Carbunaru C.,National University of Singapore |
Teo Y.M.,National University of Singapore |
Leong B.,National University of Singapore |
Ho T.,California Institute of TechnologyCA
IEEE Transactions on Parallel and Distributed Systems | Year: 2014
Given the growing popularity of peer-to-peer file distribution in commercial applications, it is important to understand the challenges of using p2p file-sharing protocols for file distribution, and how extreme conditions such as flash crowds affect the efficiency of file distribution. In this light, there is a need to understand the impact of the utilization of available bandwidth on the performance of peer-assisted file distribution systems. With a simple measurement study on PlanetLab, we identified distinct phases in peer bandwidth utilization over the download duration. Based on the evolution of the utilization of available peer bandwidth over time, we formulated an analytical model for flash crowds in homogeneous and heterogeneous bandwidth swarms. The model estimates the instantaneous download rate and the average file download time with 10 percent error for swarms up to 160 peers. Our model can be used to predict the scalability of the system when the number of peers increases, and to provision for flash crowds by estimating the server bandwidth to achieve a minimum quality of service. Lastly, we demonstrate how our model is applied to new p2p protocols to understand their design and performance problems. © 2013 IEEE.
Cherukuri A.,University of California at San Diego |
Mallada E.,California Institute of TechnologyCA |
Cortes J.,University of California at San Diego
SIAM Conference on Control and Its Applications 2015 | Year: 2015
This paper characterizes the asymptotic convergence properties of the primal-dual dynamics to the solutions of a constrained concave optimization problem using classical notions from stability analysis. We motivate our study by providing an example which rules out the possibility of employing the invariance principle for hybrid automata to analyze the asymptotic convergence. We understand the solutions of the primal-dual dynamics in the Caratheodory sense and establish their existence, uniqueness, and continuity with respect to the initial conditions. We employ the invariance principle for Caratheodory solutions of a discontinuous dynamical system to show that the primal-dual optimizers are globally asymptotically stable under the primal-dual dynamics and that each solution of the dynamics converges to an optimizer.
Dodani S.C.,California Institute of TechnologyCA |
Kiss G.,Stanford University |
Cahn J.K.B.,California Institute of TechnologyCA |
Su Y.,California Institute of TechnologyCA |
And 2 more authors.
Nature Chemistry | Year: 2016
The dynamic motions of protein structural elements, particularly flexible loops, are intimately linked with diverse aspects of enzyme catalysis. Engineering of these loop regions can alter protein stability, substrate binding and even dramatically impact enzyme function. When these flexible regions are unresolvable structurally, computational reconstruction in combination with large-scale molecular dynamics simulations can be used to guide the engineering strategy. Here we present a collaborative approach that consists of both experiment and computation and led to the discovery of a single mutation in the F/G loop of the nitrating cytochrome P450 TxtE that simultaneously controls loop dynamics and completely shifts the enzyme's regioselectivity from the C4 to the C5 position of L-tryptophan. Furthermore, we find that this loop mutation is naturally present in a subset of homologous nitrating P450s and confirm that these uncharacterized enzymes exclusively produce 5-nitro-L-tryptophan, a previously unknown biosynthetic intermediate. © 2016 Macmillan Publishers Limited. All rights reserved.
Barman S.,California Institute of TechnologyCA |
Chawla S.,University of Wisconsin - Madison |
Umboh S.,University of Wisconsin - Madison
Leibniz International Proceedings in Informatics, LIPIcs | Year: 2014
We study network design with a cost structure motivated by redundancy in data traffic. We are given a graph, g groups of terminals, and a universe of data packets. Each group of terminals desires a subset of the packets from its respective source. The cost of routing traffic on any edge in the network is proportional to the total size of the distinct packets that the edge carries. Our goal is to find a minimum cost routing. We focus on two settings. In the first, the collection of packet sets desired by source-sink pairs is laminar. For this setting, we present a primaldual based 2-approximation, improving upon a logarithmic approximation due to Barman and Chawla (2012) . In the second setting, packet sets can have non-trivial intersection. We focus on the case where each packet is desired by either a single terminal group or by all of the groups. This setting does not admit an O(log1/4-γ g)-approximation for any constant γ under a standard assumption; we present an O(log g)-approximation when the graph is unweighted. Our approximation for the second setting is based on a novel spanner-type construction in unweighted graphs that, given a collection of g vertex subsets, finds a subgraph of cost only a constant factor more than the minimum spanning tree of the graph, such that every subset in the collection has a Steiner tree in the subgraph of cost at most O(log g) that of its minimum Steiner tree in the original graph. We call such a subgraph a group spanner. © Siddharth Barman, Shuchi Chawla, and Seeun Umboh.
Coskun A.F.,California Institute of TechnologyCA |
Eser U.,Harvard Medical SchoolMA |
Islam S.,Stanford University
Molecular BioSystems | Year: 2016
A single cell creates surprising heterogeneity in a multicellular organism. While every organismal cell shares almost an identical genome, molecular interactions in cells alter the use of DNA sequences to modulate the gene of interest for specialization of cellular functions. Each cell gains a unique identity through molecular coding across the DNA, RNA, and protein conversions. On the other hand, loss of cellular identity leads to critical diseases such as cancer. Most cell identity dissection studies are based on bulk molecular assays that mask differences in individual cells. To probe cell-to-cell variability in a population, we discuss single cell approaches to decode the genetic, epigenetic, transcriptional, and translational mechanisms for cell identity formation. In combination with molecular instructions, the physical principles behind cell identity determination are examined. Deciphering and reprogramming cellular types impact biology and medicine. © The Royal Society of Chemistry 2016.
