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Items: 1 to 20 of 596

1.

Free energetics and the role of water in the permeation of methyl guanidinium across the bilayer-water interface: insights from molecular dynamics simulations using charge equilibration potentials.

Ou S, Lucas TR, Zhong Y, Bauer BA, Hu Y, Patel S.

J Phys Chem B. 2013 Apr 4;117(13):3578-92. doi: 10.1021/jp400389z. Epub 2013 Mar 26.

PMID:
23409975
2.
3.

Effect of acetone accumulation on structure and dynamics of lipid membranes studied by molecular dynamics simulations.

Posokhov YO, Kyrychenko A.

Comput Biol Chem. 2013 Oct;46:23-31. doi: 10.1016/j.compbiolchem.2013.04.005. Epub 2013 May 7.

PMID:
23764528
4.

Free energetics of arginine permeation into model DMPC lipid bilayers: coupling of effective counterion concentration and lateral bilayer dimensions.

Hu Y, Ou S, Patel S.

J Phys Chem B. 2013 Oct 3;117(39):11641-53. doi: 10.1021/jp404829y. Epub 2013 Sep 16.

5.

Molecular dynamics study of the behavior of selected nanoscale building blocks in a gel-phase lipid bilayer.

Redmill PS, McCabe C.

J Phys Chem B. 2010 Jul 22;114(28):9165-72. doi: 10.1021/jp1039942.

6.

An atomic and molecular view of the depth dependence of the free energies of solute transfer from water into lipid bilayers.

Tejwani RW, Davis ME, Anderson BD, Stouch TR.

Mol Pharm. 2011 Dec 5;8(6):2204-15. doi: 10.1021/mp2000204. Epub 2011 Nov 8.

PMID:
21988564
7.

Interaction of neurotransmitters with a phospholipid bilayer: a molecular dynamics study.

Peters GH, Werge M, Elf-Lind MN, Madsen JJ, Velardez GF, Westh P.

Chem Phys Lipids. 2014 Dec;184:7-17. doi: 10.1016/j.chemphyslip.2014.08.003. Epub 2014 Aug 23.

PMID:
25159594
8.

Phase-transfer energetics of small-molecule alcohols across the water-hexane interface: molecular dynamics simulations using charge equilibration models.

Bauer BA, Zhong Y, Meninger DJ, Davis JE, Patel S.

J Mol Graph Model. 2011 Apr;29(6):876-87. doi: 10.1016/j.jmgm.2010.09.005. Epub 2010 Oct 1.

9.

The importance of membrane defects-lessons from simulations.

Bennett WF, Tieleman DP.

Acc Chem Res. 2014 Aug 19;47(8):2244-51. doi: 10.1021/ar4002729. Epub 2014 Jun 3.

PMID:
24892900
11.

Nontrivial behavior of water in the vicinity and inside lipid bilayers as probed by molecular dynamics simulations.

Krylov NA, Pentkovsky VM, Efremov RG.

ACS Nano. 2013 Oct 22;7(10):9428-42. doi: 10.1021/nn4042392. Epub 2013 Sep 30.

PMID:
24070369
12.

Molecular dynamics simulation study of the effect of DMSO on structural and permeation properties of DMPC lipid bilayers.

Lin J, Novak B, Moldovan D.

J Phys Chem B. 2012 Feb 2;116(4):1299-308. doi: 10.1021/jp208145b. Epub 2012 Jan 18.

PMID:
22191390
13.

Orientational dependence of the affinity of guanidinium ions to the water surface.

Wernersson E, Heyda J, Vazdar M, Lund M, Mason PE, Jungwirth P.

J Phys Chem B. 2011 Nov 3;115(43):12521-6. doi: 10.1021/jp207499s. Epub 2011 Oct 10.

PMID:
21985190
14.
15.

Role of lipid charge in organization of water/lipid bilayer interface: insights via computer simulations.

Polyansky AA, Volynsky PE, Nolde DE, Arseniev AS, Efremov RG.

J Phys Chem B. 2005 Aug 11;109(31):15052-9.

PMID:
16852905
16.
17.
18.

Guanidinium Pairing Facilitates Membrane Translocation.

Allolio C, Baxova K, Vazdar M, Jungwirth P.

J Phys Chem B. 2016 Jan 14;120(1):143-53. doi: 10.1021/acs.jpcb.5b10404. Epub 2015 Dec 31.

PMID:
26673566
19.

Charge equilibration force fields for molecular dynamics simulations of lipids, bilayers, and integral membrane protein systems.

Lucas TR, Bauer BA, Patel S.

Biochim Biophys Acta. 2012 Feb;1818(2):318-29. doi: 10.1016/j.bbamem.2011.09.016. Epub 2011 Sep 24. Review.

20.

Molecular dynamics simulations of gramicidin A in a lipid bilayer: from structure-function relations to force fields.

Baştuğ T, Patra SM, Kuyucak S.

Chem Phys Lipids. 2006 Jun;141(1-2):197-204. Epub 2006 Mar 20.

PMID:
16600199

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