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Items: 1 to 20 of 68

1.

Glucose-Promoted Localization Dynamics of Excess Electrons in Aqueous Glucose Solution Revealed by Ab Initio Molecular Dynamics Simulation.

Liu J, Cukier RI, Bu Y, Shang Y.

J Chem Theory Comput. 2014 Oct 14;10(10):4189-97. doi: 10.1021/ct500238k. Epub 2014 Sep 2.

PMID:
26588118
2.

Conformational transition in signal transduction: metastable states and transition pathways in the activation of a signaling protein.

Banerjee R, Yan H, Cukier RI.

J Phys Chem B. 2015 Jun 4;119(22):6591-602. doi: 10.1021/acs.jpcb.5b02582. Epub 2015 May 19.

PMID:
25945797
3.

Dihedral angle entropy measures for intrinsically disordered proteins.

Cukier RI.

J Phys Chem B. 2015 Mar 5;119(9):3621-34. doi: 10.1021/jp5102412. Epub 2015 Feb 25.

PMID:
25679039
4.

Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details.

Wang B, Opron K, Burton ZF, Cukier RI, Feig M.

Nucleic Acids Res. 2015 Jan;43(2):1133-46. doi: 10.1093/nar/gku1370. Epub 2014 Dec 30.

5.

Simulations of potentials of mean force for separating a leucine zipper dimer and the basic region of a basic region leucine zipper dimer.

Cukier RI.

J Phys Chem B. 2014 Sep 4;118(35):10341-54. doi: 10.1021/jp504723m. Epub 2014 Aug 25.

PMID:
25124233
6.

Conformational transition of response regulator RR468 in a two-component system signal transduction process.

Banerjee R, Yan H, Cukier RI.

J Phys Chem B. 2014 May 8;118(18):4727-42. doi: 10.1021/jp4122968. Epub 2014 Apr 25.

PMID:
24731214
7.

Transition paths of Met-enkephalin from Markov state modeling of a molecular dynamics trajectory.

Banerjee R, Cukier RI.

J Phys Chem B. 2014 Mar 20;118(11):2883-95. doi: 10.1021/jp412130d. Epub 2014 Mar 10.

PMID:
24571787
8.

Bending Vibration-Governed Solvation Dynamics of an Excess Electron in Liquid Acetonitrile Revealed by Ab Initio Molecular Dynamics Simulation.

Liu J, Cukier RI, Bu Y.

J Chem Theory Comput. 2013 Nov 12;9(11):4727-34. doi: 10.1021/ct4002174. Epub 2013 Oct 31.

PMID:
26583391
9.

Variance of a potential of mean force obtained using the weighted histogram analysis method.

Cukier RI.

J Phys Chem B. 2013 Nov 27;117(47):14785-96. doi: 10.1021/jp407956c. Epub 2013 Nov 18.

PMID:
24175967
10.

Computational simulation strategies for analysis of multisubunit RNA polymerases.

Wang B, Feig M, Cukier RI, Burton ZF.

Chem Rev. 2013 Nov 13;113(11):8546-66. doi: 10.1021/cr400046x. Epub 2013 Aug 29. Review. No abstract available.

11.

Excess dielectron in an ionic liquid as a dynamic bipolaron.

Liu J, Wang Z, Zhang M, Cukier RI, Bu Y.

Phys Rev Lett. 2013 Mar 8;110(10):107602. Epub 2013 Mar 6.

PMID:
23521297
12.

The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation.

Nedialkov YA, Opron K, Assaf F, Artsimovitch I, Kireeva ML, Kashlev M, Cukier RI, Nudler E, Burton ZF.

Biochim Biophys Acta. 2013 Feb;1829(2):187-98. doi: 10.1016/j.bbagrm.2012.11.005. Epub 2012 Nov 30.

13.

Solvation and evolution dynamics of an excess electron in supercritical CO2.

Wang Z, Liu J, Zhang M, Cukier RI, Bu Y.

Phys Rev Lett. 2012 May 18;108(20):207601. Epub 2012 May 17.

PMID:
23003186
14.

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase.

Kireeva ML, Opron K, Seibold SA, Domecq C, Cukier RI, Coulombe B, Kashlev M, Burton ZF.

BMC Biophys. 2012 Jun 7;5:11. doi: 10.1186/2046-1682-5-11.

15.

Simulations of temperature and salt concentration effects on bZIP, a basic region leucine zipper.

Cukier RI.

J Phys Chem B. 2012 May 31;116(21):6071-86. doi: 10.1021/jp300836t. Epub 2012 May 21.

PMID:
22559083
16.

Ferreting out correlations from trajectory data.

Cukier RI.

J Chem Phys. 2011 Dec 14;135(22):225103. doi: 10.1063/1.3666007.

PMID:
22168728
17.

A hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper.

Cukier RI.

J Chem Phys. 2011 Jan 28;134(4):045104. doi: 10.1063/1.3548074.

PMID:
21280805
18.

How many atoms are required to characterize accurately trajectory fluctuations of a protein?

Cukier RI.

J Chem Phys. 2010 Jun 28;132(24):245101. doi: 10.1063/1.3435207.

PMID:
20590215
19.

Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase.

Seibold SA, Singh BN, Zhang C, Kireeva M, Domecq C, Bouchard A, Nazione AM, Feig M, Cukier RI, Coulombe B, Kashlev M, Hampsey M, Burton ZF.

Biochim Biophys Acta. 2010 Aug;1799(8):575-87. doi: 10.1016/j.bbagrm.2010.05.002. Epub 2010 May 15.

20.

Exploration of the biological micro-surrounding effect on the excited states of the size-expanded fluorescent base x-cytosine in DNA.

Zhang L, Chen X, Liu H, Han L, Cukier RI, Bu Y.

J Phys Chem B. 2010 Mar 18;114(10):3726-34. doi: 10.1021/jp9117503.

PMID:
20175554
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