Location

Jereld R. Nicholson Library

Subject Area

Physics

Description

AMBER (Assisted Model Building with Energy Refinement) is a force field that allows for the simulation of proteins. Basic proteins were folded by a Monte-Carlo algorithm parameterized by AMBER on MATLAB. Simulations exhibited self-organized critical (SOC) behavior and are shown to be stable throughout the simulations by use of pairwise distance matrixes. Frequency shifting is explored as a possible explanation of the mechanisms behind structure inducing probes (SIPs) in the solid phase synthesis of proteins. This also provides a mechanistic link to many other SOC systems.

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May 16th, 4:30 PM May 16th, 6:00 PM

Self-Organized Criticality in Protein Folding Simulations with AMBER Parameters

Jereld R. Nicholson Library

AMBER (Assisted Model Building with Energy Refinement) is a force field that allows for the simulation of proteins. Basic proteins were folded by a Monte-Carlo algorithm parameterized by AMBER on MATLAB. Simulations exhibited self-organized critical (SOC) behavior and are shown to be stable throughout the simulations by use of pairwise distance matrixes. Frequency shifting is explored as a possible explanation of the mechanisms behind structure inducing probes (SIPs) in the solid phase synthesis of proteins. This also provides a mechanistic link to many other SOC systems.

 

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