unique m/z ratio and retention time are routinely detected from most biological samples in an untargeted profiling experiment. Each peak, termed a metabolomic feature, can be characterized on the basis of its accurate mass, retention time and tandem mass spectral fragmentation pattern. Here a seven-step protocol is suggested for such a characterization by using the METLIN metabolite database. The protocol starts from untargeted metabolomic LC-Q-TOF-MS data that have been analyzed with the bioinformatics program XCMS, and it describes a strategy for selecting interesting features as well as performing subsequent targeted tandem MS. The seven steps described will require 2-4 h to complete per feature, depending on the compound. © 2013 Nature America, Inc. All rights reserved.

Matyskiela M.E.,University of California at Berkeley | Lander G.C.,Lawrence Berkeley National Laboratory | Lander G.C.,Scripps Research Institute | Martin A.,University of California at Berkeley
Nature Structural and Molecular Biology | Year: 2013

The 26S proteasome is the major eukaryotic ATP-dependent protease, responsible for regulating the proteome through degradation of ubiquitin-tagged substrates. Its regulatory particle, containing the heterohexameric AAA+ ATPase motor and the essential deubiquitinase Rpn11, recognizes substrates, removes their ubiquitin chains and translocates them into the associated peptidase after unfolding, but detailed mechanisms remain unknown. Here we present the 26S proteasome structure from Saccharomyces cerevisiae during substrate degradation, showing that the regulatory particle switches from a preengaged to a translocation-competent conformation. This conformation is characterized by a rearranged ATPase ring with uniform subunit interfaces, a widened central channel coaxially aligned with the peptidase and a spiral orientation of pore loops that suggests a rapid progression of ATP-hydrolysis events around the ring. Notably, Rpn11 moves from an occluded position to directly above the central pore, thus facilitating substrate deubiquitination concomitant with translocation.

Korneev V.A.,Lawrence Berkeley National Laboratory
Geophysics | Year: 2011

The Krauklis wave is a slow dispersive wave mode that propagates in a fluid layer bounded by elastic media. In a model of alternating fluid and elastic layers, two interface waves can exist at low frequencies: The first wave propagates mostly in the elastic layer and has little dispersion, while the second wave can have strong dispersion and propagates as a Krauklis wave for some parameter combinations. Analytical conditions predict appearance of the Krauklis wave for higher frequencies and low porosities. Interface-wave velocities depend on model porosity, which potentially can be used for fracture mapping. © 2011 Society of Exploration Geophysicists.

DePaolo D.J.,Lawrence Berkeley National Laboratory
Geochimica et Cosmochimica Acta | Year: 2011

A surface reaction kinetic model is developed for predicting Ca isotope fractionation and metal/Ca ratios of calcite as a function of rate of precipitation from aqueous solution. The model is based on the requirements for dynamic equilibrium; i.e. proximity to equilibrium conditions is determined by the ratio of the net precipitation rate (Rp) to the gross forward precipitation rate (Rf), for conditions where ionic transport to the growing crystal surface is not rate-limiting. The value of Rp has been experimentally measured under varying conditions, but the magnitude of Rf is not generally known, and may depend on several factors. It is posited that, for systems with no trace constituents that alter the surface chemistry, Rf can be estimated from the bulk far-from-equilibrium dissolution rate of calcite (Rb or kb), since at equilibrium Rf=Rb, and Rp=0. Hence it can be inferred that Rf≈Rp+Rb. The dissolution rate of pure calcite is measureable and is known to be a function of temperature and pH. At given temperature and pH, equilibrium precipitation is approached when Rp (=Rf-Rb)≪Rb. For precipitation rates high enough that Rp≫Rb, both isotopic and trace element partitioning are controlled by the kinetics of ion attachment to the mineral surface, which tend to favor more rapid incorporation of the light isotopes of Ca and discriminate weakly between trace metals and Ca. With varying precipitation rate, a transition region between equilibrium and kinetic control occurs near Rp≈Rb for Ca isotopic fractionation. According to this model, Ca isotopic data can be used to estimate Rf for calcite precipitation. Mechanistic models for calcite precipitation indicate that the molecular exchange rate is not constant at constant T and pH, but rather is dependent also on solution saturation state and hence Rp. Allowing Rb to vary as Rp1/2, consistent with available precipitation rate studies, produces a better fit to some trace element and isotopic data than a model where Rb is constant. This model can account for most of the experimental data in the literature on the dependence of 44Ca/40Ca and metal/Ca fractionation in calcite as a function of precipitation rate and temperature, and also accounts for 18O/16O variations with some assumptions. The apparent temperature dependence of Ca isotope fractionation in calcite may stem from the dependence of Rb on temperature; there should be analogous pH dependence at pH<6. The proposed model may be valuable for predicting the behavior of isotopic and trace element fractionation for a range of elements of interest in low-temperature aqueous geochemistry. The theory presented is based on measureable thermo-kinetic parameters in contrast to models that require hyper-fast diffusivity in near-surface layers of the solid. © 2010 Elsevier Ltd.

Brown D.N.,Lawrence Berkeley National Laboratory
AIP Conference Proceedings | Year: 2012

We describe a proposed experiment to search for Charged Lepton Flavor Violation (CLFV) using stopped muons at Fermilab. A primary Proton beam will strike a gold target, producing pions which decay to muons. Low-momentum negative muons will be collected, selected, and transported by a custom arrangement of solenoidal magnets and collimators. Muons will stop in thin foil targets, creating muonic atoms with significant nuclear overlap. Mu2e will search for the coherent conversion of nuclear bound muons to electrons, with an experimental signature of a single mono-energetic electron. Conversion electrons will be detected and measured in a low-mass straw tracker and a crystal calorimeter. Mu2e will have a sensitivity four orders of magnitude better than the most sensitive published result for μ → e conversion, and will have complementary physics reach to LHC experiments and μ → eγ decay experiments such as MEG. © 2012 American Institute of Physics.

Mueller A.H.,Columbia University | Xiao B.-W.,Central China Normal University | Xiao B.-W.,Pennsylvania State University | Yuan F.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2013

Through an explicit calculation of massive scalar particle (e.g., Higgs boson) production in high energy pA collisions up to one-loop order, we demonstrate, for the first time, that the Sudakov-type logarithms in hard processes in the small-x saturation formalism can be systematically separated from the small-x logarithms. The generic feature of the Sudakov logarithms and all order resummation is derived. This calculation shall provide us deep insights into the understanding of factorizations in the saturation formalism. We further comment on the phenomenological implications in the LHC energy regime and extension to other hard processes in small-x calculations. © 2013 American Physical Society.

Huang Z.,SLAC | Ding Y.,SLAC | Schroeder C.B.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2012

Compact laser-plasma accelerators can produce high energy electron beams with low emittance, high peak current but a rather large energy spread. The large energy spread hinders the potential applications for coherent free-electron laser (FEL) radiation generation. We discuss a method to compensate the effects of beam energy spread by introducing a transverse field variation into the FEL undulator. Such a transverse gradient undulator together with a properly dispersed beam can greatly reduce the effects of electron energy spread and jitter on FEL performance. We present theoretical analysis and numerical simulations for self-amplified spontaneous emission and seeded extreme ultraviolet and soft x-ray FELs based on laser plasma accelerators. © 2012 American Physical Society.

Koven C.D.,Lawrence Berkeley National Laboratory
Nature Geoscience | Year: 2013

Climate change can be thought of in terms of geographical shifts in climate properties. Examples include assessments of shifts in habitat distributions, of the movement needed to maintain constant temperature or precipitation, and of the emergence and disappearance of climate zones. Here I track the movement of analogue climates within climate models. From the model simulations, I define a set of vectors that link a historical reference climate for each location to the location in a changed climate whose seasonal temperature and precipitation cycles best match the reference climate. I use these vectors to calculate the change in vegetation carbon storage with climate change due to ecosystems following climate analogues. Comparing the derived carbon content change to direct carbon projections by coupled carbon-climate models reveals two regions of divergence. In the tropical forests, vector projections are fundamentally uncertain because of a lack of close climatic analogues. In the southern boreal forest, carbon losses are projected in the vector perspective because low-carbon ecosystems shift polewards. However, the majority of carbon-climate models - typically without explicit simulation of the disturbance and mortality processes behind such shifts - instead project vegetation carbon gains throughout the boreal region. Southern boreal carbon loss as a result of ecosystem shift is likely to offset carbon gains from northern boreal forest expansion. © 2013 Macmillan Publishers Limited. All rights reserved.

Atkins E.,University of California at Berkeley | Morzfeld M.,Lawrence Berkeley National Laboratory | Chorin A.J.,University of California at Berkeley
Monthly Weather Review | Year: 2013

The implicit particle filter is a sequential Monte Carlo method for data assimilation that guides the particles to the high-probability regions via a sequence of steps that includes minimizations. A new and more general derivation of this approach is presented and the method is extended to particle smoothing as well as to data assimilation for perfect models. Minimizations required by implicit particle methods are shown to be similar to those that one encounters in variational data assimilation, and the connection of implicit particle methods with variational data assimilation is explored. In particular, it is argued that existing variational codes can be converted into implicit particle methods at a low additional cost, often yielding better estimates that are also equipped with quantitative measures of the uncertainty. A detailed example is presented. © 2013 American Meteorological Societ.

Lee H.Y.,University of California at Berkeley | Doudna J.A.,University of California at Berkeley | Doudna J.A.,Howard Hughes Medical Institute | Doudna J.A.,Lawrence Berkeley National Laboratory
RNA | Year: 2012

MicroRNAs play central roles in controlling gene expression in human cells. Sequencing data show that many miRNAs are produced at different levels and as multiple isoforms that can vary in length at their 5′ or 3′ ends, but the biogenesis and functional significance of these RNAs are largely unknown. We show here that the human trans-activation response (TAR) RNA binding protein (TRBP), a known molecular partner of the miRNA processing enzyme Dicer, changes the rates of pre-miRNA cleavage in an RNA-structure-specific manner. Furthermore, TRBP can trigger the generation of iso-miRNAs (isomiRs) that are longer than the canonical sequence by one nucleotide. We show that this change in miRNA processing site can alter guide strand selection, resulting in preferential silencing of a different mRNA target. These results implicate TRBP as a key regulator of miRNA processing and targeting in humans. Copyright © 2012 RNA Society.

Yang W.,University of California at San Diego | Chen I.H.,University of California at San Diego | Gludovatz B.,University of California at Berkeley | Zimmermann E.A.,University of California at Berkeley | And 3 more authors.
Advanced Materials | Year: 2013

Fish, reptiles, and mammals can possess flexible dermal armor for protection. Here we seek to find the means by which Nature derives its protection by examining the scales from several fish (Atractosteus spatula, Arapaima gigas, Polypterus senegalus, Morone saxatilis, Cyprinius carpio), and osteoderms from armadillos, alligators, and leatherback turtles. Dermal armor has clearly been developed by convergent evolution in these different species. In general, it has a hierarchical structure with collagen fibers joining more rigid units (scales or osteoderms), thereby increasing flexibility without significantly sacrificing strength, in contrast to rigid monolithic mineral composites. These dermal structures are also multifunctional, with hydrodynamic drag (in fish), coloration for camouflage or intraspecies recognition, temperature and fluid regulation being other important functions. The understanding of such flexible dermal armor is important as it may provide a basis for new synthetic, yet bioinspired, armor materials. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Furukawa H.,University of California at Berkeley | Gandara F.,University of California at Berkeley | Zhang Y.-B.,University of California at Berkeley | Jiang J.,University of California at Berkeley | And 3 more authors.
Journal of the American Chemical Society | Year: 2014

Water adsorption in porous materials is important for many applications such as dehumidification, thermal batteries, and delivery of drinking water in remote areas. In this study, we have identified three criteria for achieving high performing porous materials for water adsorption. These criteria deal with condensation pressure of water in the pores, uptake capacity, and recyclability and water stability of the material. In search of an excellently performing porous material, we have studied and compared the water adsorption properties of 23 materials, 20 of which are metal-organic frameworks (MOFs). Among the MOFs are 10 zirconium(IV) MOFs with a subset of these, MOF-801-SC (single crystal form), -802, -805, -806, -808, -812, and -841 reported for the first time. MOF-801-P (microcrystalline powder form) was reported earlier and studied here for its water adsorption properties. MOF-812 was only made and structurally characterized but not examined for water adsorption because it is a byproduct of MOF-841 synthesis. All the new zirconium MOFs are made from the Zr 6O4(OH)4(-CO2)n secondary building units (n = 6, 8, 10, or 12) and variously shaped carboxyl organic linkers to make extended porous frameworks. The permanent porosity of all 23 materials was confirmed and their water adsorption measured to reveal that MOF-801-P and MOF-841 are the highest performers based on the three criteria stated above; they are water stable, do not lose capacity after five adsorption/desorption cycles, and are easily regenerated at room temperature. An X-ray single-crystal study and a powder neutron diffraction study reveal the position of the water adsorption sites in MOF-801 and highlight the importance of the intermolecular interaction between adsorbed water molecules within the pores. © 2014 American Chemical Society.

Whitelam S.,Lawrence Berkeley National Laboratory | Jack R.L.,University of Bath
Annual Review of Physical Chemistry | Year: 2015

This review describes some important physical characteristics of the pathways (i.e., dynamical processes) by which molecular, nanoscale, and micrometer-scale self-assembly occurs. We highlight the existence of features of self-assembly pathways that are common to a wide range of physical systems, even though those systems may differ with respect to their microscopic details. We summarize some existing theoretical descriptions of self-assembly pathways and highlight areas-notably, the description of self-assembly pathways that occur far from equilibrium-that are likely to become increasingly important. © 2015 by Annual Reviews. All rights reserved.

Tokunaga T.K.,Lawrence Berkeley National Laboratory
Langmuir | Year: 2012

When supercritical carbon dioxide (scCO 2) is injected into deep subsurface reservoirs, much of the affected volume consists of pores containing both water and scCO 2, with water films remaining as the mineral-wetting phase. Although water films can affect multiphase flow and mediate reactions at mineral surfaces, little is known about how film thicknesses depend on system properties. Here, the thicknesses of water films were estimated on the basis of considerations of capillary pressure needed for the entry of CO 2 and disjoining pressures in films resulting from van der Waals and electric double-layer interactions. Depth-dependent CO 2 and water properties were used to estimate Hamaker constants for water films on silica and smectite surfaces under CO 2 confinement. Dispersion interactions were combined with approximate solutions to the electric double layer film thickness-pressure relationship in a Derjaguin-Landau-Verwey- Overbeek (DLVO) analysis, with CO 2 as the confining fluid. Under conditions of elevated pressure, temperature, and salinity commonly associated with CO 2 sequestration, adsorbed water films in reservoir rock surfaces are typically predicted to be less than 10 nm in thickness. Decreased surface charge of silica under the acidic pH of CO 2-equilibrated water and elevated salinity is predicted to compress the electric double layer substantially, such that the dispersion contribution to the film thickness is dominant. Relative to silica, smectite surfaces are predicted to support thicker water films under CO 2 confinement because of greater electrostatic and dispersion stabilization. © 2012 American Chemical Society.

Cabana J.,Lawrence Berkeley National Laboratory | Cabana J.,Alistore European Research Institute | Monconduit L.,Charles Gerhardt Institute | Monconduit L.,Alistore European Research Institute | And 3 more authors.
Advanced Materials | Year: 2010

Despite the imminent commercial introduction of Li-ion batteries in electric drive vehicles and their proposed use as enablers of smart grids based on renewable energy technologies, an intensive quest for new electrode materials that bring about improvements in energy density, cycle life, cost, and safety is still underway. This Progress Report highlights the recent developments and the future prospects of the use of phases that react through conversion reactions as both positive and negative electrode materials in Li-ion batteries. By moving beyond classical intercalation reactions, a variety of low cost compounds with gravimetric specific capacities that are two-to-five times larger than those attained with currently used materials, such as graphite and LiCoO2, can be achieved. Nonetheless, several factors currently handicap the applicability of electrode materials entailing conversion reactions. These factors, together with the scientific breakthroughs that are necessary to fully assess the practicality of this concept, are reviewed in this report. © 2010 WILEY-VCH Verlag GmbH & Co. KGaA.

Scholes G.D.,University of Toronto | Fleming G.R.,University of California at Berkeley | Fleming G.R.,Lawrence Berkeley National Laboratory | Olaya-Castro A.,University College London | Van Grondelle R.,VU University Amsterdam
Nature Chemistry | Year: 2011

Solar fuel production often starts with the energy from light being absorbed by an assembly of molecules; this electronic excitation is subsequently transferred to a suitable acceptor. For example, in photosynthesis, antenna complexes capture sunlight and direct the energy to reaction centres that then carry out the associated chemistry. In this Review, we describe the principles learned from studies of various natural antenna complexes and suggest how to elucidate strategies for designing light-harvesting systems. We envisage that such systems will be used for solar fuel production, to direct and regulate excitation energy flow using molecular organizations that facilitate feedback and control, or to transfer excitons over long distances. Also described are the notable properties of light-harvesting chromophores, spatial-energetic landscapes, the roles of excitonic states and quantum coherence, as well as how antennas are regulated and photoprotected. © 2011 Macmillan Publishers Ltd.

