Published 6 issues per year
ISSN Print: 1543-1649
ISSN Online: 1940-4352
Indexed in
Simulation of Biomolecular Systems at Multiple Length and Time Scales
ABSTRACT
A novel multiscale simulation methodology is presented that is capable of modeling complex biomolecular systems across disparate time and length-scales. The methodology presented here employs novel mesoscopic simulation methods combined with nonequilibrium molecular dynamics at the atomistic level. The resulting disparate length and time scales associated with biological assemblies are thus effectively bridged. As an example, results for the multiscale simulation of Large Unilamellar Vesicles (LUVs) immersed in solvent are presented. It is found that in all cases the LUVs slightly contract to a smaller radius, as compared to the initial perfectly round state, to one where thermal undulations persist. In cases where the effective osmotic stress is altered, the LUVs are observed to expand or contract mesoscopically.
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Ayton Gary S., McWhirter J. Liam, Voth Gregory A., A second generation mesoscopic lipid bilayer model: Connections to field-theory descriptions of membranes and nonlocal hydrodynamics, The Journal of Chemical Physics, 124, 6, 2006. Crossref
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Ayton Gary S., McWhirter J. Liam, McMurtry Patrick, Voth Gregory A., Coupling Field Theory with Continuum Mechanics: A Simulation of Domain Formation in Giant Unilamellar Vesicles, Biophysical Journal, 88, 6, 2005. Crossref
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Chu J.-W., Ayton G. S., Izvekov S., Voth G. A., Emerging methods for multiscale simulation of biomolecular systems, Molecular Physics, 105, 2-3, 2007. Crossref
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Ayton Gary S., Voth Gregory A., Multiscale simulation of protein mediated membrane remodeling, Seminars in Cell & Developmental Biology, 21, 4, 2010. Crossref
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Ayton Gary S., Voth Gregory A., Multiscale simulation of transmembrane proteins, Journal of Structural Biology, 157, 3, 2007. Crossref
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Ayton Gary S., Izvekov Sergei, Noid W.G., Voth Gregory A., Chapter 7 Multiscale Simulation of Membranes and Membrane Proteins: Connecting Molecular Interactions to Mesoscopic Behavior, in Computational Modeling of Membrane Bilayers, 60, 2008. Crossref
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Ayton Gary S., Blood Philip D., Voth Gregory A., Membrane Remodeling from N-BAR Domain Interactions: Insights from Multi-Scale Simulation, Biophysical Journal, 92, 10, 2007. Crossref
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Ayton Gary S., Voth Gregory A., Mesoscopic Lateral Diffusion in Lipid Bilayers, Biophysical Journal, 87, 5, 2004. Crossref
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Stottrup Benjamin L., Keller Sarah L., Phase Behavior of Lipid Monolayers Containing DPPC and Cholesterol Analogs, Biophysical Journal, 90, 9, 2006. Crossref
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Badu Shyam, Melnik Roderick, Prabhakar Sanjay, RNA Nanostructures in Physiological Solutions: Multiscale Modeling and Applications, in Physics of Liquid Matter: Modern Problems, 171, 2015. Crossref
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Ayton Gary S., Voth Gregory A., Hybrid Coarse-Graining Approach for Lipid Bilayers at Large Length and Time Scales, The Journal of Physical Chemistry B, 113, 13, 2009. Crossref