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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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66 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
2024 Grelier M, Sivak DA, Ehrich J. Unlocking the potential of information flow: Maximizing free-energy transduction in a model of an autonomous rotary molecular motor. Physical Review. E. 109: 034115. PMID 38632770 DOI: 10.1103/PhysRevE.109.034115  0.809
2024 Leighton MP, Sivak DA. Jensen bound for the entropy production rate in stochastic thermodynamics. Physical Review. E. 109: L012101. PMID 38366465 DOI: 10.1103/PhysRevE.109.L012101  0.8
2023 Jones EW, Derrick J, Nisbet RM, Ludington WB, Sivak DA. First-passage-time statistics of growing microbial populations carry an imprint of initial conditions. Scientific Reports. 13: 21340. PMID 38049502 DOI: 10.1038/s41598-023-48726-w  0.728
2023 Gupta D, Klapp SHL, Sivak DA. Efficient control protocols for an active Ornstein-Uhlenbeck particle. Physical Review. E. 108: 024117. PMID 37723713 DOI: 10.1103/PhysRevE.108.024117  0.385
2023 Saha TK, Ehrich J, Gavrilov M, Still S, Sivak DA, Bechhoefer J. Information Engine in a Nonequilibrium Bath. Physical Review Letters. 131: 057101. PMID 37595211 DOI: 10.1103/PhysRevLett.131.057101  0.775
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  0.798
2023 Dodge R, Jones EW, Zhu H, Obadia B, Martinez DJ, Wang C, Aranda-Díaz A, Aumiller K, Liu Z, Voltolini M, Brodie EL, Huang KC, Carlson JM, Sivak DA, Spradling AC, et al. A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota. Nature Communications. 14: 1557. PMID 36944617 DOI: 10.1038/s41467-023-36942-x  0.756
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  0.794
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  0.757
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  0.802
2022 Saha TK, Lucero JNE, Ehrich J, Sivak DA, Bechhoefer J. Bayesian Information Engine that Optimally Exploits Noisy Measurements. Physical Review Letters. 129: 130601. PMID 36206430 DOI: 10.1103/PhysRevLett.129.130601  0.769
2022 Leighton MP, Sivak DA. Dynamic and Thermodynamic Bounds for Collective Motor-Driven Transport. Physical Review Letters. 129: 118102. PMID 36154431 DOI: 10.1103/PhysRevLett.129.118102  0.778
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  0.812
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  0.797
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  0.774
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  0.807
2022 Jones EW, Carlson JM, Sivak DA, Ludington WB. Stochastic microbiome assembly depends on context. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35135881 DOI: 10.1073/pnas.2115877119  0.768
2021 Lucero JNE, Ehrich J, Bechhoefer J, Sivak DA. Maximal fluctuation exploitation in Gaussian information engines. Physical Review. E. 104: 044122. PMID 34781582 DOI: 10.1103/PhysRevE.104.044122  0.789
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  0.442
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  0.797
2021 Saha TK, Lucero JNE, Ehrich J, Sivak DA, Bechhoefer J. Maximizing power and velocity of an information engine. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 33972432 DOI: 10.1073/pnas.2023356118  0.772
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  0.807
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  0.805
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  0.795
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  0.472
2020 Blaber S, Sivak DA. Optimal control of protein copy number. Physical Review. E. 101: 022118. PMID 32168689 DOI: 10.1103/Physreve.101.022118  0.765
2019 Brown AI, Sivak DA. Theory of Nonequilibrium Free Energy Transduction by Molecular Machines. Chemical Reviews. PMID 31411455 DOI: 10.1021/Acs.Chemrev.9B00254  0.738
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  0.735
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  0.815
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  0.697
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  0.825
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  0.79
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  0.775
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  0.751
2018 Quenneville M, Sivak D. Energy Dissipation and Information Flow in Coupled Markovian Systems Entropy. 20: 707. DOI: 10.3390/E20090707  0.454
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  0.738
2017 Babcock NS, Sivak DA, Keedy D, Fraser JS. Model Comparison to Identify Structural Heterogeneity in Protein X-Ray Crystallography Biophysical Journal. 112: 486a. DOI: 10.1016/J.Bpj.2016.11.2628  0.748
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  0.737
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  0.752
2015 Sokolik C, Liu Y, Bauer D, McPherson J, Broeker M, Heimberg G, Qi LS, Sivak DA, Thomson M. Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise. Cell Systems. 1: 117-129. PMID 26405695 DOI: 10.1016/J.Cels.2015.08.001  0.686
2014 Sivak DA, Thomson M. Environmental statistics and optimal regulation. Plos Computational Biology. 10: e1003826. PMID 25254493 DOI: 10.1371/Journal.Pcbi.1003826  0.724
2014 Woldeyes RA, Sivak DA, Fraser JS. E pluribus unum, no more: from one crystal, many conformations. Current Opinion in Structural Biology. 28: 56-62. PMID 25113271 DOI: 10.1016/J.Sbi.2014.07.005  0.492
2014 Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS. Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR. Structure (London, England : 1993). 22: 899-910. PMID 24882744 DOI: 10.1016/J.Str.2014.04.016  0.522
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  0.786
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  0.78
2014 Woldeyes RA, Sivak DA, Fraser JS. E pluribus unum, no more: From one crystal, many conformations Current Opinion in Structural Biology. 28: 56-62. DOI: 10.1016/j.sbi.2014.07.005  0.383
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  0.807
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  0.706
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  0.799
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  0.798
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  0.798
2012 Sivak DA, Crooks GE. Thermodynamic metrics and optimal paths. Physical Review Letters. 108: 190602. PMID 23003019 DOI: 10.1103/Physrevlett.108.190602  0.713
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  0.738
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  0.609
2012 Still S, Sivak DA, Bell AJ, Crooks GE. Thermodynamics of prediction Physical Review Letters. 109. DOI: 10.1103/PhysRevLett.109.120604  0.75
2012 Sivak DA, Crooks GE. Thermodynamic metrics and optimal paths Physical Review Letters. 108. DOI: 10.1103/PhysRevLett.108.190602  0.633
2012 Sivak DA, Crooks GE. Near-equilibrium measurements of nonequilibrium free energy Physical Review Letters. 108. DOI: 10.1103/PhysRevLett.108.150601  0.69
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  0.521
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  0.69
2010 Sivak DA, Crooks GE. Thermodynamic Efficiency Out of Equilibrium Biophysical Journal. 98: 388a-389a. DOI: 10.1016/J.Bpj.2009.12.2094  0.75
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  0.61
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  0.606
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  0.738
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  0.723
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