Whitelam S.,Lawrence Berkeley National Laboratory
Advanced Materials | Year: 2015

The self-assembly of molecules at surfaces can be caused by a range of physical mechanisms. Assembly can be driven by intermolecular forces, or molecule-surface forces, or both; it can result in structures that are in equilibrium or that are kinetically trapped. Here we review examples of self-assembly at surfaces focusing on a physical understanding of what causes patterns seen in experiment. Some apparently disparate systems can be described in similar physical terms, indicating that simple factors - such as the geometry and energy scale of intermolecular binding - are key to understanding the self-assembly of those systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Yang J.-M.,University of California at Berkeley | Yang H.,Lawrence Berkeley National Laboratory | Yang H.,Princeton University | Lin L.,University of California at Berkeley
ACS Nano | Year: 2011

The local temperature response inside single living cells upon external chemical and physical stimuli was characterized using quantum dots as nano thermometers. The photoluminescence spectral shifts from endocytosed quantum dots were used to map intracellular heat generation in NIH/3T3 cells following Ca2+ stress and cold shock. The direct observation of inhomogeneous intracellular temperature progression raises interesting new possibilities, including further innovations in nanomaterials for sensing local responses, as well as the concept of subcellular temperature gradient for signaling and regulation in cells. © 2011 American Chemical Society.

Oldenburg C.M.,Lawrence Berkeley National Laboratory | Rinaldi A.P.,Italian National Institute of Geophysics and Volcanology
Transport in Porous Media | Year: 2011

Upward displacement of brine from deep reservoirs driven by pressure increases resulting from CO2 injection for geologic carbon sequestration may occur through improperly sealed abandoned wells, through permeable faults, or through permeable channels between pinch-outs of shale formations. The concern about upward brine flow is that, upon intrusion into aquifers containing groundwater resources, the brine may degrade groundwater. Because both salinity and temperature increase with depth in sedimentary basins, upward displacement of brine involves lifting fluid that is saline but also warm into shallower regions that contain fresher, cooler water. We have carried out dynamic simulations using TOUGH2/EOS7 of upward displacement of warm, salty water into cooler, fresher aquifers in a highly idealized two-dimensional model consisting of a vertical conduit (representing a well or permeable fault) connecting a deep and a shallow reservoir. Our simulations show that for small pressure increases and/or high-salinity-gradient cases, brine is pushed up the conduit to a new static steady-state equilibrium. On the other hand, if the pressure rise is large enough that brine is pushed up the conduit and into the overlying upper aquifer, flow may be sustained if the dense brine is allowed to spread laterally. In this scenario, dense brine only contacts the lower-most region of the upper aquifer. In a hypothetical case in which strong cooling of the dense brine occurs in the upper reservoir, the brine becomes sufficiently dense that it flows back down into the deeper reservoir from where it came. The brine then heats again in the lower aquifer and moves back up the conduit to repeat the cycle. Parameter studies delineate steady-state (static) and oscillatory solutions and reveal the character and period of oscillatory solutions. Such oscillatory solutions are mostly a curiosity rather than an expected natural phenomenon because in nature the geothermal gradient prevents the cooling in the upper aquifer that occurs in the model. The expected effect of upward brine displacement is either establishment of a new hydrostatic equilibrium or sustained upward flux into the bottom-most region of the upper aquifer. © 2010 Springer Science+Business Media B.V. (outside the USA).

Jiang F.,University of California at Berkeley | Zhou K.,Howard Hughes Medical Institute | Ma L.,Howard Hughes Medical Institute | Gressel S.,Max Planck Institute for Biophysical Chemistry | And 3 more authors.
Science | Year: 2015

Bacterial adaptive immunity uses CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) proteins together with CRISPR transcripts for foreign DNA degradation. In type II CRISPR-Cas systems, activation of Cas9 endonuclease for DNA recognition upon guide RNA binding occurs by an unknown mechanism. Crystal structures of Cas9 bound to single-guide RNA reveal a conformation distinct from both the apo and DNA-bound states, in which the 10-nucleotide RNA "seed" sequence required for initial DNA interrogation is preordered in an A-form conformation. This segment of the guide RNA is essential for Cas9 to form a DNA recognition-competent structure that is poised to engage double-stranded DNA target sequences. We construe this as convergent evolution of a "seed" mechanism reminiscent of that used by Argonaute proteins during RNA interference in eukaryotes. © 2015, American Association for the Advancement of Science. All rights reserved.

Li M.,Shantou University | Li D.,Shantou University | O'Keeffe M.,Arizona State University | O'Keeffe M.,KAIST | And 2 more authors.
Chemical Reviews | Year: 2014

A consistent approach to the description on the structures of metal-organic frameworks (MOFs) and related materials are studied in terms of their underlying nets for cases in which these nets have more than two kinds of vertices. For MOFs formed from polytopic linkers, identifying both the basic net in which the linker is considered as a single node and the derived net in which branch points are identified explicitly, is recommended. The intrinsic symmetry of the crystal is that of the derived net, which may be lower than that of the basic net. The net gwg, derived from cds, is an example in which a tetragonal basic net has only a monoclinic derived net of minimal transitivity. Structures with different derived nets that may have the same symmetry can be differentiated. The basic nets with transitivity 3 2 (type iv of section 7) are particularly important in this regard. Several MOFs have been constructed using an octatopic linker with symmetrical shapes.

Ghadiali J.E.,Imperial College London | Cohen B.E.,Lawrence Berkeley National Laboratory | Stevens M.M.,Imperial College London
ACS Nano | Year: 2010

Bioconjugates of quantum dot nanocrystals possess unique optical properties that allow them to serve as exceptional biological imaging and sensing reagents. Protein kinases are an important family of enzymes that phosphorylate serine, threonine, or tyrosine side chains and are critical in cell signaling and cancer biology, but despite their biomedical and pharmaceutical significance, their activity has been little explored using quantum dot technology. We demonstrate that self-assembled peptide - quantum dot conjugates can serve as surrogate substrates in a simple homogeneous assay for protein kinase activity. Enzymatic phosphorylation of the peptide-conjugates is detected by means of a complementary FRET-acceptor labeled antiphosphotyrosine antibody, with formation of the immunocomplex resulting in energy transfer between the quantum dot and FRET acceptor molecules. This approach should facilitate the development of new assays for protein kinases and other enzymes based on quantum dot FRET donors. © 2010 American Chemical Society.

McMurray C.T.,Lawrence Berkeley National Laboratory | McMurray C.T.,Molecular Therapeutics | McMurray C.T.,Mayo Medical School
Nature Reviews Genetics | Year: 2010

Trinucleotide expansion underlies several human diseases. Expansion occurs during multiple stages of human development in different cell types, and is sensitive to the gender of the parent who transmits the repeats. Repair and replication models for expansions have been described, but we do not know whether the pathway involved is the same under all conditions and for all repeat tract lengths, which differ among diseases. Currently, researchers rely on bacteria, yeast and mice to study expansion, but these models differ substantially from humans. We need now to connect the dots among human genetics, pathway biochemistry and the appropriate model systems to understand the mechanism of expansion as it occurs in human disease. © 2010 Macmillan Publishers Limited. All rights reserved.

Kim S.-K.,Seoul National University | Kim S.-K.,Lawrence Berkeley National Laboratory
Journal of Physics D: Applied Physics | Year: 2010

Current needs for further advances in the nanotechnologies of information-storage and-processing devices have attracted a great deal of interest in spin (magnetization) dynamics in nanometre-scale patterned magnetic elements. For instance, the unique dynamic characteristics of non-uniform magnetic microstructures such as various types of domain walls, magnetic vortices and antivortices, as well as spin wave dynamics in laterally restricted thin-film geometries, have been at the centre of extensive and intensive researches. Understanding the fundamentals of their unique spin structure as well as their robust and novel dynamic properties allows us to implement new functionalities into existing or future devices. Although experimental tools and theoretical approaches are effective means of understanding the fundamentals of spin dynamics and of gaining new insights into them, the limitations of those same tools and approaches have left gaps of unresolved questions in the pertinent physics. As an alternative, however, micromagnetic modelling and numerical simulation has recently emerged as a powerful tool for the study of a variety of phenomena related to spin dynamics of nanometre-scale magnetic elements. In this review paper, I summarize the recent results of simulations of the excitation and propagation and other novel wave characteristics of spin waves, highlighting how the micromagnetic computer simulation approach contributes to an understanding of spin dynamics of nanomagnetism and considering some of the merits of numerical simulation studies. Many examples of micromagnetic modelling for numerical calculations, employing various dimensions and shapes of patterned magnetic elements, are given. The current limitations of continuum micromagnetic modelling and of simulations based on the Landau-Lifshitz-Gilbert equation of motion of magnetization are also discussed, along with further research directions for spin-wave studies. © 2010 IOP Publishing Ltd.

Anders A.,Lawrence Berkeley National Laboratory
Surface and Coatings Technology | Year: 2014

High power impulse magnetron sputtering (HiPIMS) has been at the center of attention over the last years as it is an emerging physical vapor deposition (PVD) technology that combines advantages of magnetron sputtering with various forms of energetic deposition of films such as ion plating and cathodic arc plasma deposition. It should not come as a surprise that many extension and variations of HiPIMS make use, intentionally or unintentionally, of previously discovered approaches to film processing such as substrate surface preparation by metal ion sputtering and phased biasing for film texture and stress control. Therefore, in this review, an overview is given on some historical developments and features of cathodic arc and HiPIMS plasmas, showing commonalities and differences. To limit the scope, emphasis is put on plasma properties, as opposed to surveying the vast literature on specific film materials and their properties. © 2014 Elsevier B.V.

Obermeyer A.C.,University of California at Berkeley | Jarman J.B.,University of California at Berkeley | Francis M.B.,University of California at Berkeley | Francis M.B.,Lawrence Berkeley National Laboratory
Journal of the American Chemical Society | Year: 2014

The synthetic modification of proteins plays an important role in chemical biology and biomaterials science. These fields provide a constant need for chemical tools that can introduce new functionality in specific locations on protein surfaces. In this work, an oxidative strategy is demonstrated for the efficient modification of N-terminal residues on peptides and N-terminal proline residues on proteins. The strategy uses o-aminophenols or o-catechols that are oxidized to active coupling species in situ using potassium ferricyanide. Peptide screening results have revealed that many N-terminal amino acids can participate in this reaction, and that proline residues are particularly reactive. When applied to protein substrates, the reaction shows a stronger requirement for the proline group. Key advantages of the reaction include its fast second-order kinetics and ability to achieve site-selective modification in a single step using low concentrations of reagent. Although free cysteines are also modified by the coupling reaction, they can be protected through disulfide formation and then liberated after N-terminal coupling is complete. This allows access to doubly functionalized bioconjugates that can be difficult to access using other methods. © 2014 American Chemical Society.

Mony L.,University of California at Berkeley | Berger T.K.,University of California at Berkeley | Isacoff E.Y.,University of California at Berkeley | Isacoff E.Y.,Lawrence Berkeley National Laboratory
Nature Structural and Molecular Biology | Year: 2015

The Hv1 proton channel is unique among voltage-gated channels for containing the pore and gate within its voltage-sensing domain. Pore opening has been proposed to include assembly of the selectivity filter between an arginine (R3) of segment S4 and an aspartate (D1) of segment S1. We determined whether gating involves motion of S1, using Ciona intestinalis Hv1. We found that channel opening is concomitant with solution access to the pore-lining face of S1, from the cytoplasm to deep inside the pore. Voltage- and patch-clamp fluorometry showed that this involves a motion of S1 relative to its surroundings. S1 motion and the S4 motion that precedes it are each influenced by residues on the other helix, thus suggesting a dynamic interaction between S1 and S4. Our findings suggest that the S1 of Hv1 has specialized to function as part of the channel's gate. © 2015 Nature America, Inc. All rights reserved.

Larabell C.A.,University of California at San Francisco | Larabell C.A.,Lawrence Berkeley National Laboratory | Nugent K.A.,University of Melbourne
Current Opinion in Structural Biology | Year: 2010

X-ray imaging of biological samples is progressing rapidly. In this paper we review the progress to date in high-resolution imaging of cellular architecture. In particular we survey the progress in soft X-ray tomography and argue that the field is coming of age and that important biological insights are starting to emerge. We then review the new ideas based on coherent diffraction. These methods are at a much earlier stage of development but, as they eliminate the need for X-ray optics, have the capacity to provide substantially better spatial resolution than zone plate-based methods. © 2010 Elsevier Ltd.

Krishna R.,University of Amsterdam | Long J.R.,University of California at Berkeley | Long J.R.,Lawrence Berkeley National Laboratory
Journal of Physical Chemistry C | Year: 2011

Metal-organic frameworks (MOFs) offer considerable potential for separating a variety of mixtures that are important in applications such as CO2 capture and H2 purification. In view of the vast number of MOFs that have been synthesized, there is a need for a reliable procedure for comparing screening and ranking MOFs with regard to their anticipated performance in pressure swing adsorption (PSA) units. For this purpose, the most commonly used metrics are the adsorption selectivity and the working capacity. Here, we suggest an additional metric for comparing MOFs that is based on the analysis of the transient response of an adsorber to a step input of a gaseous mixture. For a chosen purity of the gaseous mixture exiting from the adsorber, a dimensionless breakthrough time τbreak can be defined and determined; this metric determines the frequency of required regeneration and influences the productivity of a PSA unit. The values of τbreak are dictated both by selectivity and by capacity metrics.By performing transient adsorber calculations for separation of CO2/H2, CO 2/CH4, CH4/H2, and CO 2/CH4/H2 mixtures, we compare the values of τbreak to highlight some important advantages of MOFs over conventionally used adsorbents such as zeolite NaX. For a given separation duty, such comparisons provide a more realistic ranking of MOFs than afforded by either selectivity or capacity metrics alone. We conclude that breakthrough calculations can provide an essential tool for screening MOFs. © 2011 American Chemical Society.

Hurley J.H.,University of California at Berkeley | Hurley J.H.,Lawrence Berkeley National Laboratory
EMBO Journal | Year: 2015

The ESCRT proteins are an ancient system that buds membranes and severs membrane necks from their inner face. Three "classical" functions of the ESCRTs have dominated research into these proteins since their discovery in 2001: the biogenesis of multivesicular bodies in endolysosomal sorting; the budding of HIV-1 and other viruses from the plasma membrane of infected cells; and the membrane abscission step in cytokinesis. The past few years have seen an explosion of novel functions: the biogenesis of microvesicles and exosomes; plasma membrane wound repair; neuron pruning; extraction of defective nuclear pore complexes; nuclear envelope reformation; plus-stranded RNA virus replication compartment formation; and micro- and macroautophagy. Most, and perhaps all, of the functions involve the conserved membrane-neck-directed activities of the ESCRTs, revealing a remarkably widespread role for this machinery through a broad swath of cell biology. ESCRT complexes are required for membrane remodeling and scission; this review highlights their role in cellular processes ranging from exosome generation to the reformation of the nuclear envelope. © 2015 The Author.

Pressel K.G.,University of California at Berkeley | Collins W.D.,University of California at Berkeley | Collins W.D.,Lawrence Berkeley National Laboratory
Journal of Climate | Year: 2012

The power-law scale dependence, or scaling, of first-order structure functions of the tropospheric water vapor field between 588S and 588N is investigated using observations from the Atmospheric Infrared Sounder (AIRS). Power-law scale dependence of the first-order structure function would indicate that the water vapor field exhibits statistical scale invariance. Directional and directionally independent firstorder structure functions are computed to assess the directional dependence of derived first-order structure function scaling exponents (H) for a range of scales from 50 to 500 km. In comparison to other methods of assessing statistical scale invariance, the methodology used here requires minimal assumptions regarding the homogeneity of the spatial distribution of data within regions of analysis. Additionally, the methodology facilitates the evaluation of anisotropy and quantifies the extent to which the structure functions exhibit scale invariance. The spatial and seasonal dependence of the computed scaling exponents are explored. Minimum scaling exponents at all levels are shown to occur proximate to the equator, while the global maximum is shown to occur in the middle troposphere near the tropical-subtropical margin of the winter hemisphere. From a detailed analysis of AIRS maritime scaling exponents, it is concluded that the AIRS observations suggest the existence of two scaling regimes in the extratropics. One of these regimes characterizes the statistical scale invariance the free troposphere with H approximately 5 0.55 and a second that characterizes the statistical scale invariance of the boundary layer with H approximately = 1/3. © 2012 American Meteorological Society.

Kudirka R.,Lawrence Berkeley National Laboratory
Biopolymers | Year: 2011

The design and synthesis of protein-like polymers is a fundamental challenge in materials science. A means to achieve this goal is to create synthetic polymers of defined sequence where all relevant folding information is incorporated into a single polymer strand. We present here the aqueous self-assembly of peptoid polymers (N-substituted glycines) into ultrathin, two-dimensional highly ordered nanosheets, where all folding information is encoded into a single chain. The sequence designs enforce a two-fold amphiphilic periodicity. Two sequences were considered: one with charged residues alternately positive and negative (alternating patterning), and one with charges segregated in positive and negative halves of the molecule (block patterning). Sheets form between pH 5 and 10 with the optimal conditions being pH 6 for the alternating sequence and pH 8 for the block sequence. Once assembled, the nanosheets remain stable between pH 6 and 10 with observed degradation beginning to occur below pH 6. The alternating charge nanosheets remain stable up to concentrations of 20% acetonitrile, whereas the block pattern displayed greater robustness remaining stable up to 30% acetonitrile. These observations are consistent with expectations based on considerations of the molecules' electrostatic interactions. This study represents an important step in the construction of abiotic materials founded on biological informatic and folding principles.

Cheung C.,University of California at Berkeley | Cheung C.,Lawrence Berkeley National Laboratory
Journal of High Energy Physics | Year: 2010

We show that on-shell recursion relations hold for tree amplitudes in generic two derivative theories in an arbitrary number of dimensions with multiple particle species and diverse spins. For example, in a gauge theory coupled to scalars and fermions, any amplitude with at least one gluon obeys a recursion relation. In (super)gravity coupled to scalars and fermions, the same holds for any amplitude with at least one graviton. This result pertains to a broad class of theories, including QCD, N = 4 SYM, and N = 8 supergravity.

