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Items: 21

1.

Using a system's equilibrium behavior to reduce its energy dissipation in nonequilibrium processes.

Tafoya S, Large SJ, Liu S, Bustamante C, Sivak DA.

Proc Natl Acad Sci U S A. 2019 Mar 26;116(13):5920-5924. doi: 10.1073/pnas.1817778116. Epub 2019 Mar 13.

PMID:
30867295
2.

Optimal control of rotary motors.

Lucero JNE, Mehdizadeh A, Sivak DA.

Phys Rev E. 2019 Jan;99(1-1):012119. doi: 10.1103/PhysRevE.99.012119.

PMID:
30780326
3.

Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems.

Fass J, Sivak DA, Crooks GE, Beauchamp KA, Leimkuhler B, Chodera JD.

Entropy (Basel). 2018 May;20(5). pii: 318. doi: 10.3390/e20050318. Epub 2018 Apr 26.

4.

Allocating and Splitting Free Energy to Maximize Molecular Machine Flux.

Brown AI, Sivak DA.

J Phys Chem B. 2018 Feb 1;122(4):1387-1393. doi: 10.1021/acs.jpcb.7b10621. Epub 2018 Jan 22.

PMID:
29290114
5.

Allocating dissipation across a molecular machine cycle to maximize flux.

Brown AI, Sivak DA.

Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):11057-11062. doi: 10.1073/pnas.1707534114. Epub 2017 Oct 3. Erratum in: Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):E9754.

6.

Thermodynamic geometry of minimum-dissipation driven barrier crossing.

Sivak DA, Crooks GE.

Phys Rev E. 2016 Nov;94(5-1):052106. Epub 2016 Nov 3.

PMID:
27967045
7.

Effective dissipation: Breaking time-reversal symmetry in driven microscopic energy transmission.

Brown AI, Sivak DA.

Phys Rev E. 2016 Sep;94(3-1):032137. Epub 2016 Sep 30.

PMID:
27739864
8.

Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise.

Sokolik C, Liu Y, Bauer D, McPherson J, Broeker M, Heimberg G, Qi LS, Sivak DA, Thomson M.

Cell Syst. 2015 Aug 26;1(2):117-129.

9.

Environmental statistics and optimal regulation.

Sivak DA, Thomson M.

PLoS Comput Biol. 2014 Sep 25;10(9):e1003826. doi: 10.1371/journal.pcbi.1003826. eCollection 2014 Sep. Erratum in: PLoS Comput Biol. 2014 Oct;10(10):e1003978.

10.

E pluribus unum, no more: from one crystal, many conformations.

Woldeyes RA, Sivak DA, Fraser JS.

Curr Opin Struct Biol. 2014 Oct;28:56-62. doi: 10.1016/j.sbi.2014.07.005. Epub 2014 Aug 9. Review.

11.

Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR.

Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS.

Structure. 2014 Jun 10;22(6):899-910. doi: 10.1016/j.str.2014.04.016. Epub 2014 May 29.

12.

Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems.

Sivak DA, Chodera JD, Crooks GE.

J Phys Chem B. 2014 Jun 19;118(24):6466-74. doi: 10.1021/jp411770f. Epub 2014 Mar 17.

13.

Optimal control of transitions between nonequilibrium steady states.

Zulkowski PR, Sivak DA, DeWeese MR.

PLoS One. 2013 Dec 26;8(12):e82754. doi: 10.1371/journal.pone.0082754. eCollection 2013.

14.

Geometry of thermodynamic control.

Zulkowski PR, Sivak DA, Crooks GE, DeWeese MR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Oct;86(4 Pt 1):041148. Epub 2012 Oct 26.

PMID:
23214570
15.

Thermodynamics of prediction.

Still S, Sivak DA, Bell AJ, Crooks GE.

Phys Rev Lett. 2012 Sep 21;109(12):120604. Epub 2012 Sep 19.

PMID:
23005932
16.

Thermodynamic metrics and optimal paths.

Sivak DA, Crooks GE.

Phys Rev Lett. 2012 May 11;108(19):190602. Epub 2012 May 8.

PMID:
23003019
17.

Near-equilibrium measurements of nonequilibrium free energy.

Sivak DA, Crooks GE.

Phys Rev Lett. 2012 Apr 13;108(15):150601. Epub 2012 Apr 9.

PMID:
22587237
18.

Consequences of local inter-strand dehybridization for large-amplitude bending fluctuations of double-stranded DNA.

Sivak DA, Geissler PL.

J Chem Phys. 2012 Jan 28;136(4):045102. doi: 10.1063/1.3679654.

PMID:
22299918
19.

Probing the conformational distributions of subpersistence length DNA.

Mastroianni AJ, Sivak DA, Geissler PL, Alivisatos AP.

Biophys J. 2009 Sep 2;97(5):1408-17. doi: 10.1016/j.bpj.2009.06.031.

20.
21.

[Combined chemoprophylaxis of babesiasis in cattle].

Kolabskiń≠ NA, Gań≠dukov AKh, Vorob'ev VV, Sivak DA, Voevoda NI.

Veterinariia. 1973 Feb;3:71-3. Russian. No abstract available.

PMID:
4770054

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