Water-silica force field for simulating nanodevices
Article Abstract:
A force field for amorphous silica surfaces based on their macroscopic wetting properties that is compatible with the CHARMM force field and TIP3P water model is developed using molecular dynamics (MD) simulation to study the behavior of biomolecules interacting with silica. Results reveal that minute modeling of the amorphous surface is critical for MD studies, since the particular arrangement of surface atoms controls sensitively electrostatic interactions between silica and water.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
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Molecular dynamic study of bacteriorhodopsin and the purple membrane
Article Abstract:
Bacteriorhodopsin (bR) is a membrane protein that acts as a light driven, voltage-sensitive proton pump in the purple membrane (PM) of Halobacterium salinarum and achieves its biological function by cycling through reaction sequence. BR is simple in comparison with other proton translocating bioenergetic proteins and constitutes as an ideal model for the study of fundamental energy conversion process.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2001
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Role of water in transient cytochrome c2 docking
Article Abstract:
Molecular dynamics (MD) simulations of the reaction center (RC)cyt c2 encounter complex for both redox states of cyt c2 are reported. The results revealed that single-file water molecules serve as a redox switch where water molecules could sense the change in electrostatic potential leading to facilitated undocking after oxidation.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2004
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