Oh H.,University of California at Berkeley | Habeck C.,Columbia University | Madison C.,University of California at Berkeley | Jagust W.,University of California at Berkeley | Jagust W.,Lawrence Berkeley National Laboratory
Human Brain Mapping | Year: 2014

β-Amyloid (Aβ), a feature of Alzheimer's disease (AD) pathology, may precede reduced glucose metabolism and gray matter (GM) volume and cognitive decline in patients with AD. Accumulation of Aβ, however, has been also reported in cognitively intact older people, although it remains unresolved whether and how Aβ deposition, glucose metabolism, and GM volume relate to one another in cognitively normal elderly. Fifty-two cognitively normal older adults underwent Pittsburgh Compound B-positron emission tomography (PIB-PET), [18F]fluorodeoxyglucose-PET, and structural magnetic resonance imaging to measure whole-brain amyloid deposition, glucose metabolism, and GM volume, respectively. Covariance patterns of these measures in association with global amyloid burden measured by PIB index were extracted using principal component analysis-based multivariate methods. Higher global amyloid burden was associated with relative increases of amyloid deposition and glucose metabolism and relative decreases of GM volume in brain regions collectively known as the default mode network including the posterior cingulate/precuneus, lateral parietal cortices, and medial frontal cortex. Relative increases of amyloid deposition and glucose metabolism were also noted in the lateral prefrontal cortices, and relative decreases of GM volume were pronounced in hippocampus. The degree of expression of the topographical patterns of the PIB data was further associated with visual memory performance when controlling for age, sex, and education. The present findings suggest that cognitively normal older adults with greater amyloid deposition are relatively hypermetabolic in frontal and parietal brain regions while undergoing GM volume loss in overlapping brain regions. Hum Brain Mapp 35:297-308, 2014. © 2012 Wiley Periodicals, Inc.

Glaeser R.M.,Lawrence Berkeley National Laboratory | Hall R.J.,University of California at Berkeley
Biophysical Journal | Year: 2011

Although cryo-electron microscopy (cryo-EM) of biological macromolecules has made important advances in the past few years, the level of current technical performance is still well below what the physics of electron scattering would allow. It should be possible, for example, to use cryo-EM to solve protein structures at atomic resolution for particle sizes well below 80 kDa, but currently this has been achieved only for particles at least 10 times larger than that. In this review, we first examine some of the reasons for this large gap in performance. We then give an overview of work that is currently in progress to 1), improve the signal/noise ratio for area detectors; 2), improve the signal transfer between the scattered electrons and the corresponding images; and 3), reduce the extent to which beam-induced movement causes a steep fall-off of signal at high resolution. In each case, there is substantial reason to think that cryo-EM can indeed be made to approach the estimated physical limits. © 2011 by the Biophysical Society.

Mills E.,Lawrence Berkeley National Laboratory
Science | Year: 2012

Insurance industry trends show how market-based mechanisms support climate change mitigation and adaptation.

Ramkrishna D.,Purdue University | Singh M.R.,Purdue University | Singh M.R.,University of California at Berkeley | Singh M.R.,Lawrence Berkeley National Laboratory
Annual Review of Chemical and Biomolecular Engineering | Year: 2014

Population balance modeling is undergoing phenomenal growth in its applications, and this growth is accompanied by multifarious reviews. This review aims to fortify the model's fundamental base, as well as point to a variety of new applications, including modeling of crystal morphology, cell growth and differentiation, gene regulatory processes, and transfer of drug resistance. This is accomplished by presenting the many faces of population balance equations that arise in the foregoing applications. © 2014 by Annual Reviews.

Luntz A.C.,SLAC | McCloskey B.D.,University of California at Berkeley | McCloskey B.D.,Lawrence Berkeley National Laboratory
Chemical Reviews | Year: 2014

The major issue confronting complete electrification of road transport is simply a battery problem. While both metrics are undoubtedly important, which of the two is the most important for EV applications is somewhat debated, even among the different EV manufacturers. Traditional car companies emphasize more the importance of energy density, while Tesla emphasizes more the specific energy since they tend to design a car around the battery pack. The history of rechargeable non-aqueous Li-air batteries at this stage is so short that the field must be considered a work in progress. In fact, even the basic mechanisms and rationale for many of the fundamental properties of Li-air are still in dispute among many of the researchers in the field.

Park J.Y.,Korea Basic Science Institute | Park J.Y.,Korea Advanced Institute of Science and Technology | Salmeron M.,Lawrence Berkeley National Laboratory | Salmeron M.,University of California at Berkeley
Chemical Reviews | Year: 2014

Recent experimental and theoretical findings of the effect of bulk properties, conductance, surface structure, and point defects in energy dissipation in various systems, including metals, semiconductors, quasicrystals, two-dimensional sheets, and organic molecular films is reported. A host of new phenomena, including friction anisotropy, superlubricity, and velocity dependence, have been uncovered and studied. In these experiments, the probe is brought into contact with an electron transparent sample and the interface is imaged in the TEM during contact while the probe simultaneously measures electrical (STM) or mechanical signals. In situ TEM techniques have already made it possible to directly measure electrical and mechanical properties of gold contacts, including atomic-sized contacts that exhibit quantized conductance steps associated with atomic rearrangements and high-resolution visualization of the deformation of nm-sized gold interfaces via slip and twinning.

Williams P.T.,Lawrence Berkeley National Laboratory | Franklin B.A.,Beaumont Health Center
PLoS ONE | Year: 2013

Purpose:Walking is purported to reduce the risk of atrial fibrillation by 48%, whereas jogging is purported to increase its risk by 53%, suggesting a strong anti-arrhythmic benefit of walking over running. The purpose of these analyses is to compare incident self-reported physician-diagnosed cardiac arrhythmia to baseline energy expenditure (metabolic equivalent hours per day, METhr/d) from walking, running and other exercise.Methods:Proportional hazards analysis of 14,734 walkers and 32,073 runners.Results:There were 1,060 incident cardiac arrhythmias (412 walkers, 648 runners) during 6.2 years of follow-up. The risk for incident cardiac arrhythmias declined 4.4% per baseline METhr/d walked by the walkers, or running in the runners (P = 0.0001). Specifically, the risk declined 14.2% (hazard ratio: 0.858) for 1.8 to 3.6 METhr/d, 26.5% for 3.6 to 5.4 METhr/d, and 31.7% for ≥5.4 METhr/d, relative to <1.8 METhr/d. The risk reduction per METhr/d was significantly greater for walking than running (P<0.01), but only because walkers were at 34% greater risk than runners who fell below contemporary physical activity guideline recommendations; otherwise the walkers and runners had similar risks for cardiac arrhythmias. Cardiac arrhythmias were unrelated to walking and running intensity, and unrelated to marathon participation and performance.Conclusions:The risk for cardiac arrhythmias was similar in walkers and runners who expended comparable METhr/d during structured exercise. We found no significant risk increase for self-reported cardiac arrhythmias associated with running distance, exercise intensity, or marathon participation. Rhythm abnormalities were based on self-report, precluding definitive categorization of the nature of the rhythm disturbance. However, even if the runners' arrhythmias include sinus bradycardia due to running itself, there was no increase in arrhythmias with greater running distance.

Ryu H.,Lawrence Berkeley National Laboratory
Nature Physics | Year: 2016

We provide direct evidence for the existence of isolated, one-dimensional charge density waves at mirror twin boundaries (MTBs) of single-layer semiconducting MoSe2. Such MTBs have been previously observed by transmission electron microscopy and have been predicted to be metallic in MoSe2 and MoS2. Our low-temperature scanning tunnelling microscopy/spectroscopy measurements revealed a substantial bandgap of 100 meV opening at the Fermi energy in the otherwise metallic one-dimensional structures. We found a periodic modulation in the density of states along the MTB, with a wavelength of approximately three lattice constants. In addition to mapping the energy-dependent density of states, we determined the atomic structure and bonding of the MTB through simultaneous high-resolution non-contact atomic force microscopy. Density functional theory calculations based on the observed structure reproduced both the gap opening and the spatially resolved density of states. © 2016 Nature Publishing Group

Blow M.J.,Lawrence Berkeley National Laboratory
Nature genetics | Year: 2010

Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme noncoding-sequence conservation has successfully predicted enhancers that are active in many tissues but has failed to identify substantial numbers of heart-specific enhancers. Here, we used ChIP-Seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over 3,000 candidate heart enhancers genome wide. Compared to enhancers active in other tissues we studied at this time point, most candidate heart enhancers were less deeply conserved in vertebrate evolution. Nevertheless, transgenic mouse assays of 130 candidate regions revealed that most function reproducibly as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary conservation of embryonic enhancers can vary depending on tissue type.

Newman G.A.,Lawrence Berkeley National Laboratory
Surveys in Geophysics | Year: 2014

Many geoscientific applications exploit electrostatic and electromagnetic fields to interrogate and map subsurface electrical resistivity-an important geophysical attribute for characterizing mineral, energy, and water resources. In complex three-dimensional geologies, where many of these resources remain to be found, resistivity mapping requires large-scale modeling and imaging capabilities, as well as the ability to treat significant data volumes, which can easily overwhelm single-core and modest multicore computing hardware. To treat such problems requires large-scale parallel computational resources, necessary for reducing the time to solution to a time frame acceptable to the exploration process. The recognition that significant parallel computing processes must be brought to bear on these problems gives rise to choices that must be made in parallel computing hardware and software. In this review, some of these choices are presented, along with the resulting trade-offs. We also discuss future trends in high-performance computing and the anticipated impact on electromagnetic (EM) geophysics. Topics discussed in this review article include a survey of parallel computing platforms, graphics processing units to multicore CPUs with a fast interconnect, along with effective parallel solvers and associated solver libraries effective for inductive EM modeling and imaging. © 2013 Springer Science+Business Media Dordrecht (outside the USA).

Martin L.W.,University of Illinois at Urbana - Champaign | Chu Y.-H.,National Chiao Tung University | Ramesh R.,University of California at Berkeley | Ramesh R.,Lawrence Berkeley National Laboratory
Materials Science and Engineering R: Reports | Year: 2010

The growth and characterization of functional oxide thin films that are ferroelectric, magnetic, or both at the same time are reviewed. The evolution of synthesis techniques and how advances in in situ characterization have enabled significant acceleration in improvements to these materials are described. Methods for enhancing the properties of functional materials or creating entirely new functionality at interfaces are covered, including strain engineering and layering control at the atomic-layer level. Emerging applications of these functional oxides such as achieving electrical control of ferromagnetism and the future of these complex functional oxides is discussed. © 2010 Elsevier B.V. All rights reserved.

Dangkulwanich M.,Howard Hughes Medical Institute | Ishibashi T.,Howard Hughes Medical Institute | Ishibashi T.,Hong Kong University of Science and Technology | Bintu L.,Howard Hughes Medical Institute | And 3 more authors.
Chemical Reviews | Year: 2014

A review of the various aspects of transcription that have been addressed using methods of single-molecule detection and manipulation is studied. Whereas single-subunit viral polymerases such as T7 and SP6 RNAP can start transcription at a promoter region without additional cofactors, multi subunit bacterial and eukaryotic RNA polymerase (RNAPs) require transcription factors that aid the enzyme to recognize and bind to the promoter. Through the combination of single molecule manipulation and single-molecule fluorescence methods in the same experiment, it should be possible to follow, the internal dynamics of the polymerase or the binding of a regulatory factor and simultaneously monitor the mechanical variables of position, force, and torque. The result of these efforts will be a multidimensional picture of transcription that will provide crucial information about the relative timing of various molecular events and therefore reveal their causal connection.

Williams P.T.,Lawrence Berkeley National Laboratory
Medicine and Science in Sports and Exercise | Year: 2011

Purpose: The high prevalence of obesity in Western societies has been attributed in part to high-fat low-CHO food consumption. However, people have also become less active, and inactivity may have increased the risk for weight gain from poor dietary choices. Analyses were performed to test whether diet-weight relationships were attenuated by vigorous exercise. Methods: Age-and education-adjusted cross-sectional regression analyses of 62,042 men and 44,695 women recruited for the National Runners' Health Study were conducted. Reported meat and fruit intakes were analyzed separately and as indicators of high-risk diets. Results: The runners were generally lean (mean ± SD: males = 24.15 ± 2.81 kg•m -2, females = 21.63 ± 2.70 kg•m -2) as measured by body mass index (BMI), educated (males = 16.42 ± 2.47 yr, females = 16.04 ± 2.32 yr), and middle-aged (males = 44.40 ± 10.83 yr, females = 38.21 ± 10.08 yr), who ran 5.30 ± 3.23 km•d if male and 4.79 ± 3.00 km•d if female. Running significantly attenuated BMI's relationship to reported meat and fruit intakes in men (P < 10 and P < 10, respectively) and women (P < 10 and P < 10, respectively). Specifically, compared with running <2 km•d, running >8 km•d reduced the apparent BMI increase per serving of meat by 43% in men (slope ± SE = from 0.74 ± 0.10 to 0.42 ± 0.06) and 55% in women (from 1.26 ± 0.13 to 0.57 ± 0.09) and reduced the apparent BMI reduction per serving of fruit by 75% in men (from-0.28 ± 0.04 to-0.07 ± 0.02) and 94% in women (from-0.16 ± 0.05 to-0.01 ± 0.02). Running also significantly attenuated the concordant relationship between reported meat intake and waist and chest circumferences in men (P < 10 and P = 0.0002, respectively) and women (P = 0.0004 and P < 10, respectively) and the concordant relationship between meat intake and hip circumference in women (P < 10). Conclusions: Vigorous exercise may mitigate diet-induced weight gain, albeit not guaranteeing protection from poor dietary choices. © 2011 by the American College of Sports Medicine.

Hartwig J.F.,Lawrence Berkeley National Laboratory
Journal of the American Chemical Society | Year: 2016

This Perspective presents the fundamental principles, the elementary reactions, the initial catalytic systems, and the contemporary catalysts that have converted C-H bond functionalization from a curiosity to a reality for synthetic chemists. Many classes of elementary reactions involving transition-metal complexes cleave C-H bonds at typically unreactive positions. These reactions, coupled with a separate or simultaneous functionalization process lead to products containing new C-C, C-N, and C-O bonds. Such reactions were initially studied for the conversion of light alkanes to liquid products, but they have been used (and commercialized in some cases) most often for the synthesis of the more complex structures of natural products, medicinally active compounds, and aromatic materials. Such a change in direction of research in C-H bond functionalization is remarkable because the reactions must occur at an unactivated C-H bond over functional groups that are more reactive than the C-H bond toward classical reagents. The scope of reactions that form C-C bonds or install functionality at an unactivated C-H bond will be presented, and the potential future utility of these reactions will be discussed. © 2015 American Chemical Society.

Rycroft C.H.,University of California at Berkeley | Rycroft C.H.,Lawrence Berkeley National Laboratory | Bouchbinder E.,Weizmann Institute of Science
Physical Review Letters | Year: 2012

Quantitative understanding of the fracture toughness of metallic glasses, including the associated ductile-to-brittle (embrittlement) transitions, is not yet available. Here, we use a simple model of plastic deformation in glasses, coupled to an advanced Eulerian level set formulation for solving complex free-boundary problems, to calculate the fracture toughness of metallic glasses as a function of the degree of structural relaxation corresponding to different annealing times near the glass temperature. Our main result indicates the existence of an elastoplastic crack tip instability for sufficiently relaxed glasses, resulting in a marked drop in the toughness, which we interpret as annealing-induced embrittlement transition similar to experimental observations. © 2012 American Physical Society.

Foley R.J.,Harvard - Smithsonian Center for Astrophysics | Kasen D.,University of California at Berkeley | Kasen D.,Lawrence Berkeley National Laboratory
Astrophysical Journal | Year: 2011

We use a sample of 121 spectroscopically normal Type Ia supernovae (SNe Ia) to show that their intrinsic color is correlated with their ejecta velocity, as measured from the blueshift of the Si II λ6355 feature near maximum brightness, v Si II. The SN Ia sample was originally used by Wang et al. to show that the relationship between color excess and peak magnitude, which in the absence of intrinsic color differences describes a reddening law, was different for two subsamples split by v Si II (defined as "Normal" and "High Velocity"). We verify this result, but find that the two subsamples have the same reddening law when extremely reddened events (E(B - V)>0.35mag) are excluded. We also show that (1) the High-Velocity subsample is offset by ∼0.06mag to the red from the Normal subsample in the (B max - V max)-MV plane, (2) the B max - V max cumulative distribution functions of the two subsamples have nearly identical shapes, but the High-Velocity subsample is offset by ∼0.07mag to the red in B max - V max, and (3) the bluest High-Velocity SNe Ia are 0.10mag redder than the bluest Normal SNe Ia. Together, this evidence indicates a difference in intrinsic color for the subsamples. Accounting for this intrinsic color difference reduces the scatter in Hubble residuals from 0.190mag to 0.130mag for SNe Ia with A V ≲ 0.7mag. The scatter can be further reduced to 0.109mag by exclusively using SNe Ia from the Normal subsample. Additionally, this result can at least partially explain the anomalously low values of RV found in large SN Ia samples. We explain the correlation between ejecta velocity and color as increased line blanketing in the High-Velocity SNe Ia, causing them to become redder. We discuss some implications of this result, and stress the importance of spectroscopy for future SN Ia cosmology surveys, with particular focus on the design of WFIRST. © 2011. The American Astronomical Society. All rights reserved..

