Faculty Sponsor(s)
Joelle Murray
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.
Recommended Citation
Sim, Yura, "Self-Organized Criticality in Protein Folding Simulations with AMBER Parameters" (2014). Linfield University Student Symposium: A Celebration of Scholarship and Creative Achievement. Event. Submission 47.
https://digitalcommons.linfield.edu/symposium/2014/all/47
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.
