Protein simulations in confined environments

Murat Cetinkaya, Jorge Sofo, Melik C. Demirel

Research output: Contribution to journalConference articlepeer-review


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.

Original languageEnglish (US)
Article number14
Pages (from-to)133-137
Number of pages5
JournalProceedings of SPIE - The International Society for Optical Engineering
StatePublished - 2004
EventNanomodeling - Denver, CO, United States
Duration: Aug 2 2004Aug 3 2004

All Science Journal Classification (ASJC) codes

  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics
  • Computer Science Applications
  • Applied Mathematics
  • Electrical and Electronic Engineering


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