Dobbs T.A.,University of Calgary | Tainer J.A.,Scripps Research Institute | Tainer J.A.,Lawrence Berkeley National Laboratory | Lees-Miller S.P.,University of Calgary
DNA Repair | Year: 2010

The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and Ku heterodimer together form the biologically critical DNA-PK complex that plays key roles in the repair of ionizing radiation-induced DNA double-strand breaks through the non-homologous end-joining (NHEJ) pathway. Despite elegant and informative electron microscopy studies, the mechanism by which DNA-PK co-ordinates the initiation of NHEJ has been enigmatic due to limited structural information. Here, we discuss how the recently described small angle X-ray scattering structures of full-length Ku heterodimer and DNA-PKcs in solution, combined with a breakthrough DNA-PKcs crystal structure, provide significant insights into the early stages of NHEJ. Dynamic structural changes associated with a functionally important cluster of autophosphorylation sites play a significant role in regulating the dissociation of DNA-PKcs from Ku and DNA. These new structural insights have implications for understanding the formation and control of the DNA-PK synaptic complex, DNA-PKcs activation and initiation of NHEJ. More generally, they provide prototypic information for the phosphatidylinositol-3 kinase-like (PIKK) family of serine/threonine protein kinases that includes Ataxia Telangiectasia-Mutated (ATM) and ATM-, Rad3-related (ATR) as well as DNA-PKcs. © 2010 Elsevier B.V.

Mueller A.H.,Columbia University | Xiao B.-W.,Central China Normal University | Yuan F.,Lawrence Berkeley National Laboratory
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

In this manuscript, we present a complete study of the Sudakov double logarithms resummation for various hard processes in eA and pA collisions in the small-x saturation formalism. We first employ a couple of slightly different formalisms to perform the one-loop analysis of the Higgs boson production process in pA collisions, and demonstrate that Sudakov-type logarithms arise as the leading correction and that they can be systematically resummed in addition to the usual small-x resummation. We further study the Sudakov double logarithms for other processes such as heavy quark pair production and back-to-back dijet production in eA and pA collisions through detailed calculation of the corresponding one-loop diagrams. As the most important contribution from the one-loop correction, the Sudakov factor should play an important role in the phenomenological study of saturation physics in the pA programs at RHIC and the LHC. © 2013 American Physical Society.

Arkin A.P.,University of California at Berkeley | Arkin A.P.,Lawrence Berkeley National Laboratory
Current Opinion in Chemical Biology | Year: 2013

The next generation of synthetic biology applications will increasingly involve engineered organisms that exist in intimate contact with humans, animals and the rest of the environment. Examples include cellular and viral approaches for maintaining and improving health in humans and animals. The need for reliable and specific function in these environments may require more complex system designs than previously. In these cases the uncertainties in the behavior of biological building blocks, their hosts and their environments present a challenge for design of predictable and safe systems. Here, we review systematic methods for the effective characterization of these uncertainties that are lowering the barriers to predictive design of reliable complex biological systems. © 2013 The Author.

Kharin V.V.,Environment Canada | Zwiers F.W.,University of Victoria | Zhang X.,Environment Canada | Wehner M.,Lawrence Berkeley National Laboratory
Climatic Change | Year: 2013

Twenty-year temperature and precipitation extremes and their projected future changes are evaluated in an ensemble of climate models participating in the Coupled Model Intercomparison Project Phase 5 (CMIP5), updating a similar study based on the CMIP3 ensemble. The projected changes are documented for three radiative forcing scenarios. The performance of the CMIP5 models in simulating 20-year temperature and precipitation extremes is comparable to that of the CMIP3 ensemble. The models simulate late 20th century warm extremes reasonably well, compared to estimates from reanalyses. The model discrepancies in simulating cold extremes are generally larger than those for warm extremes. Simulated late 20th century precipitation extremes are plausible in the extratropics but uncertainty in extreme precipitation in the tropics and subtropics remains very large, both in the models and the observationally-constrained datasets. Consistent with CMIP3 results, CMIP5 cold extremes generally warm faster than warm extremes, mainly in regions where snow and sea-ice retreat with global warming. There are tropical and subtropical regions where warming rates of warm extremes exceed those of cold extremes. Relative changes in the intensity of precipitation extremes generally exceed relative changes in annual mean precipitation. The corresponding waiting times for late 20th century extreme precipitation events are reduced almost everywhere, except for a few subtropical regions. The CMIP5 planetary sensitivity in extreme precipitation is about 6 %/°C, with generally lower values over extratropical land. © 2013 Crown Copyright.

Haxton D.J.,Lawrence Berkeley National Laboratory
Physical Review A - Atomic, Molecular, and Optical Physics | Year: 2013

Total and partial cross sections for breakup of the ground rovibronic state of H2+ by photon impact are calculated using the exact nonadiabatic nonrelativistic Hamiltonian without approximation. The converged results span six orders of magnitude. The breakup cross section is divided into dissociative excitation and dissociative ionization. The dissociative excitation channels are divided into contributions from principal quantum numbers 1-4. For dissociative ionization, the fully differential cross section is calculated using a formally exact expression. These results are compared with approximate expressions. The Born-Oppenheimer expression for the dissociative ionization amplitude is shown to be deficient near onset. A Born-Oppenheimer approximation to the final state is shown to give accurate results for the sharing of kinetic energy between the electronic and the internuclear degrees of freedom - the doubly differential cross section. To accurately calculate the triply differential cross section, including the angular behavior, it is shown that nonadiabatic wave functions for both initial and final states are required at low electron energies. © 2013 American Physical Society.

Schmidt A.-C.,Friedrich - Alexander - University, Erlangen - Nuremberg | Heinemann F.W.,Friedrich - Alexander - University, Erlangen - Nuremberg | Lukens W.W.,Lawrence Berkeley National Laboratory | Meyer K.,Friedrich - Alexander - University, Erlangen - Nuremberg
Journal of the American Chemical Society | Year: 2014

In a multiple-bond metathesis reaction, the triazacyclononane (tacn)-anchored methyl- and neopentyl (nP)-substituted tris(aryloxide) U III complex [((nP,MeArO)3tacn)UIII] (1) reacts with mesityl azide and CO2 to form mesityl isocyanate and the dinuclear bis(μ-oxo)-bridged UV/UV complex [{((nP,MeArO)3tacn)UV}2(μ-O) 2] (3). This reaction proceeds via the mononuclear UV imido intermediate [((nP,MeArO)3tacn)UV(NMes)] (2), which has been synthesized and fully characterized independently. The dimeric UV oxo species shows rich redox behavior: complex 3 can be reduced by one and two electrons, respectively, yielding the mixed-valent U IV/UV bis(μ-oxo) complex [K(crypt)][{(( nP,MeArO)3tacn)UIV/V}2(μ-O) 2] (7) and the UIV/UIV bis(μ-oxo) complex K2[{((nP,MeArO)3tacn)UIV} 2(μ-O)2] (6). In addition, complex 3 can be oxidized to provide the mononuclear uranium(VI) oxo complexes [((nP,MeArO) 3tacn)UVI(O)eq(OTf)ax] (8) and [((nP,MeArO)3tacn)UVI(O)eq]SbF 6 (9). The unique series of bis(μ-oxo) complexes also shows notable magnetic behavior, which was investigated in detail by UV/vis/NIR and EPR spectroscopy as well as SQUID magnetization studies. In order to understand possible magnetic exchange phenomena, the mononuclear terminal oxo complexes [((nP,MeArO)3tacn)UV(O)(O-pyridine)] (4) and [((nP,MeArO)3tacn)UV(O)(O-NMe3)] (5) were synthesized and fully characterized. The magnetic study revealed an unusually strong antiferromagnetic exchange coupling between the two U V ions in 3. Examination of the 18O-labeled bis(μ-oxo)-bridged dinuclear complexes 3, 6, and 7 allowed for the first time the unambiguous assignment of the vibrational signature of the [U(μ-O) 2U] diamond core structural motif. © 2014 American Chemical Society.

Persaud A.,Lawrence Berkeley National Laboratory
Journal of Applied Physics | Year: 2013

In electron field emission experiments, a linear relationship in plots of slope vs. intercept obtained from Fowler-Nordheim analysis is commonly observed for single tips or tip arrays. By simulating samples with many tips, it is shown here that the observed linear relationship results from the distribution of input parameters, assuming a log-normal distribution for the radius of each tip. Typically, a shift from the lower-left to the upper-right of a slope-intercept plot has been correlated with a shift in work function. However, as shown in this paper, the same effect can result from a variation in the number of emitters. © 2013 AIP Publishing LLC.

Denes P.,Lawrence Berkeley National Laboratory
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2014

Our ability to harness the advances in microelectronics over the past decade(s) for X-ray detection has resulted in significant improvements in the state of the art. Biology with X-ray free-electron lasers present daunting detector challenges: all of the photons arrive at the same time, and individual high peak power pulses must be read out shot-by-shot. Direct X-ray detection in silicon pixel detectors-monolithic or hybrid-are the standard for XFELs today. For structural biology, improvements are needed for today's 10-100 Hz XFELs, and further improvements are required for tomorrow's 10+ kHz XFELs. This article will discuss detector challenges, why they arise and ways to overcome them, along with the current state of the art. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Randrup J.,Lawrence Berkeley National Laboratory | Moller P.,Los Alamos National Laboratory
Physical Review C - Nuclear Physics | Year: 2013

The recently developed treatment of Brownian shape evolution is refined to take account of the gradual decrease in microscopic effects as the nuclear excitation energy is raised. We construct effective potential-energy surfaces by multiplying the shell-plus-pairing correction term by a suppression factor that depends on the local excitation energy. While this approach is equivalent to the modification of the Fermi-gas level density parameter suggested by Ignatyuk, we adopt a more general functional form for the suppression factor, which is adjusted to measured charge yields for 234U(E*≈11MeV). The resulting model is benchmarked by comparison with 70 measured yields. © 2013 American Physical Society.

Korneev V.A.,Lawrence Berkeley National Laboratory | Demcenko A.,University of Twente
Journal of the Acoustical Society of America | Year: 2014

There exist ten possible nonlinear elastic wave interactions for an isotropic solid described by three constants of the third order. All other possible interactions out of 54 combinations (triplets) of interacting and resulting waves are prohibited, because of restrictions of various kinds. The considered waves include longitudinal and two shear waves polarized in the interacting plane and orthogonal to it. The amplitudes of scattered waves have simple analytical forms, which can be used for experimental setup and design. The analytic results are verified by comparison with numerical solutions of initial equations. Amplitude coefficients for all ten interactions are computed as functions of frequency for polyvinyl chloride, together with interaction and scattering angles. The nonlinear equation of motion is put into a general vector form and can be used for any coordinate system. © 2014 U.S. Government.

Liliental-Weber Z.,Lawrence Berkeley National Laboratory
Journal of Crystal Growth | Year: 2010

A short review of the structural perfection of high-pressure grown bulk crystals is given. As-grown undoped and Mg-doped crystals are described. The dependence of defect arrangement and quality of the surface on growth polarity is described. A high perfection of homoepitaxial layers grown on these substrates is shown. However, growth of thick layers by HVPE may lead to the formation of differently arranged dislocations and the formation of low angle grain boundaries associated with cracks. It is shown that the introduction of dopant or growth of mismatched layers on undoped high-pressure substrates may lead to the formation of additional defects. © 2010 Elsevier B.V. All rights reserved.

Zhuang T.,Vanderbilt University | Jap B.K.,Lawrence Berkeley National Laboratory | Sanders C.R.,Vanderbilt University
Journal of the American Chemical Society | Year: 2011

Solution NMR provides a powerful approach for detecting complex formation involving weak to moderate intermolecular affinity. However, solution NMR has only rarely been used to detect complex formation between two membrane proteins in model membranes. The impact of specific binding on the NMR spectrum of a membrane protein can be difficult to distinguish from spectral changes that are induced by nonspecific binding and/or by changes that arise from forced cohabitation of the two proteins in a single model membrane assembly. This is particularly the case when solubility limits make it impossible to complete a titration to the point of near saturation of complex formation. In this work experiments are presented that provide the basis for establishing whether specific complex formation occurs between two membrane proteins under conditions where binding is not of high avidity. Application of these methods led to the conclusion that the membrane protein CD147 (also known as EMMPRIN or basigin) forms a specific heterodimeric complex in the membrane with the 99-residue transmembrane C-terminal fragment of the amyloid precursor protein (C99 or APP-βCTF), the latter being the immediate precursor of the amyloid-β polypeptides that are closely linked to the etiology of Alzheimer's disease. © 2011 American Chemical Society.

Lian Y.,Yale University | Bergman R.G.,Lawrence Berkeley National Laboratory | Lavis L.D.,Howard Hughes Medical Institute | Ellman J.A.,Yale University
Journal of the American Chemical Society | Year: 2013

An efficient, one-step, and highly functional group-compatible synthesis of substituted N-aryl-2H-indazoles is reported via the rhodium(III)-catalyzed C-H bond addition of azobenzenes to aldehydes. The regioselective coupling of unsymmetrical azobenzenes was further demonstrated and led to the development of a new removable aryl group that allows for the preparation of indazoles without N-substitution. The 2-aryl-2H-indazole products also represent a new class of readily prepared fluorophores for which initial spectroscopic characterization has been performed. © 2013 American Chemical Society.

Korneev V.,Lawrence Berkeley National Laboratory
Geophysics | Year: 2010

Low-frequency analytical solutions have been obtained for phase velocities of symmetrical fluid waves within both an infinite fracture and a pipe filled with a viscous fluid. Three different fluid wave regimes can exist in such objects, depending on the various combinations of parameters, such as fluid density, fluid viscosity, walls shear modulus, channel thickness, and frequency. Equations for velocities of all these regimes have explicit forms and are verified by comparisons with the exact solutions. The dominant role of fractures in rock permeability at field scales and the strong amplitude and frequency effects of Stoneley guided waves suggest the importance of including these wave effects into poroelastic theories. © 2010 Society of Exploration Geophysicists.

Zimmermann S.,Lawrence Berkeley National Laboratory
Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment | Year: 2013

A new adaptive filtering technique to reduce microphonic noise in radiation detectors is presented. The technique is based on system identification that actively cancels the microphonic noise. A sensor is used to measures mechanical disturbances that cause vibration on the detector assembly, and the digital adaptive filtering estimates the impact of these disturbances on the microphonic noise. The noise then can be subtracted from the actual detector measurement. In this paper the technique is presented and simulations are used to support this approach. © 2013 Elsevier B.V.

Ricca B.L.,University of California at Berkeley | Venugopalan G.,University of California at Berkeley | Fletcher D.A.,University of California at Berkeley | Fletcher D.A.,Lawrence Berkeley National Laboratory
Current Opinion in Cell Biology | Year: 2013

A cell embedded in a multicellular organism will experience a wide range of mechanical stimuli over the course of its life. Fluid flows and neighboring cells actively exert stresses on the cell, while the cell's environment presents a set of passive mechanical properties that constrain its physical behavior. Cells respond to these varied mechanical cues through biological responses that regulate activities such as differentiation, morphogenesis, and proliferation, as well as material responses involving compression, stretching, and relaxation. Here, we break down recent studies of mechanotransduction on the basis of the input mechanical stimuli acting upon the cell and the output response of the cell. This framework provides a useful starting point for identifying overlaps in molecular players and sensing modalities, and it highlights how different timescales involved in biological and material responses to mechanical inputs could serve as a means for filtering important mechanical signals from noise. © 2013 .

Luo Y.,Beijing Normal University | Wang L.-W.,Lawrence Berkeley National Laboratory
ACS Nano | Year: 2010

The electronic structures of the CdSe/CdS core-shell nanorods are systemically investigated by large-scale first-principles quality calculations. The effects of band alignment, quantum confinement, piezoelectric field, and dipole moments are analyzed and delineated by comparing the results of systems with or without some of these attributes. We found complicated interplays between these effects in determining the nanorod band gap and electron hole wave function localizations. The hole wave function is found to be localized inside the CdSe core, while the electron wave function is localized in the CdS shell, with its distance to the CdSe core depending on the surface passivation. The permanent dipole moment induced by different surface passivations can change the electron hole separation, while the piezoelectric effect plays a relatively minor role. Finally, we demonstrate that it is straightforward to manipulate the nanorod electronic structure by changing its CdSe core position. © 2010 American Chemical Society.

Berryman J.G.,Lawrence Berkeley National Laboratory
International Journal of Engineering Science | Year: 2016

A survey is provided of some of the better known examples of quantitative results during fluid injection on number, quality, and weakening effects for fractures in earth reservoirs along with some comparisons to either well-known or better-known theories of both fracture arrival and/or new growth of existing fractures through both fluid injection and stress application. The detailed analyses presented focus on reservoirs having (at worst) orthotropic symmetry. © 2016 Elsevier Ltd. All rights reserved.

Sathre R.,Lawrence Berkeley National Laboratory | Masanet E.,Northwestern University
RSC Advances | Year: 2013

Metal-organic frameworks (MOFs) are promising new material media for carbon dioxide (CO2) capture. Their tunable adsorption patterns may allow relatively efficient separation of gases, e.g. from power plant exhaust. Here we conduct scenario-based prospective life-cycle system modeling to estimate the potentials and implications of large-scale MOF application for post-combustion carbon capture and storage (CCS), and estimate the source and magnitude of uncertainties. The methodological approach includes parametric system modeling to quantify relations between system components; scenario projections of plausible pathways for system scale-up; proxy data on analogous materials and processes; and uncertainty analysis of parameter significance. We estimate the system-wide material and energy flows and economic costs associated with projected large-scale CCS deployment. We compare the performance of a MOF-based system to currently more mature amine-based capture technology. We discuss balancing two critical factors that determine the success of CO2 capture media: thermodynamic efficiency of the capture/regeneration cycle, and life-cycle embodied energy and cost of the material and its ancillary systems. © 2013 The Royal Society of Chemistry.

