Mixed monte carlo/molecular dynamics simulations in explicit solvent
نویسندگان
چکیده
منابع مشابه
Inter-DNA electrostatics from explicit solvent molecular dynamics simulations.
Electrostatic interactions drive a compaction of many biomolecules, such as RNA and DNA.1,2 For example, DNA is compacted a million-fold into a highly organized structure in eukaryotic cells, called chromatin.2-5 Understanding the mechanism of chromatin folding is of great biological importance, since it mediates the extent of accessibility of specific DNA sequences, which in turn, controls imp...
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Sulfated glycosaminoglycans (GAGs) are an important class of biomacromolecules involved in many biological functions. Due to the inherent limitations of experimental techniques in assessing the aspects related to their dynamics and interactions in solution, theoretical approaches like molecular dynamics simulations found extended applicability in complementing the experimental field. Recognizin...
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pH is an important parameter in condensed-phase systems, because it determines the protonation state of titratable groups and thus influences the structure, dynamics, and function of molecules in solution. In most force field simulation protocols, however, the protonation state of a system (rather than its pH) is kept fixed and cannot adapt to changes of the local environment. Here, we present ...
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End-to-end contact formation rates of several peptides were recently measured by tryptophan triplet quenching (Lapidus et al. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 7220). Motivated by these experiments, we study loop-closure kinetics for two peptides of different lengths, Cys-(Ala-Gly-Gln)n-Trp (n = 1, 2), in multiple all-atom explicit-solvent molecular dynamics simulations with different ini...
متن کاملCompression of high grafting density opposing polymer brushes using molecular dynamics simulations in explicit solvent.
Opposing polymer brush layers at high grafting density were examined under confinement and characterized with respect to structure and interaction forces using molecular dynamics simulations in an explicit solvent. The brush system underwent a static compression, where the system is simulated at several discrete separation distances. These simulations are all at the same solvent chemical potent...
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ژورنال
عنوان ژورنال: Journal of Computational Chemistry
سال: 2012
ISSN: 0192-8651
DOI: 10.1002/jcc.22925