66. Flow of energy and information in molecular machines
MP Leighton and DA Sivak
Ann Rev Phys Chem, in press (2025).
65. Information thermodynamics of transition paths between multiple mesostates
MD Louwerse and DA Sivak
Phys Rev E 109, 064112 (2024).
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64. Performance limits of information engines
J du Buisson, DA Sivak,* and J Bechhoefer*
Adv Phys X 9, 2352112 (2024).
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63. Unlocking the potential of information flow: Maximizing free-energy transduction in a model of an autonomous rotary molecular motor
M Grelier, DA Sivak, and J Ehrich
Phys Rev E 109, 034115 (2024).
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62. Jensen bound for the entropy production rate in stochastic thermodynamics
MP Leighton and DA Sivak
Phys Rev E (Letter) 109, L012101 (2024).
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61. Signal in the noise: temporal variation in exponentially growing populations
EW Jones, J Derrick, RM Nisbet, W Ludington, and DA Sivak
Sci Rep 13, 21340 (2023).
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60. Efficient control protocols for an active Ornstein-Uhlenbeck particle
D Gupta, SHL Klapp, and DA Sivak
Phys Rev E 108, 024117 (2023).
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59. Information engine in a nonequilibrium bath
TK Saha,* J Ehrich,* M Gavrilov, S Still, DA Sivak, and J Bechhoefer
Phys Rev Lett 131, 057101 (2023).
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58. Energetic cost of feedback control
J Ehrich, S Still, and DA Sivak
Phys Rev Res 5, 023080 (2023).
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57. Inferring subsystem efficiencies in bipartite molecular machines
MP Leighton and DA Sivak
Phys Rev Lett 130, 178401 (2023).
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56. Energy and information flows in autonomous systems
J Ehrich and DA Sivak
Front Phys 11, 1108357 (2023).
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55. Optimal control in stochastic thermodynamics
S Blaber and DA Sivak
J Phys Commun 7, 033001 (2023).
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54. A gut commensal niche regulates stable association of a multispecies microbiota
R Dodge, EW Jones, Z Haolong, ..., DA Sivak, AC Spradling, and WB Ludington
Nat Commun 14, 1557 (2023).
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53. Remembering the work of Phillip L. Geissler: A coda to his scientific trajectory
GR Bowman, ..., DA Sivak, ..., A Widmer-Cooper
Ann Rev Phys Chem 74, 11.1 (2023).
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52. Optimal control of the F1-ATPase motor
D Gupta, SJ Large, S Toyabe, and DA Sivak
J Phys Chem Lett 13, 11844 (2022).
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51. Connections between efficient control and spontaneous transitions in an Ising model
MD Louwerse and DA Sivak
Phys Rev E 106, 064124 (2022).
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50. Bayesian information engine that optimally exploits noisy measurements
TK Saha, JNE Lucero, J Ehrich, DA Sivak, and J Bechhoefer
Phys Rev Lett 129, 130601 (2022).
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49. Dynamic and thermodynamic bounds for collective motor-driven transport
MP Leighton and DA Sivak
Phys Rev Lett 129, 118102 (2022).
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48. Optimal control with a strong harmonic trap
S Blaber and DA Sivak
Phys Rev E (Letter) 106, L022103 (2022).
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47. Efficient two-dimensional control of barrier crossing
S Blaber and DA Sivak
Europhys Lett 139, 17001 (2022).
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46. Multidimensional minimum-work control of a 2D Ising model
MD Louwerse and DA Sivak
J Chem Phys 156, 194108 (2022).
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45. Information thermodynamics of the transition-path ensemble
MD Louwerse and DA Sivak
Phys Rev Lett 128, 170602 (2022).
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44. Internal energy and information flows mediate input and output power in bipartite molecular machines
E Lathouwers and DA Sivak
Phys Rev E 105, 024136 (2022).
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43. Stochastic microbiome assembly depends on context
EW Jones, JM Carlson, DA Sivak, and WB Ludington
Proc Natl Acad Sci USA 119 (7), e2115877119 (2022).
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42. Performance scaling and trade-offs for collective motor-driven transport
MP Leighton and DA Sivak
New J Phys 24, 013009 (2022).
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41. Maximal fluctuation exploitation in Gaussian information engines
JNE Lucero, J Ehrich, J Bechhoefer, and DA Sivak
Phys Rev E 104, 044122 (2021).
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40. Heat fluctuations in a harmonic chain of active particles
D Gupta and DA Sivak
Phys Rev E 104, 024605 (2021).
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39. Steps minimize dissipation in rapidly driven stochastic systems
S Blaber, MD Louwerse, and DA Sivak
Phys Rev E (Letter) 104, L022101 (2021).
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38. Maximizing power and velocity of an information engine
TK Saha, JNE Lucero, J Ehrich, DA Sivak, and J Bechhoefer
Proc Natl Acad Sci USA 118 (20), e2023356118 (2021).
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37. Hidden energy flows in strongly coupled nonequilibrium systems
SJ Large and DA Sivak
Europhys Lett 133, 10003 (2021).
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36. Free energy transduction within autonomous systems
SJ Large, J Ehrich, and DA Sivak
Phys Rev E 103, 022140 (2021).
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35. Skewed thermodynamic geometry and optimal free energy estimation
S Blaber and DA Sivak
J Chem Phys 153, 244119 (2020).
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34. Apparent superballistic dynamics in one-dimensional random walks with biased detachment
CS Korosec, DA Sivak, and NR Forde
Phys Rev Res, 2, 033520 (2020).
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33. Nonequilibrium energy transduction in stochastic strongly coupled rotary motors
E Lathouwers, JNE Lucero, and DA Sivak
J Phys Chem Lett, 11, 5273-5378 (2020).