Yu C.,Lawrence Berkeley National Laboratory
Methods in molecular biology (Clifton, N.J.) | Year: 2011

We describe a method for high-throughput production of protein expression-ready clones. Open-reading frames (ORFs) are amplified by PCR from sequence-verified cDNA clones and subcloned into an appropriate loxP-containing donor vector. Each ORF is represented by two types of clones, one containing the native stop codon for expression of the native protein or amino-terminal fusion constructs and the other made without the stop codon to allow for carboxy-terminal fusion constructs. The expression-ready clone is sequenced to verify that no PCR errors have been introduced. We have made over 11,000 clones ranging in size from 78-6,699 bp with a median of 1,056 bp. This is the largest set of fully sequence-verified-"movable ORFs" of any model organism genome project. The donor clone facilitates rapid and simple transfer of the ORF into any expression vector of choice. Vectors are available for expressing these ORFs in bacteria, cell lines, or transgenic animals. The flexibility of this ORF clone collection makes possible a variety of proteomic applications, including protein interaction mapping, high-throughput cell-based expression screens, and functional studies. We have transferred 5,800 ORFs to a vector that allows production of a FLAG-HA tagged protein in Drosophila tissue culture cells with a metallothionein-inducible promoter. These clones are being used to produce a protein complex map of Drosophila from Schneider cells.

Purpose: The guideline physical activity levels are prescribed in terms of time, frequency, and intensity (e.g., 30 minutes brisk walking, five days a week or its energy equivalence) and assume that different activities may be combined to meet targeted goals (exchangeability premise). Habitual runners and walkers may quantify exercise in terms of distance (km/day), and for them, the relationship between activity dose and health benefits may be better assessed in terms of distance rather than time. Analyses were therefore performed to test: 1) whether time-based or distance-based estimates of energy expenditure provide the best metric for relating running and walking to hypertensive, high cholesterol, and diabetes medication use (conditions known to be diminished by exercise), and 2) the exchangeability premise. Methods: Logistic regression analyses of medication use (dependent variable) vs. metabolic equivalent hours per day (METhr/d) of running, walking and other exercise (independent variables) using cross-sectional data from the National Runners' (17,201 male, 16,173 female) and Walkers' Health Studies (3,434 male, 12,384 female). Results: Estimated METhr/d of running and walking activity were 38% and 31% greater, respectively, when calculated from self-reported time than distance in men, and 43% and 37% greater in women, respectively. Percent reductions in the odds for hypertension and high cholesterol medication use per METhr/d run or per METhr/d walked were ≥2-fold greater when estimated from reported distance (km/wk) than from time (hr/wk). The per METhr/d odds reduction was significantly greater for the distance- than the time-based estimate for hypertension (runners: P<10-5 for males and P = 0.003 for females; walkers: P = 0.03 for males and P<10-4 for females), high cholesterol medication use in runners (P<10-4 for males and P = 0.02 for females) and male walkers (P = 0.01 for males and P = 0.08 for females) and for diabetes medication use in male runners (P<10-3). Conclusions: Although causality between greater exercise and lower prevalence of hypertension, high cholesterol and diabetes cannot be inferred from these cross-sectional data, the results do suggest that distance-based estimates of METhr/d run or walked provide superior metrics for epidemiological analyses to their traditional time-based estimates.

DePaolo D.J.,Lawrence Berkeley National Laboratory | Cole D.R.,Ohio State University
Reviews in Mineralogy and Geochemistry | Year: 2013

Geochemistry plays a significant role in many aspects of geologic carbon sequestration, from dissolution and precipitation of minerals in the reservoir and seal rocks, to modification of the properties of mineral surfaces and their effects on fluid flow and capillary trapping. The properties of supercritical CO2, brines, and their mixtures are also critical to designing, predicting the behavior, and monitoring sequestration systems and sites. In this volume, there are illustrations of many of the important geochemical challenges relating to carbon sequestration. The contributions also showcase modern techniques and approaches that are being employed to advance knowledge of these fluid-rock systems that may be critical to mitigation of carbon emissions. Copyright © 2013 Mineralogical Society of America.

Ritchie R.O.,Lawrence Berkeley National Laboratory
Nature Materials | Year: 2011

The attainment of both strength and toughness is a vital requirement for most structural materials; unfortunately these properties are generally mutually exclusive. Although the quest continues for stronger and harder materials, these have little to no use as bulk structural materials without appropriate fracture resistance. It is the lower-strength, and hence higher-toughness, materials that find use for most safety-critical applications where premature or, worse still, catastrophic fracture is unacceptable. For these reasons, the development of strong and tough (damage-tolerant) materials has traditionally been an exercise in compromise between hardness versus ductility. Drawing examples from metallic glasses, natural and biological materials, and structural and biomimetic ceramics, we examine some of the newer strategies in dealing with this conflict. Specifically, we focus on the interplay between the mechanisms that individually contribute to strength and toughness, noting that these phenomena can originate from very different lengthscales in a material's structural architecture. We show how these new and natural materials can defeat the conflict of strength versus toughness and achieve unprecedented levels of damage tolerance within their respective material classes. © 2011 Macmillan Publishers Limited. All rights reserved.

Hesp K.D.,Yale University | Bergman R.G.,Lawrence Berkeley National Laboratory | Bergman R.G.,University of California at Berkeley | Ellman J.A.,Yale University
Organic Letters | Year: 2012

Rhodium-catalyzed addition of benzamide C-H bonds to a range of aromatic N-sulfonyl aldimines has been developed and proceeds with high functional group compatibility. The synthetic utility of the resulting branched amine products has also been demonstrated by the preparation of isoindoline and isoindolinone frameworks. © 2012 American Chemical Society.

Yoo J.,University of Zurich | Yoo J.,Lawrence Berkeley National Laboratory | Desjacques V.,University of Geneva
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

We perform an all-sky analysis of the general relativistic galaxy power spectrum using the well-developed spherical Fourier decomposition. Spherical Fourier analysis expresses the observed galaxy fluctuation in terms of the spherical harmonics and spherical Bessel functions that are angular and radial eigenfunctions of the Helmholtz equation, providing a natural orthogonal basis for all-sky analysis of the large-scale mode measurements. Accounting for all the relativistic effects in galaxy clustering, we compute the spherical power spectrum and its covariance matrix and compare it to the standard three-dimensional power spectrum to establish a connection. The spherical power spectrum recovers the three-dimensional power spectrum at each wave number k with its angular dependence μk encoded in angular multipole l, and the contributions of the line-of-sight projection to galaxy clustering such as the gravitational lensing effect can be readily accommodated in the spherical Fourier analysis. A complete list of formulas for computing the relativistic spherical galaxy power spectrum is also presented. © 2013 American Physical Society.

Randrup J.,Lawrence Berkeley National Laboratory | Moller P.,Los Alamos National Laboratory
Physical Review Letters | Year: 2011

Although nuclear fission can be understood qualitatively as an evolution of the nuclear shape, a quantitative description has proven to be very elusive. In particular, until now, there existed no model with demonstrated predictive power for the fission-fragment mass yields. Exploiting the expected strongly damped character of nuclear dynamics, we treat the nuclear shape evolution in analogy with Brownian motion and perform random walks on five-dimensional fission potential-energy surfaces which were calculated previously and are the most comprehensive available. Test applications give good reproduction of highly variable experimental mass yields. This novel general approach requires only a single new global parameter, namely, the critical neck size at which the mass split is frozen in, and the results are remarkably insensitive to its specific value. © 2011 American Physical Society.

Donev A.,Courant Institute of Mathematical Sciences | Bell J.B.,Lawrence Berkeley National Laboratory | De La Fuente A.,San Jose State University | Garcia A.L.,San Jose State University
Physical Review Letters | Year: 2011

We study the contribution of advection by thermal velocity fluctuations to the effective diffusion coefficient in a mixture of two identical fluids. We find good agreement between a simple fluctuating hydrodynamics theory and particle and finite-volume simulations. The enhancement of the diffusive transport depends on the system size L and grows as ln(L/L0) in quasi-two-dimensional systems, while in three dimensions it scales as L0-1-L-1, where L0 is a reference length. Our results demonstrate that fluctuations play an important role in the hydrodynamics of small-scale systems. © 2011 American Physical Society.

Yan L.,French National Center for Scientific Research | Ollitrault J.-Y.,French National Center for Scientific Research | Poskanzer A.M.,Lawrence Berkeley National Laboratory
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2015

Elliptic flow in ultrarelativistic heavy-ion collisions results from the hydrodynamic response to the spatial anisotropy of the initial density profile. A long-standing problem in the interpretation of flow data is that uncertainties in the initial anisotropy are mingled with uncertainties in the response. We argue that the non-Gaussianity of flow fluctuations in small systems with large fluctuations can be used to disentangle the initial state from the response. We apply this method to recent measurements of anisotropic flow in Pb+Pb and p+Pb collisions at the LHC, assuming linear response to the initial anisotropy. The response coefficient is found to decrease as the system becomes smaller and is consistent with a low value of the ratio of viscosity over entropy of η/. s≃. 0.19. Deviations from linear response are studied. While they significantly change the value of the response coefficient they do not change the rate of decrease with centrality. Thus, we argue that the estimate of η/. s is robust against non-linear effects. © 2015 The Authors.

Chon M.J.,Brown University | Sethuraman V.A.,Brown University | McCormick A.,Brown University | Srinivasan V.,Lawrence Berkeley National Laboratory | Guduru P.R.,Brown University
Physical Review Letters | Year: 2011

Crystalline to amorphous phase transformation during initial lithiation in (100) Si wafers is studied in an electrochemical cell with Li metal as the counter and reference electrode. During initial lithiation, a moving phase boundary advances into the wafer starting from the surface facing the lithium electrode, transforming crystalline Si into amorphous LixSi. The resulting biaxial compressive stress in the amorphous layer is measured insitu, and it was observed to be ca. 0.5GPa. High-resolution TEM images reveal a very sharp crystalline-amorphous phase boundary, with a thickness of ∼1nm. Upon delithiation, the stress rapidly reverses and becomes tensile, and the amorphous layer begins to deform plastically at around 0.5GPa. With continued delithiation, the yield stress increases in magnitude, culminating in a sudden fracture of the amorphous layer into microfragments, and the cracks extend into the underlying crystalline Si. © 2011 American Physical Society.

Bousso R.,University of California at Berkeley | Bousso R.,Lawrence Berkeley National Laboratory
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

The firewall paradox is often presented as arising from double entanglement, but I argue that more generally the paradox is double purity. Near-horizon modes are purified by the interior, in the infalling vacuum. Hence, they cannot also be pure alone, or in combination with any third system, as demanded by unitarity. This conflict arises independently of the Page time, for entangled and for pure states. It implies that identifications of Hilbert spaces cannot resolve the paradox. Traditional complementarity requires the unitary identification of infalling matter with a scrambled subsystem of the Hawking radiation. Extending this map to the infalling vacuum overdetermines the out-state. More general complementarity maps ("A=RB," "ER=EPR") necessarily fail when the near-horizon zone is pure. I argue that pure-zone states span the microcanonical ensemble, and that this suffices to make the horizon a special place. I advocate that the ability to detect the horizon locally, rather than the degree or probability of violence, is what makes firewalls problematic. Conversely, if the production of matter at the horizon can be dynamically understood and shown to be consistent, then firewalls do not constitute a violation of the equivalence principle. © 2013 American Physical Society.

Jack R.L.,University of Bath | Hedges L.O.,Lawrence Berkeley National Laboratory | Garrahan J.P.,University of Nottingham | Chandler D.,University of California at Berkeley
Physical Review Letters | Year: 2011

We prepare metastable glassy states in a model glass former made of Lennard-Jones particles by sampling biased ensembles of trajectories with low dynamical activity. These trajectories form an inactive dynamical phase whose "fast" vibrational degrees of freedom are maintained at thermal equilibrium by contact with a heat bath, while the "slow" structural degrees of freedom are located in deep valleys of the energy landscape. We examine the relaxation to equilibrium and the vibrational properties of these metastable states. The glassy states we prepare by our trajectory sampling method are very stable to thermal fluctuations and also more mechanically rigid than low-temperature equilibrated configurations. © 2011 American Physical Society.

Chanowitz M.S.,Lawrence Berkeley National Laboratory
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

If the Higgs-like particle at 125 GeV is the Standard Model (SM) Higgs boson, then SM4, the simplest four generation (4G) extension of the SM, is inconsistent with the most recent LHC data. However, 4G variations (BSM4) are possible if the new particle is not the SM Higgs boson and/or if other new quanta modify its production and decay rates. Since LHC searches have pushed 4G quarks to high mass and strong coupling where perturbation theory eventually fails, we examine the leading nondecoupling electroweak (EW) corrections at two loop order to estimate the domain of validity for perturbation theory. We find that the two loop hypercharge correction, which has not been included in previous EW fits of 4G models, makes the largest quark sector contribution to the rho parameter, much larger even than the nominally leading one loop term. Because it is large and negative, it has a big effect on the EW fits. It does not invalidate perturbation theory since it only first appears at two loop order and is large because it does not vanish for equal quark doublet masses, unlike the one loop term. We estimate that perturbation theory is useful for m Q 600 GeV but begins to become marginal for mQ 900 GeV. The results apply directly to BSM4 models that retain the SM Higgs sector but must be reevaluated for non-SM Higgs sectors. © 2013 American Physical Society.

Kang Z.-B.,Brookhaven National Laboratory | Xiao B.-W.,Pennsylvania State University | Yuan F.,Brookhaven National Laboratory | Yuan F.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2011

We study the transverse momentum dependent factorization for single spin asymmetries in Drell-Yan and semi-inclusive deep inelastic scattering processes at one-loop order. The next-to-leading order hard factors are calculated in the Ji-Ma-Yuan factorization scheme. We further derive the QCD resummation formalisms for these observables following the Collins-Soper-Sterman method. The results are expressed in terms of the collinear correlation functions from initial and/or final state hadrons coupled with the Sudakov form factor containing all order soft-gluon resummation effects. The scheme-independent coefficients are calculated up to one-loop order. © 2011 American Physical Society.

Bailey S.,Lawrence Berkeley National Laboratory
Publications of the Astronomical Society of the Pacific | Year: 2012

We present a method for performing principal component analysis (PCA) on noisy datasets with missing values. Estimates of the measurement error are used to weight the input data such that the resulting eigenvectors, when compared to classic PCA, are more sensitive to the true underlying signal variations rather than being pulled by heteroskedastic measurement noise. Missing data are simply limiting cases of weight 1/4 0. The underlying algorithm is a noise weighted expectation maximization (EM) PCA, which has additional benefits of implementation speed and flexibility for smoothing eigenvectors to reduce the noise contribution. We present applications of this method on simulated data and QSO spectra from the Sloan Digital Sky Survey (SDSS). © 2012. The Astronomical Society of the Pacific.

This study reveals the interrelationships among a variety of policies supporting solar energy adoption in the U.S. and then calculates the amount of financial subsidies required to support mandatory policies such as Renewable Portfolio Standard (RPS). To illuminate interrelationships among these policies, this study proposes three tiers of descriptive model: the top tier includes mandatory policies such as the Renewable Portfolio Standard (RPS); the middle tier is composed of financial support mechanisms, such as tax credit and rebates; and the bottom tier comprises policies that provide funding sources, such as Public Benefit funds. Based on our proposed model, this study further builds a model which calculates the amount of financial subsidies required to support RPS targets of distributed photovoltaics (PV) adoption. The model is applied to the case study of idential PV adoption in the state of Arizona by 2025. The financial requirements are calculated considering of the uncertainty of federal tax credits (extension or termination after 2016) and compared with planned funds that support PV adoption. This study points out that if states would pursue a sustainable PV adoption targets, they should make more efforts on financial support programs. © 2013 Elsevier Ltd.

Anders A.,Lawrence Berkeley National Laboratory
Surface and Coatings Technology | Year: 2011

High power impulse magnetron sputtering (HIPIMS) is pulsed sputtering where the peak power exceeds the time-averaged power by typically two orders of magnitude. The peak power density, averaged over the target area, can reach or exceed 107W/m2, leading to plasma conditions that make ionization of the sputtered atoms very likely. A brief review of HIPIMS operation is given in a tutorial manner, illustrated by some original data related to the self-sputtering of niobium in argon and krypton. Emphasis is put on the current-voltage-time relationships near the threshold of self-sputtering runaway. The great variety of current pulse shapes delivers clues on the very strong gas rarefaction, self-sputtering runaway conditions, and the stopping of runaway due to the evolution of atom ionization and ion return probabilities as the gas plasma is replaced by metal plasma. The discussions are completed by considering instabilities and the special case of "gasless" self-sputtering. © 2011 Elsevier B.V.

Zhang Q.,Lawrence Berkeley National Laboratory
Computer Methods in Applied Mechanics and Engineering | Year: 2011

The author presents a polynomial-based algorithm for high-order multidimensional interpolation at the coarse-fine interface in the context of adaptive mesh refinement on structured Cartesian grids. The proposed algorithm reduces coarse-fine interpolation to matrix-vector products by exploiting the static mesh geometry and a family of nonsingularity-preserving stencil transformations. As such, no linear system is solved at the runtime and the ill-conditioning of Vandermonde matrix is avoided. The algorithm is also generic in that D, the dimensionality of the computational domain, and p, the degree of the interpolating polynomial, are both arbitrary positive integers. Stability and accuracy are verified by interpolating simple functions, and by applying the proposed method to adaptively solving Poisson's equation and the convection-diffusion equation. The companion MATLAB® package, AMRCFI, is also freely available for convenience and more implementation details. © 2011 Elsevier B.V.

Lee D.-H.,University of California at Berkeley | Lee D.-H.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2011

We study the Sz-conserving quantum spin Hall insulator in the presence of Hubbard U from a field theory point of view. The main findings are the following. (1) For arbitrarily small U the edges possess power-law correlated antiferromagnetic XY local moments. Gapless charge excitations arise from the Goldstone-Wilczek mechanism. (2) Electron tunneling between opposite edges allows vortex instantons to proliferate when K, the XY stiffness constant, satisfies 4πK+(4πK)-1<4. When the preceding inequality is violated, the edge modes remain gapless despite the sample width being finite. (3) The phase transition from the topological insulator to the large U antiferromagnetic insulator is triggered by the condensation of magnetic excitons. (4) In the large U antiferromagnetic insulating phase the magnetic vortices carry charges proportional to the square magnitude of the antiferromagnetic order parameter. © 2011 American Physical Society.

