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Results: 1 to 20 of 62

1.

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
[PubMed - in process]
2.

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
[PubMed - in process]
3.

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
[PubMed]
4.

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.

PMID:
23987500
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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
[PubMed]
6.

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.

PMID:
23202476
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
[PubMed - indexed for MEDLINE]
8.

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.

PMID:
22676913
[PubMed]
Free PMC Article
9.

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
[PubMed - indexed for MEDLINE]
10.

Ferreting out correlations from trajectory data.

Cukier RI.

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

PMID:
22168728
[PubMed]
11.

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
[PubMed - indexed for MEDLINE]
12.

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
[PubMed - indexed for MEDLINE]
13.

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.

PMID:
20478425
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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
[PubMed - indexed for MEDLINE]
15.

States and migration of an excess electron in a pyridinium-based, room-temperature ionic liquid: an ab initio molecular dynamics simulation exploration.

Wang Z, Zhang L, Cukier RI, Bu Y.

Phys Chem Chem Phys. 2010 Feb 28;12(8):1854-61. doi: 10.1039/b921104g. Epub 2010 Jan 7.

PMID:
20145852
[PubMed]
16.

Hamiltonian replica exchange method study of Escherichia coli and Yersinia pestis HPPK.

Su L, Cukier RI.

J Phys Chem B. 2009 Dec 17;113(50):16197-208. doi: 10.1021/jp903861a.

PMID:
19924845
[PubMed - indexed for MEDLINE]
17.

Hamiltonian replica exchange method studies of a leucine zipper dimer.

Su L, Cukier RI.

J Phys Chem B. 2009 Jul 16;113(28):9595-605. doi: 10.1021/jp900309q.

PMID:
19586073
[PubMed - indexed for MEDLINE]
18.

Excess electron solvation in an imidazolium-based room-temperature ionic liquid revealed by ab initio molecular dynamics simulations.

Wang Z, Zhang L, Chen X, Cukier RI, Bu Y.

J Phys Chem B. 2009 Jun 18;113(24):8222-6. doi: 10.1021/jp902575s.

PMID:
19469567
[PubMed - indexed for MEDLINE]
19.

Effect of metal ions on radical type and proton-coupled electron transfer channel: sigma-radical vs pi-radical and sigma-channel vs pi-channel in the imide units.

Chen X, Xing D, Zhang L, Cukier RI, Bu Y.

J Comput Chem. 2009 Dec;30(16):2694-705. doi: 10.1002/jcc.21284.

PMID:
19399771
[PubMed - indexed for MEDLINE]
20.

Hetero-ring-expansion design for adenine-based DNA motifs: evidence from DFT calculations and molecular dynamics simulations.

Han L, Li H, Cukier RI, Bu Y.

J Phys Chem B. 2009 Apr 2;113(13):4407-12. doi: 10.1021/jp8088726.

PMID:
19245224
[PubMed - indexed for MEDLINE]

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