64. Information thermodynamics of transition paths between multiple mesostates
MD Louwerse and DA Sivak
Phys Rev E, in press (2024).
arXiv
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).
Journal | PDF | arXiv
62. Jensen bound for the entropy production rate in stochastic thermodynamics
MP Leighton and DA Sivak
Phys Rev E (Letter) 109, L012101 (2024).
Journal | PDF | arXiv
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).
Journal | PDF | arXiv
60. Efficient control protocols for an active Ornstein-Uhlenbeck particle
D Gupta, SHL Klapp, and DA Sivak
Phys Rev E 108, 024117 (2023).
Journal | PDF | arXiv
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).
Journal | PDF | arXiv
58. Energetic cost of feedback control
J Ehrich, S Still, and DA Sivak
Phys Rev Res 5, 023080 (2023).
Journal | PDF | arXiv
57. Inferring subsystem efficiencies in bipartite molecular machines
MP Leighton and DA Sivak
Phys Rev Lett 130, 178401 (2023).
Journal | PDF | arXiv
56. Energy and information flows in autonomous systems
J Ehrich and DA Sivak
Front Phys 11, 1108357 (2023).
Journal | PDF | arXiv
55. Optimal control in stochastic thermodynamics
S Blaber and DA Sivak
J Phys Commun 7, 033001 (2023).
Journal | PDF | arXiv
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).
Journal | bioRxiv
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).
Journal | PDF | arXiv
52. Optimal control of the F1-ATPase motor
D Gupta, SJ Large, S Toyabe, and DA Sivak
J Phys Chem Lett 13, 11844 (2022).
Journal | arXiv
51. Connections between efficient control and spontaneous transitions in an Ising model
MD Louwerse and DA Sivak
Phys Rev E 106, 064124 (2022).
Journal | PDF | arXiv
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).
Journal | PDF | arXiv
49. Dynamic and thermodynamic bounds for collective motor-driven transport
MP Leighton and DA Sivak
Phys Rev Lett 129, 118102 (2022).
Journal | PDF | arXiv
48. Optimal control with a strong harmonic trap
S Blaber and DA Sivak
Phys Rev E (Letter) 106, L022103 (2022).
Journal | PDF | arXiv
47. Efficient two-dimensional control of barrier crossing
S Blaber and DA Sivak
Europhys Lett 139, 17001 (2022).
Journal | PDF | arXiv
46. Multidimensional minimum-work control of a 2D Ising model
MD Louwerse and DA Sivak
J Chem Phys 156, 194108 (2022).
Journal | PDF | arXiv
45. Information thermodynamics of the transition-path ensemble
MD Louwerse and DA Sivak
Phys Rev Lett 128, 170602 (2022).
Journal | PDF | arXiv
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).
Journal | PDF | arXiv
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).
Journal | bioRxiv
42. Performance scaling and trade-offs for collective motor-driven transport
MP Leighton and DA Sivak
New J Phys 24, 013009 (2022).
Journal | PDF | arXiv
41. Maximal fluctuation exploitation in Gaussian information engines
JNE Lucero, J Ehrich, J Bechhoefer, and DA Sivak
Phys Rev E 104, 044122 (2021).
Journal | PDF | arXiv
40. Heat fluctuations in a harmonic chain of active particles
D Gupta and DA Sivak
Phys Rev E 104, 024605 (2021).
Journal | PDF | arXiv
39. Steps minimize dissipation in rapidly driven stochastic systems
S Blaber, MD Louwerse, and DA Sivak
Phys Rev E (Letter) 104, L022101 (2021).
Journal | PDF | arXiv
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).
Journal | arXiv
37. Hidden energy flows in strongly coupled nonequilibrium systems
SJ Large and DA Sivak
Europhys Lett 133, 10003 (2021).
Journal | PDF | arXiv
36. Free energy transduction within autonomous systems
SJ Large, J Ehrich, and DA Sivak
Phys Rev E 103, 022140 (2021).
Journal | PDF | arXiv
35. Skewed thermodynamic geometry and optimal free energy estimation
S Blaber and DA Sivak
J Chem Phys 153, 244119 (2020).
Journal | arXiv
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).
Journal | PDF | arXiv
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).