Watanabe H.,University of California at Berkeley | Murayama H.,University of California at Berkeley | Murayama H.,Lawrence Berkeley National Laboratory | Murayama H.,University of Tokyo
Physical Review Letters | Year: 2013

We propose a simple criterion to identify when Nambu-Goldstone bosons for different symmetries are redundant. It solves an old mystery why crystals have phonons for spontaneously broken translations but no gapless excitations for equally spontaneously broken rotations. Similarly for a superfluid, the Nambu-Goldstone boson for spontaneously broken Galilean symmetry is redundant with phonons. The most nontrivial example is Tkachenko mode for a vortex lattice in a superfluid, where phonons are redundant to the Tkachenko mode which is identified as the Boboliubov mode. © 2013 American Physical Society.

Orenstein J.,University of California at Berkeley | Orenstein J.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2011

Rotation of the plane of polarization of reflected light (Kerr effect) is a direct manifestation of broken time-reversal symmetry and is generally associated with the appearance of a ferromagnetic moment. Here I identify magnetic structures that may arise within the unit cell of cuprate superconductors that generate polarization rotation despite the absence of a net moment. For these magnetic symmetries the Kerr effect is mediated by magnetoelectric coupling, which can arise when antiferromagnetic order breaks inversion symmetry. The structures identified are candidates for a time-reversal breaking phase in the pseudogap regime of the cuprates. © 2011 American Physical Society.

Berryman J.G.,Lawrence Berkeley National Laboratory | Hoversten G.M.,Chevron
Geophysical Prospecting | Year: 2013

Effective-medium theories for either highly conductive or more resistive electrical inclusions in a moderately conducting background medium are presented for modelling macroscopic (i.e., large-scale) fluid-filled fractures or cracks in a potential reservoir rock or granular medium. Conductive fluids are most often brine and the resistive fluids of interest are oil, gas, air and/or CO2. Novel features of the presentation for conductive fluids include results for both non-interacting inclusions (using a Maxwell approximation) and for interacting inclusions (via a self-consistent effective-medium scheme). The anisotropic analysis is specifically designed to handle reservoirs with multiple orientations (usually three orthogonal sets) of oblate spheroidal cracks/fractures, while also having arbitrary aspect ratios. But these aspect ratios are strictly <1, thus excluding spherical pores and simple granular media - both already widely studied by others. Results show that the self-consistent approximation depends on fracture aspect ratio α and that this approximation becomes important when fracture porosity is about φ= 1% for aspect ratio α≃ 0.05, or φ= 3% for aspect ratio α≃ 0.10. It is shown that the self-consistent analysis is most important when the fractures have a very small aspect ratio - the inferred reason being that the fracture (or crack) number density (ρc≡φ/α) then becomes very high and the fracture relative spacing correspondingly very small for any fixed value of porosity (but with decreasing values of the aspect ratio). Hybrid methods (combining self-consistent and non-self consistent formulas) are also developed to deal with high volume fractions and multiple sets of fractures having different aspect ratios. Whenever possible and appropriate, the results are also compared to rigorous bounds, including the Wiener bounds and the Hashin-Shtrikman bounds, in order to provide one type of partial validation of the methods being developed. © 2012 European Association of Geoscientists & Engineers.

Purpose: Current physical activity recommendations assume that different activities can be exchanged to produce the same weight-control benefits so long as total energy expended remains the same (exchangeability premise). To this end, they recommend calculating energy expenditure as the product of the time spent performing each activity and the activity's metabolic equivalents (MET), which may be summed to achieve target levels. The validity of the exchangeability premise was assessed using data from the National Runners' Health Study. Methods: Physical activity dose was compared to body mass index (BMI) and body circumferences in 33,374 runners who reported usual distance run and pace, and usual times spent running and other exercises per week. MET hours per day (METhr/d) from running was computed from: a) time and intensity, and b) reported distance run (1.02 MET•hours per km). Results: When computed from time and intensity, the declines (slope±SE) per METhr/d were significantly greater (P<10-15) for running than non-running exercise for BMI (slopes±SE, male: -0.12±0.00 vs. 0.00±0.00; female: -0.12±0.00 vs. -0.01±0.01 kg/m2 per METhr/d) and waist circumference (male: -0.28±0.01 vs. -0.07±0.01; female: -0. 31±0.01 vs. -0.05±0.01 cm per METhr/d). Reported METhr/d of running was 38% to 43% greater when calculated from time and intensity than distance. Moreover, the declines per METhr/d run were significantly greater when estimated from reported distance for BMI (males: -0.29±0.01; females: -0.27±0.01 kg/m2 per METhr/d) and waist circumference (males: -0.67±0.02; females: -0.69±0.02 cm per METhr/d) than when computed from time and intensity (cited above). Conclusion: The exchangeability premise was not supported for running vs. non-running exercise. Moreover, distance-based running prescriptions may provide better weight control than time-based prescriptions for running or other activities. Additional longitudinal studies and randomized clinical trials are required to verify these results prospectively.

Ishizaki A.,University of California at Berkeley | Fleming G.R.,Lawrence Berkeley National Laboratory
Journal of Physical Chemistry B | Year: 2011

The observation of long-lived electronic quantum coherence in a photosynthetic light harvesting system [Engel et al. Nature2007, 446, 782] has led to much effort being devoted to elucidation of the quantum mechanisms of the photosynthetic excitation energy transfer. In this paper we examine the question of whether the decay of the coherent beating signal is due to quantum mechanical decoherence or ensemble dephasing (also called "fake decoherence"). We compare results based on the quantum master equation description of the time-evolution of the reduced density matrix with a mixed quantum/classical approach where the ensemble average is calculated after the dynamics. The two methods show good agreement with results from the quantum master equation in terms of the decay of quantum coherent oscillations when ensemble average is considered for the mixed quantum/classical approach. However, the results also demonstrate it remains possible that the quantum coherent motion is robust under individual realizations of the environment-induced fluctuations contrary to intuition obtained from the reduced density matrices, indicating that the decay of the observed quantum coherence should be understood as ensemble dephasing. Our calculations imply that coherence is a property of the pigment-protein system, not simply the preparation method of the electronic excitation. © 2011 American Chemical Society.

Hall L.J.,Lawrence Berkeley National Laboratory | Nomura Y.,University of California at Berkeley
Journal of High Energy Physics | Year: 2014

With minimal field content and for an interesting range of the supersymmetric Higgs mixing parameter, 0.5 ≲ tan2β ≲ 2, the superpartner mass scale, m, is found to be at the intermediate scale, ∼ 1010±1 GeV, near where the Standard Model Higgs quartic coupling passes through zero. For any 4d supersymmetric grand unified symmetry spontaneously broken by a vacuum expectation value (∑), if superpotential interactions for ∑ are forbidden e.g. by R symmetries, the uneaten color octet, ∑8, and weak triplet, ∑3, have masses of order m. The combination of superpartner and∑8,3 states leads to successful gauge coupling unification, removing the disastrously high proton decay rate of minimal Standard Model unification. Proton decay could be seen in future experiments if m 1011 GeV, but not if it is lower. If the reheating temperature after inflation, TR, is less than m dark matter may be axions. If TR > m, thermal LSP dark matter may lead to the environmental selection of a TeV-scale LSP, either wino or Higgsino, which could comprise all or just one component of dark matter. In the Higgsino case, the dark matter is found to behave inelastically in direct detection experiments, and gauge coupling unification occurs accurately without the need of any threshold corrections. Open Access, © 2014 The Authors.

Williams P.T.,Lawrence Berkeley National Laboratory
PLoS ONE | Year: 2012

Objective: Physical activity has been shown to attenuate the effect of the FTO polymorphism on body weight, and the heritability of body weight in twin and in family studies. The dose-response relationship between activity and the risk for inherited obesity is not well known, particularly for higher doses of vigorous exercise. Such information is needed to best prescribe an exercise dose for obesity prevention in those at risk due to their family history. Design: We therefore analyzed self-reported usual running distance, body mass index (BMI), waist circumference, and mother's and father's adiposity (1 = lean, 2 = normal, 3 = overweight, and 4 = very overweight) from survey data collected on 33,480 male and 14,211 female runners. Age-, education-, and alcohol-adjusted regression analyses were used to estimate the contribution of parental adiposities to the BMI and waist circumferences in runners who ran an average of <3, 3-6, 6-9, ≥9 km/day. Results: BMI and waist circumferences of runners who ran <3 km/day were significantly related to their parents adiposity (P<10 -15 and P<10 -11, respectively). These relationships (i.e., kg/m 2 or cm per increment in parental adiposity) diminished significantly with increasing running distance for both BMI (inheritance×exercise interaction, males: P<10 -10; females: P<10 -5) and waist circumference (inheritance×exercise interaction, males: P<10 -9; females: P = 0.004). Compared to <3 km/day, the parental contribution to runners who averaged ≥9 km/day was diminished by 48% for male BMI, 58% for female BMI, 55% for male waist circumference, and 58% for female waist circumference. These results could not be attributed to self-selection. Conclusions: Exceeding the minimum exercise dose currently recommended for general health benefits (energy equivalent to running 2-3 km/day) may substantially diminish the risk for inherited obesity. The results are consistent with other research suggesting the physical activity dose required to prevent unhealthy weight gain is greater than that recommended for other health benefits.

Bousso R.,University of California at Berkeley | Bousso R.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2014

If information escapes from an evaporating black hole, then field modes just outside the horizon must be thermally entangled with distant Hawking radiation. But for an infalling observer to find empty space at the horizon, the same modes would have to be entangled with the black hole interior. Thus, unitarity appears to require a "firewall" at the horizon. Identifying the interior with the distant radiation promises to resolve the entanglement conflict and restore the vacuum. But the map must adjust for any interactions, or else the firewall will reappear if the Hawking radiation scatters off the cosmic microwave background. Such a map produces a "frozen vacuum," a phenomenon that is arguably worse than a firewall. An infalling observer is unable to excite the vacuum near the horizon. This allows the horizon to be locally detected and so violates the equivalence principle. © 2014 American Physical Society.

Groom D.E.,Lawrence Berkeley National Laboratory
Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment | Year: 2013

The DREAM collaboration has introduced the Q/S Method for obtaining the energy estimator from simultaneous Cherenkov and scintillator readouts of individual hadronic events. I show that the algorithm is equivalent to an elementary method.

O'Brien K.,University of California at Berkeley | Macklin C.,University of California at Berkeley | Siddiqi I.,University of California at Berkeley | Zhang X.,University of California at Berkeley | Zhang X.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2014

We propose a technique to overcome phase mismatch in Josephson-junction traveling wave parametric amplifiers in order to achieve high gain over a broad bandwidth. Using "resonant phase matching," we design a compact superconducting device consisting of a transmission line with subwavelength resonant inclusions that simultaneously achieves a gain of 20 dB, an instantaneous bandwidth of 3 GHz, and a saturation power of -98dBm. Such an amplifier is well suited to cryogenic broadband microwave measurements such as the multiplexed readout of quantum coherent circuits based on superconducting, semiconducting, or nanomechanical elements, as well as traditional astronomical detectors. © 2014 American Physical Society.

Yan H.,North Carolina State University | Wang C.,Lawrence Berkeley National Laboratory | McCarn A.R.,North Carolina State University | Ade H.,North Carolina State University
Physical Review Letters | Year: 2013

A practical and accurate method to obtain the index of refraction, especially the decrement δ, across the carbon 1s absorption edge is demonstrated. The combination of absorption spectra scaled to the Henke atomic scattering factor database, the use of the doubly subtractive Kramers-Kronig relations, and high precision specular reflectivity measurements from thin films allow the notoriously difficult-to-measure δ to be determined with high accuracy. No independent knowledge of the film thickness or density is required. High confidence interpolation between relatively sparse measurements of δ across an absorption edge is achieved. Accurate optical constants determined by this method are expected to greatly improve the simulation and interpretation of resonant soft x-ray scattering and reflectivity data. The method is demonstrated using poly(methyl methacrylate) and should be extendable to all organic materials. © 2013 American Physical Society.

Diz-Munoz A.,University of California at Berkeley | Diz-Munoz A.,University of California at San Francisco | Fletcher D.A.,University of California at Berkeley | Fletcher D.A.,Lawrence Berkeley National Laboratory | Weiner O.D.,University of California at San Francisco
Trends in Cell Biology | Year: 2013

Many cell phenomena that involve shape changes are affected by the intrinsic deformability of the plasma membrane (PM). Far from being a passive participant, the PM is now known to physically, as well as biochemically, influence cell processes ranging from vesicle trafficking to actin assembly. Here we review current understanding of how changes in PM tension regulate cell shape and movement, as well as how cells sense PM tension. © 2012 Elsevier Ltd.

Lu Y.-M.,University of California at Berkeley | Lu Y.-M.,Lawrence Berkeley National Laboratory | Wang Z.,Boston College
Physical Review Letters | Year: 2013

Realizations of Majorana fermions in solid state materials have attracted great interest recently in connection to topological order and quantum information processing. We propose a novel way to create Majorana fermions in superconductors. We show that an incipient noncollinear magnetic order turns a spin-singlet superconductor with nodes into a topological superconductor with a stable Majorana bound state in the vortex core, at a topologically stable magnetic point defect, and on the edge. We argue that such an exotic non-Abelian phase can be realized in extended t-J models on the triangular and square lattices. It is promising to search for Majorana fermions in correlated electron materials where nodal superconductivity and magnetism are two common caricatures. © 2013 American Physical Society.

Hochberg Y.,Lawrence Berkeley National Laboratory | Hochberg Y.,University of California at Berkeley | Kuflik E.,Tel Aviv University | Volansky T.,Tel Aviv University | Wacker J.G.,SLAC
Physical Review Letters | Year: 2014

We present a new paradigm for achieving thermal relic dark matter. The mechanism arises when a nearly secluded dark sector is thermalized with the standard model after reheating. The freeze-out process is a number-changing 3→2 annihilation of strongly interacting massive particles (SIMPs) in the dark sector, and points to sub-GeV dark matter. The couplings to the visible sector, necessary for maintaining thermal equilibrium with the standard model, imply measurable signals that will allow coverage of a significant part of the parameter space with future indirect- and direct-detection experiments and via direct production of dark matter at colliders. Moreover, 3→2 annihilations typically predict sizable 2→2 self-interactions which naturally address the "core versus cusp" and "too-big-to-fail" small-scale structure formation problems. © 2014 American Physical Society.

Groom D.E.,Lawrence Berkeley National Laboratory
Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment | Year: 2013

If the scintillator response to a hadronic shower in a semi-infinite uniform calorimeter structure is S relative to the electronic response, then S/E=[fem+(1-fem)(h/e)], where E is the incident hadron energy, fem is the electronic shower fraction, and h/e is the hadron/electron response ratio. If there is also a simultaneous readout with a different h/e, say a Cherenkov signal C, then a linear combination of the two signals provides an estimator of E that is proportional to the incident energy and whose distribution is nearly Gaussian - even though the S and C distributions are non-linear in E, wide, and skewed. Since an estimator of fem is also obtained, it is no longer a stochastic variable. Much of the remaining resolution variance is due to sampling fluctuations. These can be avoided in a homogeneous calorimeter. The energy resolution depends upon the contrast in h/e between the two channels. h/e is small in the Cherenkov channel. Mechanisms that increase h/e in sampling calorimeters with organic scintillator readout are not available in a homogeneous inorganic scintillator calorimeter. The h/e contrast is very likely too small to provide the needed energy resolution. © 2012 Elsevier B.V.

Campisi J.,Buck Institute for Research on Aging | Campisi J.,Lawrence Berkeley National Laboratory
Annual Review of Physiology | Year: 2013

For most species, aging promotes a host of degenerative pathologies that are characterized by debilitating losses of tissue or cellular function. However, especially among vertebrates, aging also promotes hyperplastic pathologies, the most deadly of which is cancer. In contrast to the loss of function that characterizes degenerating cells and tissues, malignant (cancerous) cells must acquire new (albeit aberrant) functions that allow them to develop into a lethal tumor. This review discusses the idea that, despite seemingly opposite characteristics, the degenerative and hyperplastic pathologies of aging are at least partly linked by a common biological phenomenon: a cellular stress response known as cellular senescence. The senescence response is widely recognized as a potent tumor suppressive mechanism. However, recent evidence strengthens the idea that it also drives both degenerative and hyperplastic pathologies, most likely by promoting chronic inflammation. Thus, the senescence response may be the result of antagonistically pleiotropic gene action. Copyright © 2013 by Annual Reviews. All rights reserved.

Gregorich K.E.,Lawrence Berkeley National Laboratory
Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment | Year: 2013

A computer code has been developed to simulate the production of heavy element compound nucleus recoils and their trajectories through gas-filled magnetic separators. The simulation is carried out in three steps: positions and trajectories of heavy element recoils in the target layer, propagation through remaining target material, and trajectories through the gas-filled separator. Separators with quite different magnetic configurations are modeled: the Berkeley gas-filled separator (BGS) and two magnetic configurations for the TransActinide separator and chemistry apparatus (TASCA). While computing trajectories through the gas-filled separator, special attention is paid to the charge exchange/equilibration and scattering in the gas. New features of these simulations include mixed He/H2/N2 gas operation and a gas density (pressure) effect. Numerical procedures used in the simulations are explained in detail. Results of the simulations are presented, showing the gas mixtures/pressures that result in the highest efficiency for collecting compound nucleus recoils at the focal plane of the gas-filled separator. Comparison between simulation and experimental results are presented for average recoil ion charge in various gases, focal plane image size, and magnetic rigidity dispersion.

