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David A. Sivak, Ph.D. - Publications

Affiliations: 
2014- Physics Simon Fraser University, Burnaby, British Columbia, Canada 
Area:
Biophysics, Theoretical Chemistry
Website:
http://www.sfu.ca/physics/sivakgroup.html
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50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Leighton MP, Sivak DA. Inferring Subsystem Efficiencies in Bipartite Molecular Machines. Physical Review Letters. 130: 178401. PMID 37172234 DOI: 10.1103/PhysRevLett.130.178401  0.31
2023 Louwerse MD, Sivak DA. Connections between efficient control and spontaneous transitions in an Ising model. Physical Review. E. 106: 064124. PMID 36671088 DOI: 10.1103/PhysRevE.106.064124  0.792
2022 Bowman GR, Cox SJ, Dellago C, DuBay KH, Eaves JD, Fletcher DA, Frechette LB, Grünwald M, Klymko K, Ku J, Omar A, Rabani E, Reichman DR, Rogers JR, Rosnik AM, ... ... Sivak DA, et al. Remembering the Work of Phillip L. Geissler: A Coda to His Scientific Trajectory. Annual Review of Physical Chemistry. PMID 36719975 DOI: 10.1146/annurev-physchem-101422-030127  0.736
2022 Gupta D, Large SJ, Toyabe S, Sivak DA. Optimal Control of the F-ATPase Molecular Motor. The Journal of Physical Chemistry Letters. 13: 11844-11849. PMID 36520417 DOI: 10.1021/acs.jpclett.2c03033  0.796
2022 Blaber S, Sivak DA. Optimal control with a strong harmonic trap. Physical Review. E. 106: L022103. PMID 36110009 DOI: 10.1103/PhysRevE.106.L022103  0.806
2022 Louwerse MD, Sivak DA. Multidimensional minimum-work control of a 2D Ising model. The Journal of Chemical Physics. 156: 194108. PMID 35597666 DOI: 10.1063/5.0086079  0.793
2022 Louwerse MD, Sivak DA. Information Thermodynamics of the Transition-Path Ensemble. Physical Review Letters. 128: 170602. PMID 35570424 DOI: 10.1103/PhysRevLett.128.170602  0.76
2022 Lathouwers E, Sivak DA. Internal energy and information flows mediate input and output power in bipartite molecular machines. Physical Review. E. 105: 024136. PMID 35291132 DOI: 10.1103/PhysRevE.105.024136  0.791
2021 Gupta D, Sivak DA. Heat fluctuations in a harmonic chain of active particles. Physical Review. E. 104: 024605. PMID 34525619 DOI: 10.1103/PhysRevE.104.024605  0.369
2021 Blaber S, Louwerse MD, Sivak DA. Steps minimize dissipation in rapidly driven stochastic systems. Physical Review. E. 104: L022101. PMID 34525515 DOI: 10.1103/PhysRevE.104.L022101  0.779
2021 Large SJ, Ehrich J, Sivak DA. Free-energy transduction within autonomous systems. Physical Review. E. 103: 022140. PMID 33735999 DOI: 10.1103/PhysRevE.103.022140  0.816
2020 Blaber S, Sivak DA. Skewed thermodynamic geometry and optimal free energy estimation. The Journal of Chemical Physics. 153: 244119. PMID 33380076 DOI: 10.1063/5.0033405  0.799
2020 Lathouwers E, Lucero JNE, Sivak DA. Nonequilibrium Energy Transduction in Stochastic Strongly Coupled Rotary Motors. The Journal of Physical Chemistry Letters. 5273-5278. PMID 32501698 DOI: 10.1021/Acs.Jpclett.0C01055  0.803
2020 Kasper AKS, Sivak DA. Modeling work-speed-accuracy trade-offs in a stochastic rotary machine. Physical Review. E. 101: 032110. PMID 32289954 DOI: 10.1103/Physreve.101.032110  0.398
2020 Blaber S, Sivak DA. Optimal control of protein copy number. Physical Review. E. 101: 022118. PMID 32168689 DOI: 10.1103/Physreve.101.022118  0.753