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32. Modeling work-speed-accuracy trade-offs in a stochastic rotary machine
AKS Kasper and DA Sivak
Phys Rev E, 101, 032110 (2020).
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31. Optimal control of protein copy number
S Blaber and DA Sivak
Phys Rev E, 101, 022118 (2020).
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30. Theory of nonequilibrium free energy transduction by molecular machines
AI Brown and DA Sivak
Chem Rev, 120, 434-459 (2020).
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29. Optimal discrete control: minimizing dissipation in discretely driven nonequilibrium systems
SJ Large and DA Sivak
J Stat Mech, 083212 (2019).
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28. Pulling cargo increases the precision of molecular motor progress
AI Brown and DA Sivak
Eur Phys Lett, 126 (4), 40004 (2019).
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27. Breaking time-reversal symmetry for ratchet models of molecular machines
A Zarrin, DA Sivak, and AI Brown
Phys Rev E, 99, 062127 (2019).
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26. Using a system's equilibrium behavior to reduce its energy dissipation in non-equilibrium processes
S Tafoya,* SJ Large,* S Liu, CJ Bustamante, and DA Sivak
Proc Natl Acad Sci USA, 102 (7), 2310-2315 (2019).
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25. Optimal control of rotary motors
JNE Lucero, A Mehdizadeh, and DA Sivak
Phys Rev E, 99, 012119 (2019).
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24. Stochastic control in microscopic nonequilibrium systems
SJ Large, R Chetrite, and DA Sivak
Europhys Lett, 124 (2), 20001 (2018).
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23. Energy dissipation and information flow in coupled Markovian systems
M Quenneville and DA Sivak
Entropy, 20 (9), 707 (2018).
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22. Quantifying configuration-sampling error in Langevin simulations of complex molecular systems
J Fass, DA Sivak, GE Crooks, KA Beauchamp, B Leimkuhler, and JD Chodera
Entropy, 20 (5), 318 (2018).
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21. Allocating and splitting free energy to maximize molecular machine flux
AI Brown and DA Sivak
J Phys Chem B, 122 (4), 1387-1393 (2018). | PDF |
20. Toward the design principles of molecular machines
AI Brown and DA Sivak
Physics in Canada, 73 (2), 61-66 (2017).
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19. Allocating dissipation across a molecular machine cycle to maximize steady-state flux
AI Brown and DA Sivak
Proc Natl Acad Sci USA, 114 (42), 11057-11062 (2017).
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18. Thermodynamic geometry of minimum-dissipation driven barrier crossing
DA Sivak and GE Crooks
Phys Rev E, 94, 052106 (2016).
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17. Effective dissipation: Breaking time-reversal symmetry in driven microscopic energy transmission
AI Brown and DA Sivak
Phys Rev E, 94, 032137 (2016).
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16. Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise
C Sokolik,* J McPherson,* Y Liu, D Bauer, M Broeker, G Heimberg, S Qi,* DA Sivak,* and M Thomson.*
Cell Sys, 1, 117-129 (2015).
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15. Environmental statistics and optimal regulation
DA Sivak* and M Thomson*
PLoS Comp Biol, 10 (9), e1003826 (2014).
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14. E pluribus unum, no more: From one crystal, many conformations
R Woldeyes, DA Sivak, JS Fraser
Curr Opin Struct Biol, 28, 56-62 (2014).
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13. 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, and JS Fraser
Structure, 22 (6), 899-910 (2014).
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12. Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems
DA Sivak, JD Chodera, and GE Crooks
J Phys Chem B, 118, 6466-6474 (2014).
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11. Optimal control of transitions between nonequilibrium steady states
PR Zulkowski, DA Sivak, and MR DeWeese
PLoS ONE, 8 (12), e82754 (2013).
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10. Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium simulations of discrete Langevin dynamics
DA Sivak, JD Chodera, and GE Crooks
Phys Rev X, 3, 011007 (2013).
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9. Geometry of thermodynamic control
PR Zulkowski, DA Sivak, GE Crooks, and MR DeWeese
Phys Rev E, 86, 041148 (2012).
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8. Thermodynamics of prediction
S Still, DA Sivak, AJ Bell, and GE Crooks
Phys Rev Lett, 109, 120604 (2012).
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7. Thermodynamic metrics and optimal paths
DA Sivak and GE Crooks
Phys Rev Lett, 108, 190602 (2012).
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6. Near-equilibrium measurements of nonequilibrium free energy
DA Sivak and GE Crooks
Phys Rev Lett, 108, 150601 (2012).
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5. Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA
DA Sivak and PL Geissler
J Chem Phys, 136, 045102 (2012).
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4. Measures of trajectory ensemble disparity in nonequilibrium statistical dynamics
GE Crooks and DA Sivak
J Stat Mech, P06003 (2011).
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3. Probing the conformational distributions of sub-persistence length DNA
AJ Mastroianni,* DA Sivak,* PL Geissler, and AP Alivisatos
Biophys J, 97, 1408-1417 (2009).
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2. Optical measurement of mechanical forces inside short DNA loops
H Shroff,* DA Sivak,* JJ Siegel,* AL McEvoy, M Siu, AJ Spakowitz, PL Geissler, and JT Liphardt
Biophys J, 94, 2179-2186 (2008).
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1. Controlling DNA capture and propagation through artificial nanopores
EH Trepagnier, A Radenovic, DA Sivak, PL Geissler, and JT Liphardt
Nano Lett, 7 (9), 2824-2830 (2007).
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* Asterisks: marked authors contributed equally to publication.
Underline: author was in Sivak research group.