Balitsky I.,Old Dominion University | Balitsky I.,Jefferson Lab | Chirilli G.A.,Lawrence Berkeley National Laboratory
Physical Review D - Particles, Fields, Gravitation and Cosmology | Year: 2013

The photon impact factor for the Balitsky-Fadin-Kuraev-Lipatov pomeron is calculated in the next-to-leading order approximation using the operator expansion in Wilson lines. The result is represented as a next-to-leading order kT-factorization formula for the structure functions of small-x deep inelastic scattering. © 2013 American Physical Society.

Iyer-Biswas S.,James Franck Institute | Crooks G.E.,Lawrence Berkeley National Laboratory | Scherer N.F.,James Franck Institute | Dinner A.R.,James Franck Institute
Physical Review Letters | Year: 2014

Recent imaging data for single bacterial cells reveal that their mean sizes grow exponentially in time and that their size distributions collapse to a single curve when rescaled by their means. An analogous result holds for the division-time distributions. A model is needed to delineate the minimal requirements for these scaling behaviors. We formulate a microscopic theory of stochastic exponential growth as a Master Equation that accounts for these observations, in contrast to existing quantitative models of stochastic exponential growth (e.g., the Black-Scholes equation or geometric Brownian motion). Our model, the stochastic Hinshelwood cycle (SHC), is an autocatalytic reaction cycle in which each molecular species catalyzes the production of the next. By finding exact analytical solutions to the SHC and the corresponding first passage time problem, we uncover universal signatures of fluctuations in exponential growth and division. The model makes minimal assumptions, and we describe how more complex reaction networks can reduce to such a cycle. We thus expect similar scalings to be discovered in stochastic processes resulting in exponential growth that appear in diverse contexts such as cosmology, finance, technology, and population growth. © 2014 American Physical Society.

Pletikosic I.,Princeton University | Pletikosic I.,Brookhaven National Laboratory | Ali M.N.,Princeton University | Fedorov A.V.,Lawrence Berkeley National Laboratory | And 2 more authors.
Physical Review Letters | Year: 2014

The electronic structure basis of the extremely large magnetoresistance in layered nonmagnetic tungsten ditelluride has been investigated by angle-resolved photoelectron spectroscopy. Hole and electron pockets of approximately the same size were found at low temperatures, suggesting that carrier compensation should be considered the primary source of the effect. The material exhibits a highly anisotropic Fermi surface from which the pronounced anisotropy of the magnetoresistance follows. A change in the Fermi surface with temperature was found and a high-density-of-states band that may take over conduction at higher temperatures and cause the observed turn-on behavior of the magnetoresistance in WTe2 was identified. © 2014 American Physical Society.

Kang J.,University of Minnesota | Kemper A.F.,Lawrence Berkeley National Laboratory | Fernandes R.M.,University of Minnesota
Physical Review Letters | Year: 2014

In the iron pnictides and chalcogenides, multiple orbitals participate in the superconducting state, enabling different gap structures to be realized in distinct materials. Here we argue that the spectral weights of these orbitals can, in principle, be controlled by a tetragonal symmetry-breaking uniaxial strain, due to the enhanced nematic susceptibility of many iron-based superconductors. By investigating multiorbital microscopic models in the presence of orbital order, we show that not only Tc can be enhanced, but pairs of accidental gap nodes can be annihilated and created in the Fermi surface by an increasing external strain. We explain our results as a mixture of nearly degenerate superconducting states promoted by strain, and show that the annihilation and creation of nodes can be detected experimentally via anisotropic penetration depth measurements. Our results provide a promising framework to externally control the superconducting properties of iron-based materials. © 2014 American Physical Society.

Crivellin A.,CERN | Crivellin A.,University of Bern | D'Eramo F.,University of California at Berkeley | D'Eramo F.,Lawrence Berkeley National Laboratory | Procura M.,University of Bern
Physical Review Letters | Year: 2014

We consider an effective field theory for a gauge singlet Dirac dark matter particle interacting with the standard model fields via effective operators suppressed by the scale Λ1TeV. We perform a systematic analysis of the leading loop contributions to spin-independent Dirac dark matter-nucleon scattering using renormalization group evolution between Λ and the low-energy scale probed by direct detection experiments. We find that electroweak interactions induce operator mixings such that operators that are naively velocity suppressed and spin dependent can actually contribute to spin-independent scattering. This allows us to put novel constraints on Wilson coefficients that were so far poorly bounded by direct detection. Constraints from current searches are already significantly stronger than LHC bounds, and will improve in the near future. Interestingly, the loop contribution we find is isospin violating even if the underlying theory is isospin conserving. © 2014 American Physical Society.

Heinke L.,University of Leipzig | Heinke L.,Fritz Haber Institute of the Max Planck Society | Heinke L.,Lawrence Berkeley National Laboratory | Karger J.,University of Leipzig
Physical Review Letters | Year: 2011

The rates of uptake and release of guest molecules in nanoporous solids are often strongly influenced or even controlled by transport resistances at the external surface ("surface barriers") rather than by intraparticle diffusion, which was assumed to be rate controlling in many of the earlier kinetic studies. By correlating the surface resistance with the intracrystalline diffusivity, we develop here a microkinetic model which closely reproduces the experimentally observed results for short-chain alkanes in Zn(tbip), a member of the novel metal-organic framework family of nanoporous materials. It seems likely that this mechanism, which is shown to provide a rational explanation of the commonly observed discrepancies between "macro" and "micro" measurements of intracrystalline diffusion, may be fairly general. © 2011 American Physical Society.

Lu P.,General Motors | Li C.,View Inc | Schneider E.W.,General Motors | Harris S.J.,Lawrence Berkeley National Laboratory
Journal of Physical Chemistry C | Year: 2014

The solid electrolyte interphase (SEI) forms during the initial cycles in lithium ion batteries and evolves throughout the battery life. By protecting the electrode and passing lithium ions, the SEI plays an important role in the performance and degradation of lithium ion batteries. Identifying how the SEI forms and evolves during battery cycling helps us understand and mitigate battery degradation. In this work, we address the SEI chemical and electrochemical evolution during its formation process and provide a correlation between these properties. It is found that the SEI chemistry, not just its thickness, has a distinct influence on its impedance, which may ultimately impact the battery performance. © 2013 American Chemical Society.

Crumlin E.J.,Lawrence Berkeley National Laboratory
Nature Materials | Year: 2016

Segregation and phase separation of aliovalent dopants on perovskite oxide (ABO3) surfaces are detrimental to the performance of energy conversion systems such as solid oxide fuel/electrolysis cells and catalysts for thermochemical H2O and CO2 splitting. One key reason behind the instability of perovskite oxide surfaces is the electrostatic attraction of the negatively charged A-site dopants (for example, ) by the positively charged oxygen vacancies () enriched at the surface. Here we show that reducing the surface concentration improves the oxygen surface exchange kinetics and stability significantly, albeit contrary to the well-established understanding that surface oxygen vacancies facilitate reactions with O2 molecules. We take La0.8Sr0.2CoO3 (LSC) as a model perovskite oxide, and modify its surface with additive cations that are more and less reducible than Co on the B-site of LSC. By using ambient-pressure X-ray absorption and photoelectron spectroscopy, we proved that the dominant role of the less reducible cations is to suppress the enrichment and phase separation of Sr while reducing the concentration of and making the LSC more oxidized at its surface. Consequently, we found that these less reducible cations significantly improve stability, with up to 30 times faster oxygen exchange kinetics after 54 h in air at 530 °C achieved by Hf addition onto LSC. Finally, the results revealed a ‘volcano’ relation between the oxygen exchange kinetics and the oxygen vacancy formation enthalpy of the binary oxides of the additive cations. This volcano relation highlights the existence of an optimum surface oxygen vacancy concentration that balances the gain in oxygen exchange kinetics and the chemical stability loss. © 2016 Nature Publishing Group

Frauendorf S.,University of Notre Dame | Macchiavelli A.O.,Lawrence Berkeley National Laboratory
Progress in Particle and Nuclear Physics | Year: 2014

The role of neutron-proton pairing correlations on the structure of nuclei along the N=Z line is reviewed. Particular emphasis is placed on the competition between isovector (T=1) and isoscalar (T=0) pair fields. The expected properties of these systems, in terms of pairing collective motion, are assessed by different theoretical frameworks including schematic models, realistic Shell Model and mean field approaches. The results are contrasted with experimental data with the goal of establishing clear signals for the existence of neutron-proton (np) condensates. We will show that there is clear evidence for an isovector np condensate as expected from isospin invariance. However, and contrary to early expectations, a condensate of deuteron-like pairs appears quite elusive and pairing collectivity in the T=0 channel may only show in the form of a phonon. Arguments are presented for the use of direct reactions, adding or removing an np pair, as the most promising tool to provide a definite answer to this intriguing question. © 2014 Elsevier B.V. All rights reserved.

Williams P.T.,Lawrence Berkeley National Laboratory
American Journal of Cardiology | Year: 2010

Cardiorespiratory fitness has often been interpreted as a surrogate measurement of physical activity rather than an independent coronary heart disease (CHD) risk factor per se. Fitness is also known to be highly heritable, however, and rats bred selectively for treadmill endurance have low CHD risk phenotypes even in the absence of physical activity. Therefore, I assessed whether cardiorespiratory fitness predicted CHD independent of physical activity in 29,721 men followed prospectively for 7.7 years as part of the National Runners' Health Study. Specifically, CHD deaths and incident participant-reported physician-diagnosed myocardial infarction, revascularization procedures (coronary artery bypass grafting and percutaneous coronary intervention), and angina pectoris during follow-up were compared to baseline cardiorespiratory fitness (10-km footrace performance, meters/second). Nonfatal end points for the 80% of these men who provided follow-up questionnaires included 121 nonfatal myocardial infarctions, 317 revascularization procedures, and 81 angina pectora. The National Death Index identified 44 CHD deaths. Per meter/second increment in baseline fitness, men's risks decreased 54% for nonfatal myocardial infarction (p <0.0001), 44% for combined CHD deaths and nonfatal myocardial infarction (p = 0.0003), 53% for angina pectoris (p = 0.001), and 32% for revascularizations (p = 0.002). Adjustment for physical activity (kilometer/day run) had little effect on the per meter/second risk decreases for nonfatal myocardial infarction (from 64% to 63%), combined CHD deaths and nonfatal myocardial infarction (from 34% to 33%), angina pectoris (from 53% to 47%) or revascularizations (from 32% to 26%). In conclusion, the results suggest that cardiorespiratory fitness is a CHD risk factor, largely independent of physical activity, which warrants clinical screening. © 2010 Elsevier Inc. All rights reserved.

Knowles D.W.,Lawrence Berkeley National Laboratory
Wiley interdisciplinary reviews. Developmental biology | Year: 2013

Animals comprise dynamic three-dimensional arrays of cells that express gene products in intricate spatial and temporal patterns that determine cellular differentiation and morphogenesis. A rigorous understanding of these developmental processes requires automated methods that quantitatively record and analyze complex morphologies and their associated patterns of gene expression at cellular resolution. Here we summarize light microscopy-based approaches to establish permanent, quantitative datasets-atlases-that record this information. We focus on experiments that capture data for whole embryos or large areas of tissue in three dimensions, often at multiple time points. We compare and contrast the advantages and limitations of different methods and highlight some of the discoveries made. We emphasize the need for interdisciplinary collaborations and integrated experimental pipelines that link sample preparation, image acquisition, image analysis, database design, visualization, and quantitative analysis. Copyright © 2013 Wiley Periodicals, Inc.

Veiseh M.,Lawrence Berkeley National Laboratory | Turley E.A.,University of Western Ontario
Integrative Biology | Year: 2011

Clinical and experimental evidence increasingly support the concept of cancer as a disease that emulates a component of wound healing, in particular abnormal stromal extracellular matrix remodeling. Here we review the biology and function of one remodeling process, hyaluronan (HA) metabolism, which is essential for wound resolution but closely linked to breast cancer (BCA) progression. Components of the HA metabolic cycle (HAS2, SPAM1 and HA receptors CD44, RHAMM/HMMR and TLR2) are discussed in terms of their known functions in wound healing and in breast cancer progression. Finally, we discuss recent advances in the use of HA-based platforms for developing nanoprobes to image areas of active HA metabolism and for therapeutics in breast cancer. © The Royal Society of Chemistry.

Harris S.J.,Lawrence Berkeley National Laboratory | Lu P.,General Motors
Journal of Physical Chemistry C | Year: 2013

We review work from our laboratory that suggests to us that most Li-ion battery failure can be ascribed to the presence of nano-and microscale inhomogeneities that interact at the mesoscale, as is the case with almost every material, and that these inhomogeneities act by hindering Li transport. (Li does not get to the right place at the right time.) For this purpose, we define inhomogeneities as regions with sharply varying properties -which includes interfaces -whether present by "accident" or design. We have used digital image correlation, X-ray tomography, FIB-SEM serial sectioning, and isotope tracer techniques with TOF-SIMS to observe and quantify these inhomogeneities. We propose new research approaches to make more durable, high energy density lithium-ion batteries. © 2013 American Chemical Society.

Alushin G.,University of California at Berkeley | Nogales E.,Howard Hughes Medical Institute | Nogales E.,Lawrence Berkeley National Laboratory
Current Opinion in Structural Biology | Year: 2011

Kinetochores are large macromolecular assemblies that link chromosomes to spindle microtubules (MTs) during mitosis. Here we review recent advances in the study of core MT-binding kinetochore complexes using electron microcopy methods in vitro and nanometer-accuracy fluorescence microscopy in vivo. We synthesize these findings in novel three-dimensional models of both the budding yeast and vertebrate kinetochore in different stages of mitosis. There is a growing consensus that kinetochores are highly dynamic, supra-molecular machines that undergo dramatic structural rearrangements in response to MT capture and spindle forces during mitosis. © 2011 Elsevier Ltd.

Iglesia E.,Lawrence Berkeley National Laboratory | Iglesia E.,University of California at Berkeley
Journal of Physical Chemistry C | Year: 2014

Bimetallic Pd-Au clusters with (Pd/Au)at compositions of 0.5, 1.0, and 2.0 narrowly distributed in size were prepared using colloidal methods with reagents containing only C, H, and O atoms, specifically polyvinyl alcohol (PVA) as protecting species and ethanol as the organic reductant. Synthesis protocols involved contacting a solution of Au precursors with nearly monodisperse Pd clusters. The formation of Pd-Au clusters was inferred from the monotonic growth of clusters with increasing Au content and confirmed by the in situ detection of Au plasmon bands in their UV-visible spectra during synthesis. Specifically, transmission electron microscopy (TEM) showed that growth rates were proportional to the surface area of the clusters, and rigorous deconvolution and background subtraction allowed for determination of the intensity and energy of Au-derived plasmon bands. This feature emerged during initial contact between Au precursors and Pd clusters apparently because Au 3+ species deposit as Au0 using Pd0 as the reductant in a fast galvanic displacement process consistent with their respective redox potentials. The plasmon band ultimately disappeared as a result of the subsequent slower reduction of the displaced Pd2+ species by ethanol and of their deposition onto the bimetallic clusters. Such displacement-reduction pathways are consistent with the thermodynamic redox tendencies of Au, Pd, and ethanol and lead to the conclusion that such triads (two metals and an organic reductant) can be chosen from thermodynamic data and applied generally to the synthesis of bimetallic clusters with other compositions. These bimetallic clusters were dispersed on mesoporous γ-Al2O3 supports, and PVA was removed by treatment in ozone at near-ambient temperature without any detectable changes in cluster size. The absence of strongly bound heteroatoms, ubiquitous in many other colloidal synthesis protocols, led to Al2O3-dispersed clusters with chemisorption uptakes consistent with their TEM-derived cluster size, thus demonstrating that cluster surfaces are accessible and free of synthetic debris. The infrared spectra of chemisorbed CO indicated that both Pd and Au were present at such clean surfaces but that any core-shell intracluster structure conferred by synthesis was rapidly destroyed by adsorption of catalytically relevant species, even at ambient temperature; this merely reflects the thermodynamic tendency and kinetic ability of an element to segregate and to decrease surface energies when it binds an adsorbate more strongly than another element in bimetallic particles. © 2014 American Chemical Society.

Wiley C.,Buck Institute for Research on Aging | Campisi J.,Buck Institute for Research on Aging | Campisi J.,Lawrence Berkeley National Laboratory
EMBO Journal | Year: 2014

Loss of the coenzyme NAD+, which is required for many energy-dependent cellular processes, has emerged as a potentially unifying mechanism for age-related conditions. A study in this issue of The EMBO Journal identifies a novel link between depletion of NAD+ and age-associated loss of proliferating adult neural stem/progenitor cells in the murine brain (Stein & Imai,). These data have important implications for how brain function might decline with age. Age-associated loss of NAD+ or Nampt, the rate-limiting biosynthetic step for this coenzyme, accounts for the loss of neural stem/progenitor cells self-renewal and differentiation. © 2014 The Authors.

Lv Y.,Beijing University of Chemical Technology | Lv Y.,University of California at Berkeley | Tan T.,Beijing University of Chemical Technology | Svec F.,Lawrence Berkeley National Laboratory
Biotechnology Advances | Year: 2013

This review article summarizes the preparation of polymers imprinted with proteins that exhibit antibody-like specificity due to the presence of well-defined recognition sites. We present the newest developments concerned with use of nanomaterials, such as magnetic and silica nanoparticles, nanowires, carbon nanotubes, and quantum dots as supports enabling the preparation of protein-imprinted polymers via surface imprinting techniques. As an alternative receptor-like synthetic materials, these conjugates are attracting a great deal of interest in various fields including proteomics, genomics, and fabrication of selective sensors. However, imprinting of large biomacromolecules such as proteins still remains a challenge due to the inherent limitations related to protein properties. In the text below, we also describe examples of applications focused on selective recognition of biomacromolecules. © 2013 Elsevier Inc.