2019 Brown AI, Sivak DA. Theory of Nonequilibrium Free Energy Transduction by Molecular Machines. Chemical Reviews. PMID 31411455 DOI: 10.1021/Acs.Chemrev.9B00254  0.726
2019 Zarrin A, Sivak DA, Brown AI. Breaking time-reversal symmetry for ratchet models of molecular machines. Physical Review. E. 99: 062127. PMID 31330673 DOI: 10.1103/Physreve.99.062127  0.729
2019 Tafoya S, Large SJ, Liu S, Bustamante C, Sivak DA. Using a system's equilibrium behavior to reduce its energy dissipation in nonequilibrium processes. Proceedings of the National Academy of Sciences of the United States of America. PMID 30867295 DOI: 10.1073/Pnas.1817778116  0.82
2019 Lucero JNE, Mehdizadeh A, Sivak DA. Optimal control of rotary motors. Physical Review. E. 99: 012119. PMID 30780326 DOI: 10.1103/Physreve.99.012119  0.475
2019 Brown AI, Sivak DA. Pulling cargo increases the precision of molecular motor progress Epl (Europhysics Letters). 126: 40004. DOI: 10.1209/0295-5075/126/40004  0.671
2019 Large SJ, Sivak DA. Optimal discrete control: minimizing dissipation in discretely driven nonequilibrium systems Journal of Statistical Mechanics: Theory and Experiment. 2019: 083212. DOI: 10.1088/1742-5468/Ab342B  0.828
2019 Tafoya S, Large SJ, Liu S, Bustamante C, Sivak DA. Using Equilibrium Behavior to Reduce Energy Dissipation in Non-Equilibrium Biomolecular Processes Biophysical Journal. 116: 325a. DOI: 10.1016/J.Bpj.2018.11.1765  0.787
2018 Fass J, Sivak DA, Crooks GE, Beauchamp KA, Leimkuhler B, Chodera JD. Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems. Entropy (Basel, Switzerland). 20. PMID 30393452 DOI: 10.3390/E20050318  0.732
2018 Brown AI, Sivak DA. Allocating and Splitting Free Energy to Maximize Molecular Machine Flux. The Journal of Physical Chemistry. B. PMID 29290114 DOI: 10.1021/Acs.Jpcb.7B10621  0.746
2018 Quenneville M, Sivak D. Energy Dissipation and Information Flow in Coupled Markovian Systems Entropy. 20: 707. DOI: 10.3390/E20090707  0.367
2018 Large SJ, Chetrite R, Sivak DA. Stochastic control in microscopic nonequilibrium systems Epl (Europhysics Letters). 124: 20001. DOI: 10.1209/0295-5075/124/20001  0.813
2017 Brown AI, Sivak DA. Allocating dissipation across a molecular machine cycle to maximize flux. Proceedings of the National Academy of Sciences of the United States of America. 114: 11057-11062. PMID 29073016 DOI: 10.1073/Pnas.1707534114  0.732
2016 Sivak DA, Crooks GE. Thermodynamic geometry of minimum-dissipation driven barrier crossing. Physical Review. E. 94: 052106. PMID 27967045 DOI: 10.1103/Physreve.94.052106  0.724
2016 Brown AI, Sivak DA. Effective dissipation: Breaking time-reversal symmetry in driven microscopic energy transmission. Physical Review. E. 94: 032137. PMID 27739864 DOI: 10.1103/Physreve.94.032137  0.748
2014 Sivak DA, Thomson M. Environmental statistics and optimal regulation. Plos Computational Biology. 10: e1003826. PMID 25254493 DOI: 10.1371/Journal.Pcbi.1003826  0.304
2014 Sivak DA, Chodera JD, Crooks GE. Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems. The Journal of Physical Chemistry. B. 118: 6466-74. PMID 24555448 DOI: 10.1021/Jp411770F  0.744
2014 Sivak DA, Chodera JD, Crooks GE. Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems Journal of Physical Chemistry B. 118: 6466-6474. DOI: 10.1021/jp411770f  0.722
