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24.  Stochastic control in microscopic nonequilibrium systems
SJ Large, R Chetrite, and DA Sivak
Europhys Lett 124 (2), 20001 (2018).
Journal  |  PDF

23.  Energy dissipation and information flow in coupled Markovian systems
M Quenneville and DA Sivak
Entropy 20 (9), 707 (2018).
Journal  |  PDF

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

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).
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20. Toward the design principles of molecular machines
AI Brown and DA Sivak
Physics in Canada, 73 (2), 61-66 (2017). 
arXiv  |  PDF

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).
Journal  PDF

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).  
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

11.  Optimal control of transitions between nonequilibrium steady states
PR Zulkowski, DA Sivak, and MR DeWeese
PLoS ONE, 8(12), e82754 (2013).  
Journal  PDF

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

9.  Geometry of thermodynamic control
PR Zulkowski, DA Sivak, GE Crooks, and MR DeWeese
Phys. Rev. E, 86, 041148 (2012).  
Journal  PDF

8.  Thermodynamics of prediction
S Still, DA Sivak, AJ Bell, and GE Crooks
Phys. Rev. Lett., 109, 120604 (2012).  
Journal  |  PDF

7.  Thermodynamic metrics and optimal paths
DA Sivak and GE Crooks
Phys. Rev. Lett., 108, 190602 (2012).  
Journal  PDF

6.  Near-equilibrium measurements of nonequilibrium free energy
DA Sivak and GE Crooks
Phys. Rev. Lett., 108, 150601 (2012).  
Journal  PDF

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

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



DNA bending elasticity
DA Sivak
PhD Thesis

Optimal nonequilibrium driving of a rotary mechanochemical motor
A Mehdizadeh
MSc Thesis (2016). 

Energy-speed-accuracy tradeoffs in a driven, stochastic, rotary machine
AK Kasper
MSc Thesis (2017).

Energy dissipation and information flow in coupled Markovian systems
M Quenneville
BSc Thesis (2016).

Analyzing gene-gene interactions through a renormalization of the Ising model
J Sastrillo
BSc Thesis (2017).