Asmis K.R.,Fritz Haber Institute | Neumark D.M.,University of California at Berkeley | Neumark D.M.,Lawrence Berkeley National Laboratory
Accounts of Chemical Research | Year: 2012

Conjugate-base anions are ubiquitous in aqueous solution. Understanding the hydration of these anions at the molecular level represents a long-standing goal in chemistry. A molecular-level perspective on ion hydration is also important for understanding the surface speciation and reactivity of aerosols, which are a central component of atmospheric and oceanic chemical cycles. In this Account, as a means of studying conjugate-base anions in water, we describe infrared multiple-photon dissociation spectroscopy on clusters in which the sulfate, nitrate, bicarbonate, and suberate anions are hydrated by a known number of water molecules.This spectral technique, used over the range of 550-1800 cm -1, serves as a structural probe of these clusters. The experiments follow how the solvent network around the conjugate-base anion evolves, one water molecule at a time. We make structural assignments by comparing the experimental infrared spectra to those obtained from electronic structure calculations. Our results show how changes in anion structure, symmetry, and charge state have a profound effect on the structure of the solvent network. Conversely, they indicate how hydration can markedly affect the structure of the anion core in a microhydrated cluster.Some key results include the following. The first few water molecules bind to the anion terminal oxo groups in a bridging fashion, forming two anion-water hydrogen bonds. Each oxo group can form up to three hydrogen bonds; one structural result, for example, is the highly symmetric, fully coordinated SO 4 2-(H 2O) 6 cluster, which only contains bridging water molecules. Adding more water molecules results in the formation of a solvent network comprising water-water hydrogen bonding in addition to hydrogen bonding to the anion. For the nitrate, bicarbonate, and suberate anions, fewer bridging sites are available, namely, three, two, and one (per carboxylate group), respectively. As a result, an earlier onset of water-water hydrogen bonding is observed.When there are more than three hydrating water molecules (n > 3), the formation of a particularly stable four-membered water ring is observed for hydrated nitrate and bicarbonate clusters. This ring binds in either a side-on (bicarbonate) or top-on (nitrate) fashion. In the case of bicarbonate, additional water molecules then add to this water ring rather than directly to the anion, indicating a preference for surface hydration. In contrast, doubly charged sulfate dianions are internally hydrated and characterized by the closing of the first hydration shell at n = 12. The situation is different for the -O 2C(CH 2) 6CO 2- (suberate) dianion, which adapts to the hydration network by changing from a linear to a folded structure at n > 15. This change is driven by the formation of additional solute-solvent hydrogen bonds. © 2011 American Chemical Society.

Faubel M.,Max Planck Institute for Dynamics and Self-Organization | Siefermann K.R.,Lawrence Berkeley National Laboratory | Liu Y.,University of Leipzig | Abel B.,University of Leipzig
Accounts of Chemical Research | Year: 2012

Since the pioneering work of Kai Siegbahn, electron spectroscopy for chemical analysis (ESCA) has been developed into an indispensable analytical technique for surface science. The value of this powerful method of photoelectron spectroscopy (PES, also termed photoemission spectroscopy) and Siegbahn's contributions were recognized in the 1981 Nobel Prize in Physics.The need for high vacuum, however, originally prohibited PES of volatile liquids, and only allowed for investigation of low-vapor-pressure molecules attached to a surface (or close to a surface) or liquid films of low volatility. Only with the invention of liquid beams of volatile liquids compatible with high-vacuum conditions was PES from liquid surfaces under vacuum made feasible. Because of the ubiquity of water interfaces in nature, the liquid water-vacuum interface became a most attractive research topic, particularly over the past 10 years. PES studies of these important aqueous interfaces remained significantly challenging because of the need to develop high-pressure PES methods.For decades, ESCA or PES (termed XPS, for X-ray photoelectron spectroscopy, in the case of soft X-ray photons) was restricted to conventional laboratory X-ray sources or beamlines in synchrotron facilities. This approach enabled frequency domain measurements, but with poor time resolution. Indirect access to time-resolved processes in the condensed phase was only achieved if line-widths could be analyzed or if processes could be related to a fast clock, that is, reference processes that are fast enough and are also well understood in the condensed phase. Just recently, the emergence of high harmonic light sources, providing short-wavelength radiation in ultrashort light pulses, added the dimension of time to the classical ESCA or XPS technique and opened the door to (soft) X-ray photoelectron spectroscopy with ultrahigh time resolution.The combination of high harmonic light sources (providing radiation with laserlike beam qualities) and liquid microjet technology recently enabled the first liquid interface PES experiments in the IR/UV-pump and extreme ultraviolet-probe (EUV-probe) configuration. In this Account, we highlight features of the technology and a number of recent applications, including extreme states of matter and the discovery and detection of short-lived transients of the solvated electron in water. Properties of the EUV radiation, such as its controllable polarization and features of the liquid microjet, will enable unique experiments in the near future. PES measures electron binding energies and angular distributions of photoelectrons, which comprise unique information about electron orbitals and their involvement in chemical bonding. One of the future goals is to use this information to trace molecular orbitals, over time, in chemical reactions or biological transformations. © 2011 American Chemical Society.

Faybishenko B.,Lawrence Berkeley National Laboratory
Stochastic Environmental Research and Risk Assessment | Year: 2010

Hydrogeological systems are often characterized by imprecise, vague, inconsistent, incomplete, or subjective information, which may limit the application of conventional stochastic methods in predicting hydrogeologic conditions and associated uncertainty. Instead, predictions and uncertainty analysis can be made using uncertain input parameters expressed as probability boxes, intervals, and fuzzy numbers. The objective of this paper is to present the theory for, and a case study as an application of, the fuzzy-probabilistic approach, combining probability and possibility theory for simulating soil water balance and assessing associated uncertainty in the components of a simple water-balance equation. The application of this approach is demonstrated using calculations with the RAMAS Risk Calc code, to assess the propagation of uncertainty in calculating potential evapotranspiration, actual evapotranspiration, and infiltration-in a case study at the Hanford site, Washington, USA. Propagation of uncertainty into the results of water-balance calculations was evaluated by changing the types of models of uncertainty incorporated into various input parameters. The results of these fuzzy-probabilistic calculations are compared to the conventional Monte Carlo simulation approach and estimates from field observations at the Hanford site. © 2010 U.S. Government.

Shen C.,Ohio State University | Heinz U.,Ohio State University | Huovinen P.,Goethe University Frankfurt | Song H.,Lawrence Berkeley National Laboratory
Physical Review C - Nuclear Physics | Year: 2011

A comprehensive viscous hydrodynamic fit of spectra and elliptic flow for charged hadrons and identified pions and protons from Au+Au collisions of all centralities measured at the Relativistic Heavy Ion Collider (RHIC) is performed and used as the basis for predicting the analogous observables for Pb+Pb collisions at the Large Hadron Collider (LHC) at √s=2.76 and 5.5A TeV. Comparison with recent measurements of the elliptic flow of charged hadrons by the ALICE experiment shows that the model slightly overpredicts the data if the same (constant) specific shear viscosity η/s is assumed at both collision energies. In spite of differences in our assumptions for the equation of state, the freeze-out temperature, the chemical composition at freeze-out, and the starting time for the hydrodynamic evolution, our results agree remarkably well with those of Luzum, indicating robustness of the hydrodynamic model extrapolations. Future measurements of the centrality and transverse momentum dependence of spectra and elliptic flow for identified hadrons predicted here will further test the model and shed light on possible variations of the quark-gluon transport coefficients between RHIC and LHC energies. © 2011 American Physical Society.

Kolchin P.,University of California at Berkeley | Oulton R.F.,University of California at Berkeley | Zhang X.,University of California at Berkeley | Zhang X.,Lawrence Berkeley National Laboratory
Physical Review Letters | Year: 2011

We propose a waveguide-QED system where two single photons of distinct frequency or polarization interact strongly. The system consists of a single ladder-type three level atom coupled to a waveguide. When both optical transitions are coupled strongly to the waveguide's mode, we show that a control photon tuned to the upper transition induces a π phase shift and tunneling of a probe photon tuned to the otherwise reflective lower transition. Furthermore, the system exhibits single photon scattering by a classical control beam. Waveguide-QED schemes could be an alternative to high quality cavities or dense atomic ensembles in quantum information processing. © 2011 American Physical Society.

Banerjee P.,University of Minnesota | Haxton W.C.,Lawrence Berkeley National Laboratory | Qian Y.-Z.,University of Minnesota
Physical Review Letters | Year: 2011

We revisit a ν-driven r-process mechanism in the He shell of a core-collapse supernova, finding that it could succeed in early stars of metallicity Z10 -3Z, at relatively low temperatures and neutron densities, producing A 130 and 195 abundance peaks over ∼10-20s. The mechanism is sensitive to the ν emission model and to ν oscillations. We discuss the implications of an r process that could alter interpretations of abundance data from metal-poor stars, and point out the need for further calculations that include effects of the supernova shock. © 2011 American Physical Society.

Ma R.-M.,University of California at Berkeley | Oulton R.F.,University of California at Berkeley | Sorger V.J.,University of California at Berkeley | Bartal G.,University of California at Berkeley | And 2 more authors.
Nature Materials | Year: 2011

Plasmon lasers are a new class of coherent optical amplifiersthat generate and sustain light well below its diffraction limit. Their intense, coherent and confined optical fields can enhance significantly lightĝ€"matter interactions and bring fundamentallynew capabilities to bio-sensing, data storage, photolithography and optical communications. However, metallic plasmon laser cavities generally exhibit both high metal and radiation losses, limiting the operation of plasmon lasers to cryogenic temperatures, where sufficient gain can be attained. Here, we present a room-temperature semiconductor sub-diffraction-limited laser by adopting total internal reflection of surface plasmons to mitigate the radiation loss, while using hybrid semiconductorĝ €"insulatorĝ€"metal nanosquares for strong confinement with low metal loss. High cavity quality factors, approaching 100, along with strong λ/20 mode confinement, lead to enhancements of spontaneous emission rate by up to 18-fold. By controlling the structural geometry we reduce the number of cavity modes to achieve single-mode lasing. © 2011 Macmillan Publishers Limited. All rights reserved.

We compare the heat released directly due to combustion of fossil fuels to the heat accumulated indirectly in the earth system due to the effect of greenhouse gases (GHGs) associated with the fuels. We differentiate between GHG emissions from the combustion products of fossil fuels and from the fuel cycle activities of extracting, processing, and transporting the fuels. We find that the direct release of heat from the combustion of fossil fuels is minor in relation to the indirect accumulation of heat due to radiative forcing. The quantity of indirect heat accumulated by GHGs continues to increase over time, as additional energy is accumulated in the earth system as long as the GHGs remain in the atmosphere. Fuel cycle emissions contribute significantly to total lifecycle GHG emissions and radiative forcing. © 2013 Elsevier Ltd. All rights reserved.

Lee B.C.,Lawrence Berkeley National Laboratory
ACS chemical biology | Year: 2011

For the last few decades, chemistry has played an important role in protein engineering by providing a variety of synthetic tools such as chemoselective side-chain modifications, chemical conjugation, incorporation of non-natural amino acids, and the development of protein-mimetic heteropolymers. Here we study protein backbone engineering in order to better understand the molecular mechanism of protein function and to introduce protease stable, non-natural residues into a protein structure. Using a combination of genetic engineering and chemical synthesis, we were able to introduce peptoid residues (N-substituted glycine residues) at defined positions into bovine pancreatic ribonuclease A. This results in a side-chain translocation from the Cα carbon to the neighboring backbone nitrogen atom. To generate these peptoid substitutions, we removed the N-terminal S-peptide of the protein by proteolysis and chemically conjugated synthetic peptide-peptoid hybrids to the new N-terminus. A triple peptoid mutant containing a catalytic His12 peptoid mutation was active with a k(cat)/K(m) value of 1.0 × 10(4) M(-1) s(-1). This k(cat)/K(m) value is only 10-fold lower than the control wild-type conjugate and comparable in magnitude to many other natural enzymes. The peptoid mutations increased the chain flexibility at the site of peptoid substitution and at its C-terminal neighboring residue. Our ability to translocate side chains by one atom along the proten backbone advances a synthetic mutagenesis tool and opens up a new level of protein engineering.

Phillips C.M.,Lawrence Berkeley National Laboratory
ACS chemical biology | Year: 2011

The high cost of enzymes for saccharification of lignocellulosic biomass is a major barrier to the production of second generation biofuels. Using a combination of genetic and biochemical techniques, we report that filamentous fungi use oxidative enzymes to cleave glycosidic bonds in cellulose. Deletion of cdh-1, the gene encoding the major cellobiose dehydrogenase of Neurospora crassa, reduced cellulase activity substantially, and addition of purified cellobiose dehydrogenases from M. thermophila to the Δcdh-1 strain resulted in a 1.6- to 2.0-fold stimulation in cellulase activity. Addition of cellobiose dehydrogenase to a mixture of purified cellulases showed no stimulatory effect. We show that cellobiose dehydrogenase enhances cellulose degradation by coupling the oxidation of cellobiose to the reductive activation of copper-dependent polysaccharide monooxygenases (PMOs) that catalyze the insertion of oxygen into C-H bonds adjacent to the glycosidic linkage. Three of these PMOs were characterized and shown to have different regiospecifities resulting in oxidized products modified at either the reducing or nonreducing end of a glucan chain. In contrast to previous models where oxidative enzymes were thought to produce reactive oxygen species that randomly attacked the substrate, the data here support a direct, enzyme-catalyzed oxidation of cellulose. Cellobiose dehydrogenases and proteins related to the polysaccharide monooxygenases described here are found throughout both ascomycete and basidiomycete fungi, suggesting that this model for oxidative cellulose degradation may be widespread throughout the fungal kingdom. When added to mixtures of cellulases, these proteins enhance cellulose saccharification, suggesting that they could be used to reduce the cost of biofuel production.

Williams P.T.,Lawrence Berkeley National Laboratory
Journal of Alzheimer's disease : JAD | Year: 2015

BACKGROUND: Whether lifestyle affects Alzheimer's disease (AD) risk remains controversial.OBJECTIVE: Test whether exercise, diet, or statins affect AD mortality in 153,536 participants of the National Runners' and Walkers' Health Studies.METHODS: Hazard ratios (HR) and 95% confidence intervals (95% CI) were obtained from Cox proportional hazard analyses for AD mortality versus baseline metabolic equivalent (MET) hours/d of exercise energy expenditure (1 MET equals approximately 1 km run), statin use, and fruit intake when adjusted for age, race, gender, education, and exercise mode.RESULTS: The National Death Index identified 175 subjects who died with AD listed as an underlying (n = 116) or contributing (n = 59) cause of death during 11.6-year average mortality surveillance. Relative to exercising <1.07 MET-hours/d, AD mortality was 6.0% lower for 1.07 to 1.8 MET-hours/d (HR: 0.94, 95% CI: 0.59 to 1.46, p = 0.79), 24.8% lower for 1.8 to 3.6 MET-hours/d (HR: 0.75, 95% CI: 0.50 to 1.13, p = 0.17), and 40.1% lower for ≥3.6 MET-hours/d (HR: 0.60, 95% CI: 0.37 to 0.97, p = 0.04). Relative to non-use, statin use was associated with 61% lower AD mortality (HR: 0.39, 95% CI: 0.15 to 0.82, p = 0.01), whereas use of other cholesterol-lowering medications was not (HR: 0.78, 95% CI: 0.40 to 1.38, p = 0.42). Relative to <1 piece of fruit/day, consuming 2 to 3 pieces daily was associated with 39.7% lower AD mortality (HR: 0.60, 95% CI: 0.39 to 0.91, p = 0.02) and ≥3 pieces/day with 60.7% lower AD mortality (HR: 0.39, 95% CI: 0.22 to 0.67, p = 0.0004).CONCLUSIONS: Exercise, statin, and fruit intake were associated with lower risk for AD mortality.

Aetukuri N.B.,IBM | McCloskey B.D.,IBM | McCloskey B.D.,University of California at Berkeley | McCloskey B.D.,Lawrence Berkeley National Laboratory | And 5 more authors.
Nature Chemistry | Year: 2015

Given their high theoretical specific energy, lithium-oxygen batteries have received enormous attention as possible alternatives to current state-of-the-art rechargeable Li-ion batteries. However, the maximum discharge capacity in nonaqueous lithium-oxygen batteries is limited to a small fraction of its theoretical value due to the build-up of insulating lithium peroxide (Li2O2), the battery's primary discharge product. The discharge capacity can be increased if Li2O2 forms as large toroidal particles rather than as a thin conformal layer. Here, we show that trace amounts of electrolyte additives, such as H2O, enhance the formation of Li2O2 toroids and result in significant improvements in capacity. Our experimental observations and a growth model show that the solvating properties of the additives prompt a solution-based mechanism that is responsible for the growth of Li2O2 toroids.We present a general formalism describing an additive's tendency to trigger the solution process, providing a rational design route for electrolytes that afford larger lithium-oxygen battery capacities. © 2015 Macmillan Publishers Limited.

Sternberg S.H.,University of California at Berkeley | Doudna J.A.,University of California at Berkeley | Doudna J.A.,Howard Hughes Medical Institute | Doudna J.A.,Lawrence Berkeley National Laboratory
Molecular Cell | Year: 2015

Few discoveries transform a discipline overnight, but biologists today can manipulate cells in ways never possible before, thanks to a peculiar form of prokaryotic adaptive immunity mediated by clustered regularly interspaced short palindromic repeats (CRISPR). From elegant studies that deciphered how these immune systems function in bacteria, researchers quickly uncovered the technological potential of Cas9, anRNA-guided DNA cleaving enzyme, for genome engineering. Here we highlight the recent explosion in visionary applications of CRISPR-Cas9 that promises to usher in a new era of biological understanding and control. © 2015 Elsevier Inc.

Houseworth J.E.,Lawrence Berkeley National Laboratory
Transport in Porous Media | Year: 2012