Sivak DA - Search Results

1

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. Keedy DA, et al. Among authors: sivak da. Structure. 2014 Jun 10;22(6):899-910. doi: 10.1016/j.str.2014.04.016. Epub 2014 May 29. Structure. 2014. PMID: 24882744 Free PMC article.

2

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

Woldeyes RA, Sivak DA, Fraser JS. Woldeyes RA, et al. Among authors: sivak da. Curr Opin Struct Biol. 2014 Oct;28:56-62. doi: 10.1016/j.sbi.2014.07.005. Epub 2014 Aug 9. Curr Opin Struct Biol. 2014. PMID: 25113271 Free PMC article. Review.

3

Probing the conformational distributions of subpersistence length DNA.

Mastroianni AJ, Sivak DA, Geissler PL, Alivisatos AP. Mastroianni AJ, et al. Among authors: sivak da. Biophys J. 2009 Sep 2;97(5):1408-17. doi: 10.1016/j.bpj.2009.06.031. Biophys J. 2009. PMID: 19720029 Free PMC article.

4

Controlling DNA capture and propagation through artificial nanopores.

Trepagnier EH, Radenovic A, Sivak D, Geissler P, Liphardt J. Trepagnier EH, et al. Nano Lett. 2007 Sep;7(9):2824-30. doi: 10.1021/nl0714334. Epub 2007 Aug 18. Nano Lett. 2007. PMID: 17705552 Free article.

5

Optical measurement of mechanical forces inside short DNA loops.

Shroff H, Sivak D, Siegel JJ, McEvoy AL, Siu M, Spakowitz A, Geissler PL, Liphardt J. Shroff H, et al. Biophys J. 2008 Mar 15;94(6):2179-86. doi: 10.1529/biophysj.107.114413. Epub 2007 Dec 7. Biophys J. 2008. PMID: 18065484 Free PMC article.

6

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

Sivak DA, Geissler PL. Sivak DA, et al. J Chem Phys. 2012 Jan 28;136(4):045102. doi: 10.1063/1.3679654. J Chem Phys. 2012. PMID: 22299918

7

Near-equilibrium measurements of nonequilibrium free energy.

Sivak DA, Crooks GE. Sivak DA, et al. Phys Rev Lett. 2012 Apr 13;108(15):150601. doi: 10.1103/PhysRevLett.108.150601. Epub 2012 Apr 9. Phys Rev Lett. 2012. PMID: 22587237

8

Optimal control of transitions between nonequilibrium steady states.

Zulkowski PR, Sivak DA, DeWeese MR. Zulkowski PR, et al. Among authors: sivak da. PLoS One. 2013 Dec 26;8(12):e82754. doi: 10.1371/journal.pone.0082754. eCollection 2013. PLoS One. 2013. PMID: 24386112 Free PMC article.

9

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

Sivak DA, Chodera JD, Crooks GE. Sivak DA, et al. J Phys Chem B. 2014 Jun 19;118(24):6466-74. doi: 10.1021/jp411770f. Epub 2014 Mar 17. J Phys Chem B. 2014. PMID: 24555448 Free PMC article.

10

Environmental statistics and optimal regulation.

Sivak DA, Thomson M. Sivak DA, et al. PLoS Comput Biol. 2014 Sep 25;10(9):e1003826. doi: 10.1371/journal.pcbi.1003826. eCollection 2014 Sep. PLoS Comput Biol. 2014. PMID: 25254493 Free PMC article.

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