Google Scholar page

PDF Publication List

Errata


29.  Optimal discrete control: minimizing dissipation in discretely driven nonequilibrium systems
SJ Large and DA Sivak
J Stat Mech, in press (2019).
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

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

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

25.  Optimal control of rotary motors
JNE Lucero, A Mehdizadeh, and DA Sivak
Phys Rev E, 99, 012119 (2019).
Journal  |  PDF

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).
Journal
  |  PDF

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).
Journal  |  PDF

18. Thermodynamic geometry of minimum-dissipation driven barrier crossing
DA Sivak and GE Crooks
Phys Rev.E, 94, 052106 (2016).
Journal  |  PDF

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

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

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

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


* Asterisks denote that marked authors contributed equally to publication.

Underline denotes that author is Highly Qualified Personnel from Sivak research group.