David A. Sivak
David A. Sivak
Assoc. Prof., Dept. of Physics, Simon Fraser U
Verified email at sfu.ca - Homepage
Cited by
Cited by
Thermodynamics of prediction
S Still, DA Sivak, AJ Bell, GE Crooks
Physical review letters 109 (12), 120604, 2012
Thermodynamic metrics and optimal paths
DA Sivak, GE Crooks
Physical Review Letters 108, 190602, 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
Probing the conformational distributions of subpersistence length DNA
AJ Mastroianni, DA Sivak, PL Geissler, AP Alivisatos
Biophysical journal 97 (5), 1408-1417, 2009
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
Geometry of thermodynamic control
PR Zulkowski, DA Sivak, GE Crooks, MR DeWeese
Physical Review E 86 (4), 041148, 2012
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
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
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
Near-equilibrium measurements of nonequilibrium free energy
DA Sivak, GE Crooks
Physical Review Letters 108, 150601, 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
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
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
Optimal control of transitions between nonequilibrium steady states
PR Zulkowski, DA Sivak, MR DeWeese
PloS one 8 (12), e82754, 2013
Measures of trajectory ensemble disparity in nonequilibrium statistical dynamics
GE Crooks, DA Sivak
Journal of Statistical Mechanics: Theory and Experiment 2011 (06), P06003, 2011
Thermodynamic geometry of minimum-dissipation driven barrier crossing
DA Sivak, GE Crooks
Physical Review E 94 (5), 052106, 2016
Theory of nonequilibrium free energy transduction by molecular machines
AI Brown, DA Sivak
Chemical reviews 120 (1), 434-459, 2019
Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA
DA Sivak, PL Geissler
The Journal of chemical physics 136 (4), 01B615, 2012
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
Stochastic control in microscopic nonequilibrium systems
SJ Large, R Chetrite, DA Sivak
EPL (Europhysics Letters) 124 (2), 20001, 2018
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