Kim M.,Stanford University |
Pan M.,Stanford University |
Gai Y.,Stanford University |
Pang S.,Central College |
And 3 more authors.
Lab on a Chip - Miniaturisation for Chemistry and Biology | Year: 2015
This paper describes an optofluidic droplet interrogation device capable of counting fluorescent drops at a throughput of 254 000 drops per second. To our knowledge, this rate is the highest interrogation rate published thus far. Our device consists of 16 parallel microfluidic channels bonded directly to a filter-coated two-dimensional Complementary Metal-Oxide-Semiconductor (CMOS) sensor array. Fluorescence signals emitted from the drops are collected by the sensor that forms the bottom of the channel. The proximity of the drops to the sensor facilitates efficient collection of fluorescence emission from the drops, and overcomes the trade-off between light collection efficiency and field of view in conventional microscopy. The interrogation rate of our device is currently limited by the acquisition speed of CMOS sensor, and is expected to increase further as high-speed sensors become increasingly available. © 2015 The Royal Society of Chemistry.
Noriega-Crespo A.,California Institute of TechnologyCA |
Noriega-Crespo A.,US Space Telescope Science Institute |
Raga A.C.,National Autonomous University of Mexico |
Moro-Martin A.,US Space Telescope Science Institute |
And 3 more authors.
New Journal of Physics | Year: 2014
We have used multiple mid-infrared observations at 4.5 μm obtained with the infrared array camera, of the compact (∼ 1.4′young stellar bipolar outflow Cep E to measure the proper motion of its brightest condensations. The images span a period of ∼6 yr and have been reprocessed to achieve a higher angular resolution (∼ 0.8″than their normal beam (∼2″). We found that for a distance of 730 pc, the tangential velocities of the north and south outflow lobes are and respectively, and moving away from the central source roughly along the major axis of the flow. A simple 3D hydrodynamical simulation of the H2 gas in a precessing outflow supports this idea. Observations and models confirm that the molecular hydrogen gas, traced by the pure rotational transitions, moves at highly supersonic velocities without being dissociated. This suggests either a very efficient mechanism to reform H2 molecules along these shocks or the presence of some other mechanism (e.g. strong magnetic field) that shields the H2 gas. © 2014 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.
Kourdis P.D.,California Institute of TechnologyCA |
Bellan J.,California Institute of TechnologyCA |
Bellan J.,Jet Propulsion Laboratory
International Journal of Chemical Kinetics | Year: 2016
We utilize the local self-similarity tabulation method to drastically downsize the number of species involved in a detailed kinetic mechanism of iso-cetane. Reduced-species mechanisms of 20 and 15 species are constructed, out of the 1114 species involved in the detailed mechanism, with a focus on high-pressure combustion. The performance of the two reduced mechanisms are compared to the detailed one for a lean (ϕ = 0.5), stoichiometric (ϕ = 1.0), and rich (ϕ = 1.5) iso-cetane/air mixture at initial temperatures of 900 and 1100 K and constant pressures of 20 and 40 bar. Good to very good agreement between the detailed kinetic mechanism and the two highly reduced species mechanisms are demonstrated. © 2016 Wiley Periodicals, Inc. California Institute of Technology. Government sponsorship acknowledged.
Chen B.,California Institute of TechnologyCA |
Perona P.,California Institute of TechnologyCA |
BMVC 2014 - Proceedings of the British Machine Vision Conference 2014 | Year: 2014
Poselets have been used in a variety of computer vision tasks, such as detection, segmentation, action classification, pose estimation and action recognition, often achieving state-of-the-art performance. Poselet evaluation, however, is computationally intensive as it involves running thousands of scanning window classifiers. We present an algorithm for training a hierarchical cascade of part-based detectors and apply it to speed up poselet evaluation. Our cascade hierarchy leverages common components shared across poselets. We generate a family of cascade hierarchies, including trees that grow logarithmically on the number of poselet classifiers. Our algorithm, under some reasonable assumptions, finds the optimal tree structure that maximizes speed for a given target detection rate. We test our system on the PASCAL dataset and show an order of magnitude speedup at less than 1% loss in AP. © 2014. The copyright of this document resides with its authors.
Papadakis G.T.,California Institute of TechnologyCA |
Atwater H.A.,California Institute of TechnologyCA
Physical Review B - Condensed Matter and Materials Physics | Year: 2015
We demonstrate that use of the field effect enables tuning of the effective optical parameters of a layered hyperbolic metamaterial at optical frequencies. Field-effect gating electrically modulates the permittivity in transparent conductive oxides via changes in the carrier density. These permittivity changes lead to active modulation of the effective electromagnetic parameters along with active control of the anisotropic dispersion surface of hyperbolic metamaterials and enable the opening and closing of photonic band gaps. Tunability of the effective electric permittivity and magnetic permeability also leads to topological transitions in the optical dispersion characteristics. ©2015 American Physical Society.