Sivak D - Search Results

1

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. Among authors: sivak d. 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.

2

Controlling DNA capture and propagation through artificial nanopores.

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

3

Probing the conformational distributions of subpersistence length DNA.

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

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

5

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

Tafoya S, Large SJ, Liu S, Bustamante C, Sivak DA. Tafoya S, et al. Proc Natl Acad Sci U S A. 2019 Mar 26;116(13):5920-5924. doi: 10.1073/pnas.1817778116. Epub 2019 Mar 13. Proc Natl Acad Sci U S A. 2019. PMID: 30867295 Free PMC article.

6

Geometry of thermodynamic control.

Zulkowski PR, Sivak DA, Crooks GE, DeWeese MR. Zulkowski PR, et al. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Oct;86(4 Pt 1):041148. doi: 10.1103/PhysRevE.86.041148. Epub 2012 Oct 26. Phys Rev E Stat Nonlin Soft Matter Phys. 2012. PMID: 23214570 Free article.

7

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

Woldeyes RA, Sivak DA, Fraser JS. Woldeyes RA, et al. 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.

8

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

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

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.

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