David A. Sivak

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Gavin E. CrooksNormal ComputingVerified email at berkeley.edu
Jannik EhrichSimon Fraser UniversityVerified email at sfu.ca
Aidan I BrownAssistant Professor, Toronto Metropolitan UniversityVerified email at torontomu.ca
Steve LargeSimon Fraser UniversityVerified email at sfu.ca
John BechhoeferProfessor of Physics, Simon Fraser UniversityVerified email at sfu.ca
Susanne StillUniversity of Hawaii at ManoaVerified email at hawaii.edu
Tushar K. SahaOptical Physicist, MKS InstrumentsVerified email at sfu.ca
William B LudingtonPrincipal Investigator, Carnegie Institution for Science, Dept EmbryologyVerified email at carnegiescience.edu
Joseph N. E. LuceroPhD student, Dept. of Chemistry, Stanford UniversityVerified email at stanford.edu
John D. ChoderaMemorial Sloan-Kettering Cancer CenterVerified email at mskcc.org
Jan LiphardtAssociate Professor of BioengineeringVerified email at stanford.edu
Steven BlaberPostdoctoral Researcher, University of British ColumbiaVerified email at ubc.ca
Matt ThomsonCaltechVerified email at caltech.edu
Daniel A. KeedyCUNY Advanced Science Research CenterVerified email at gc.cuny.edu
James S. FraserProfessor, University of California San FranciscoVerified email at ucsf.edu
Jean CarlsonUniversity of California Santa BarbaraVerified email at ucsb.edu
Matthew LeightonGraduate Student, Simon Fraser UniversityVerified email at sfu.ca
Miranda Danielle LouwersePhD Candidate, Simon Fraser UniversityVerified email at sfu.ca
Eric W. JonesBanting and PIMS Postdoctoral Fellow, Physics Dept @ Simon Fraser UniversityVerified email at sfu.ca
Patrick ZulkowskiBrilliant WorldwideVerified email at brilliant.org

David A. Sivak

Associate Professor, Dept. of Physics, Simon Fraser U

Verified email at sfu.ca - Homepage

Stochastic Thermodynamics Nonequilibrium Statistical Mechanics Physics of Information Biophysics


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Thermodynamic metrics and optimal paths DA Sivak, GE Crooks Physical Review Letters 108, 190602, 2012	333	2012
Thermodynamics of prediction S Still, DA Sivak, AJ Bell, GE Crooks Physical review letters 109 (12), 120604, 2012	276	2012
Controlling DNA capture and propagation through artificial nanopores EH Trepagnier, A Radenovic, D Sivak, P Geissler, J Liphardt Nano letters 7 (9), 2824-2830, 2007	161	2007
Geometry of thermodynamic control PR Zulkowski, DA Sivak, GE Crooks, MR DeWeese Physical Review E 86 (4), 041148, 2012	141	2012
Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR DA Keedy, H Van Den Bedem, DA Sivak, GA Petsko, D Ringe, MA Wilson, ... Structure 22 (6), 899-910, 2014	136	2014
Theory of nonequilibrium free energy transduction by molecular machines AI Brown, DA Sivak Chemical reviews 120 (1), 434-459, 2019	108	2019
Probing the conformational distributions of subpersistence length DNA AJ Mastroianni, DA Sivak, PL Geissler, AP Alivisatos Biophysical journal 97 (5), 1408-1417, 2009	103	2009
Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise C Sokolik, Y Liu, D Bauer, J McPherson, M Broeker, G Heimberg, LS Qi, ... Cell systems 1 (2), 117-129, 2015	81	2015
Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium simulations of discrete Langevin dynamics DA Sivak, JD Chodera, GE Crooks Physical Review X 3 (1), 011007, 2013	79	2013
Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems DA Sivak, JD Chodera, GE Crooks The Journal of Physical Chemistry B 118 (24), 6466-6474, 2014	77	2014
Near-equilibrium measurements of nonequilibrium free energy DA Sivak, GE Crooks Physical Review Letters 108, 150601, 2012	62	2012
E pluribus unum, no more: from one crystal, many conformations RA Woldeyes, DA Sivak, JS Fraser Current opinion in structural biology 28, 56-62, 2014	59	2014
Thermodynamic geometry of minimum-dissipation driven barrier crossing DA Sivak, GE Crooks Physical Review E 94 (5), 052106, 2016	53	2016
Maximizing power and velocity of an information engine TK Saha, JNE Lucero, J Ehrich, DA Sivak, J Bechhoefer Proceedings of the National Academy of Sciences 118 (20), e2023356118, 2021	46	2021
Using a system’s equilibrium behavior to reduce its energy dissipation in nonequilibrium processes S Tafoya, SJ Large, S Liu, C Bustamante, DA Sivak Proceedings of the National Academy of Sciences 116 (13), 5920-5924, 2019	46	2019
Allocating dissipation across a molecular machine cycle to maximize flux AI Brown, DA Sivak Proceedings of the National Academy of Sciences 114 (42), 11057-11062, 2017	44	2017
Optimal control of transitions between nonequilibrium steady states PR Zulkowski, DA Sivak, MR DeWeese PloS one 8 (12), e82754, 2013	44	2013
Quantifying configuration-sampling error in Langevin simulations of complex molecular systems J Fass, DA Sivak, GE Crooks, KA Beauchamp, B Leimkuhler, JD Chodera Entropy 20 (5), 318, 2018	42	2018
Optical measurement of mechanical forces inside short DNA loops H Shroff, D Sivak, JJ Siegel, AL McEvoy, M Siu, A Spakowitz, PL Geissler, ... Biophysical journal 94 (6), 2179-2186, 2008	40	2008
Stochastic microbiome assembly depends on context EW Jones, JM Carlson, DA Sivak, WB Ludington Proceedings of the National Academy of Sciences 119 (7), e2115877119, 2022	39	2022

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