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Proceedings Paper

Protein simulations in confined environments
Author(s): Murat Cetinkaya; Jorge Sofo; Melik C. Demirel
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Paper Abstract

Materials surfaces mimic cell like architecture and proteins can be encapsulated by these material surfaces (e.g. a porous glass or gold). Depending on the number and types of surface interactions, this confine environment could destroy the protein or help it maintain its bioactivity. We developed computer models and simulation tools for the understanding of surface-protein interaction at the atomistic levels. At the molecular level, molecular dynamics simulations are very powerful, but the high computational cost of molecular simulations is a drawback. A viable alternative method to study protein-surface interactions is the coarse-grained molecular simulations of simplified models, such as elastic network model. At the atomic interaction level, we used ab initio simulations to calculate the potential between surface and protein atoms.

Paper Details

Date Published: 2 August 2004
PDF: 5 pages
Proc. SPIE 5509, Nanomodeling, (2 August 2004); doi: 10.1117/12.558733
Show Author Affiliations
Murat Cetinkaya, The Pennsylvania State Univ. (United States)
Jorge Sofo, The Pennsylvania State Univ. (United States)
Melik C. Demirel, The Pennsylvania State Univ. (United States)


Published in SPIE Proceedings Vol. 5509:
Nanomodeling
Akhlesh Lakhtakia; Sergey A. Maksimenko, Editor(s)

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