2014 Sivak DA, Chodera JD, Crooks GE. Numerical Langevin Simulations: Equilibrium Dynamics and Nonequilibrium Thermodynamics Biophysical Journal. 106: 403a. DOI: 10.1016/J.Bpj.2013.11.2269  0.775
2013 Zulkowski PR, Sivak DA, DeWeese MR. Optimal control of transitions between nonequilibrium steady states. Plos One. 8: e82754. PMID 24386112 DOI: 10.1371/Journal.Pone.0082754  0.399
2013 Sivak DA, Chodera JD, Crooks GE. Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium simulations of discrete Langevin dynamics Physical Review X. 3. DOI: 10.1103/Physrevx.3.011007  0.765
2012 Zulkowski PR, Sivak DA, Crooks GE, DeWeese MR. Geometry of thermodynamic control. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 041148. PMID 23214570 DOI: 10.1103/Physreve.86.041148  0.703
2012 Still S, Sivak DA, Bell AJ, Crooks GE. Thermodynamics of prediction. Physical Review Letters. 109: 120604. PMID 23005932 DOI: 10.1103/Physrevlett.109.120604  0.679
2012 Sivak DA, Crooks GE. Thermodynamic metrics and optimal paths. Physical Review Letters. 108: 190602. PMID 23003019 DOI: 10.1103/Physrevlett.108.190602  0.703
2012 Sivak DA, Crooks GE. Near-equilibrium measurements of nonequilibrium free energy. Physical Review Letters. 108: 150601. PMID 22587237 DOI: 10.1103/Physrevlett.108.150601  0.729
2012 Sivak DA, Geissler PL. Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA. The Journal of Chemical Physics. 136: 045102. PMID 22299918 DOI: 10.1063/1.3679654  0.58
2012 Still S, Sivak DA, Bell AJ, Crooks GE. Thermodynamics of prediction Physical Review Letters. 109. DOI: 10.1103/PhysRevLett.109.120604  0.58
2012 Sivak DA, Crooks GE. Thermodynamic metrics and optimal paths Physical Review Letters. 108. DOI: 10.1103/PhysRevLett.108.190602  0.603
2012 Sivak DA, Crooks GE. Near-equilibrium measurements of nonequilibrium free energy Physical Review Letters. 108. DOI: 10.1103/PhysRevLett.108.150601  0.673
2012 Sivak DA, Geissler PL. Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA Journal of Chemical Physics. 136. DOI: 10.1063/1.3679654  0.47
2011 Crooks GE, Sivak DA. Measures of trajectory ensemble disparity in nonequilibrium statistical dynamics Journal of Statistical Mechanics: Theory and Experiment. 2011. DOI: 10.1088/1742-5468/2011/06/P06003  0.667
2010 Sivak DA, Crooks GE. Thermodynamic Efficiency Out of Equilibrium Biophysical Journal. 98: 388a-389a. DOI: 10.1016/J.Bpj.2009.12.2094  0.737
2009 Mastroianni AJ, Sivak DA, Geissler PL, Alivisatos AP. Probing the conformational distributions of subpersistence length DNA. Biophysical Journal. 97: 1408-17. PMID 19720029 DOI: 10.1016/J.Bpj.2009.06.031  0.577
2009 Sivak DA, Mastroianni AJ, Alivisatos A, Geissler PL. Equilibrium Bending Fluctuations of Short DNA Biophysical Journal. 96: 576a. DOI: 10.1016/J.Bpj.2008.12.3012  0.569
2008 Shroff H, Sivak D, Siegel JJ, McEvoy AL, Siu M, Spakowitz A, Geissler PL, Liphardt J. Optical measurement of mechanical forces inside short DNA loops. Biophysical Journal. 94: 2179-86. PMID 18065484 DOI: 10.1529/Biophysj.107.114413  0.569
2007 Trepagnier EH, Radenovic A, Sivak D, Geissler P, Liphardt J. Controlling DNA capture and propagation through artificial nanopores Nano Letters. 7: 2824-2830. PMID 17705552 DOI: 10.1021/Nl0714334  0.539
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