arXiv subjects

John P. Donohue

Publications and source records attributed to John P. Donohue.

2 recordsLinked to original sources

arXiv2004

Another Monte Carlo Renormalization Group Algorithm

A Monte Carlo Renormalization Group algorithm is used on the Ising model to derive critical exponents and the critical temperature. The algorithm is based on a minimum relative entropy iteration developed previously to derive potentials from equilibrium configurations. This previous algorithm is modified to derive useful information in an RG iteration. The method is applied in several dimensions with limited success. Required accuracy has not been achieved, but the method is interesting.

physics.comp-ph↗

arXiv2003

An Inverse Equilibrium Maximum Entropy Algorithm Applied to Proteins

A computational method is developed to work on an inverse equilibrium problem with an interest towards applications with protein folding. In general, we are given a set of equilibrium confgiurations and want to derive the most probable potential function that results in these configurations. The method is applied to polymer simulations and a simple model of proteins using protein structures obtained from the Protein Data Bank http://www.rcsb.org/pdb The resulting energy function is tested on a few decoy sets with limited success.

physics.bio-ph↗