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Items: 12

1.

Direct Measurement of the Effect of Cholesterol and 6-Ketocholestanol on the Membrane Dipole Electric Field Using Vibrational Stark Effect Spectroscopy Coupled with Molecular Dynamics Simulations.

Shrestha R, Anderson CM, Cardenas AE, Elber R, Webb LJ.

J Phys Chem B. 2017 Apr 20;121(15):3424-3436. doi: 10.1021/acs.jpcb.6b09007. Epub 2017 Jan 26.

PMID:
28071910
2.

Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning.

Cardenas AE, Elber R.

J Phys Chem B. 2016 Aug 25;120(33):8208-16. doi: 10.1021/acs.jpcb.6b01890. Epub 2016 Apr 5.

PMID:
27016332
3.

Membrane permeation of a peptide: it is better to be positive.

Cardenas AE, Shrestha R, Webb LJ, Elber R.

J Phys Chem B. 2015 May 28;119(21):6412-20. doi: 10.1021/acs.jpcb.5b02122. Epub 2015 May 13.

4.

Measurement of the membrane dipole electric field in DMPC vesicles using vibrational shifts of p-cyanophenylalanine and molecular dynamics simulations.

Shrestha R, Cardenas AE, Elber R, Webb LJ.

J Phys Chem B. 2015 Feb 19;119(7):2869-76. doi: 10.1021/jp511677j. Epub 2015 Feb 4.

5.

Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation.

Cardenas AE, Elber R.

J Chem Phys. 2014 Aug 7;141(5):054101. doi: 10.1063/1.4891305.

6.
7.

Analyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples.

Viswanath S, Kreuzer SM, Cardenas AE, Elber R.

J Chem Phys. 2013 Nov 7;139(17):174105. doi: 10.1063/1.4827495.

8.

MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU system.

Ruymgaart AP, Cardenas AE, Elber R.

J Chem Theory Comput. 2011 Aug 26;7(10):3072-3082.

9.

Unassisted transport of N-acetyl-L-tryptophanamide through membrane: experiment and simulation of kinetics.

Cardenas AE, Jas GS, DeLeon KY, Hegefeld WA, Kuczera K, Elber R.

J Phys Chem B. 2012 Mar 8;116(9):2739-50. doi: 10.1021/jp2102447. Epub 2012 Feb 22.

10.

Computer simulations of the refolding of sperm whale apomyoglobin from high-temperature denaturated state.

Dametto M, Cárdenas AE.

J Phys Chem B. 2008 Aug 7;112(31):9501-6. doi: 10.1021/jp804300w. Epub 2008 Jul 11.

PMID:
18616314
11.
12.

Kinetics of cytochrome C folding: atomically detailed simulations.

Cárdenas AE, Elber R.

Proteins. 2003 May 1;51(2):245-57.

PMID:
12660993

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