Journal | PDF | arXiv
32. Modeling work-speed-accuracy trade-offs in a stochastic rotary machine
AKS Kasper and DA Sivak
Phys Rev E, 101, 032110 (2020).
Journal | PDF | arXiv
31. Optimal control of protein copy number
S Blaber and DA Sivak
Phys Rev E, 101, 022118 (2020).
Journal | PDF | arXiv
30. Theory of nonequilibrium free energy transduction by molecular machines
AI Brown and DA Sivak
Chem Rev, 120, 434-459 (2020).
Journal | arXiv
29. Optimal discrete control: minimizing dissipation in discretely driven nonequilibrium systems
SJ Large and DA Sivak
J Stat Mech, 083212 (2019).
Journal | PDF | arXiv
28. Pulling cargo increases the precision of molecular motor progress
AI Brown and DA Sivak
Eur Phys Lett, 126 (4), 40004 (2019).
Journal | PDF | arXiv
27. Breaking time-reversal symmetry for ratchet models of molecular machines
A Zarrin, DA Sivak, and AI Brown
Phys Rev E, 99, 062127 (2019).
Journal | PDF | arXiv
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).
Journal | PDF | bioRxiv
25. Optimal control of rotary motors
JNE Lucero, A Mehdizadeh, and DA Sivak
Phys Rev E, 99, 012119 (2019).
Journal | PDF | arXiv
24. Stochastic control in microscopic nonequilibrium systems
SJ Large, R Chetrite, and DA Sivak
Europhys Lett, 124 (2), 20001 (2018).
Journal | PDF | arXiv
23. Energy dissipation and information flow in coupled Markovian systems
M Quenneville and DA Sivak
Entropy, 20 (9), 707 (2018).
Journal | PDF | arXiv
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).
Journal | PDF | bioRxiv
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).
Journal | PDF | arXiv
20. Toward the design principles of molecular machines
AI Brown and DA Sivak
Physics in Canada, 73 (2), 61-66 (2017).
Journal | PDF | arXiv
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).
Journal | PDF | arXiv
18. Thermodynamic geometry of minimum-dissipation driven barrier crossing
DA Sivak and GE Crooks
Phys Rev E, 94, 052106 (2016).
Journal | PDF | arXiv
17. Effective dissipation: Breaking time-reversal symmetry in driven microscopic energy transmission
AI Brown and DA Sivak
Phys Rev E, 94, 032137 (2016).
Journal | PDF | arXiv
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).
Journal | PDF
15. Environmental statistics and optimal regulation
DA Sivak* and M Thomson*
PLoS Comp Biol, 10 (9), e1003826 (2014).
Journal | PDF | arXiv
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).
Journal | PDF
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).
Journal | PDF
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).
Journal | PDF | arXiv
11. Optimal control of transitions between nonequilibrium steady states
PR Zulkowski, DA Sivak, and MR DeWeese
PLoS ONE, 8 (12), e82754 (2013).
Journal | PDF | arXiv
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).
Journal | PDF | arXiv
9. Geometry of thermodynamic control
PR Zulkowski, DA Sivak, GE Crooks, and MR DeWeese
Phys Rev E, 86, 041148 (2012).
Journal | PDF | arXiv
8. Thermodynamics of prediction
S Still, DA Sivak, AJ Bell, and GE Crooks
Phys Rev Lett, 109, 120604 (2012).
Journal | PDF | arXiv
7. Thermodynamic metrics and optimal paths
DA Sivak and GE Crooks
Phys Rev Lett, 108, 190602 (2012).
Journal | PDF | arXiv
6. Near-equilibrium measurements of nonequilibrium free energy
DA Sivak and GE Crooks
Phys Rev Lett, 108, 150601 (2012).
Journal | PDF | arXiv
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).
Journal | PDF | arXiv
4. Measures of trajectory ensemble disparity in nonequilibrium statistical dynamics
GE Crooks and DA Sivak
J Stat Mech, P06003 (2011).
Journal | PDF
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).
Journal | PDF
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).
Journal | PDF
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).
Journal | PDF
* Asterisks: marked authors contributed equally to publication.
Underline: author was Highly Qualified Personnel in Sivak research group.