Scratchings on biomolecular simulation and theory

George A. Pantelopulos

I am a post-doctoral scholar working under the supervision of Robert Best and the Laboratory of Chemical Physics at NIH/NIDDK.

I recently completed my PhD with John E. Straub of the Boston University Chemistry Department. My new focus is on modeling of collagen and the extracellular matrix with atomistic accuracy with a focus toward reproduction of multiscale mechanics. This website is used to occasionally catalogue write-ups on theory, analysis, and software for sharing with colleagues.

Extramembrane β-strands control homodimerization of C99

less than 1 minute read

Recently, one of the last manuscripts prepared during my PhD work was published in PNAS as

An Introduction to Bilayer Phases, Cholesterol, Amyloid Precursor Protein, and their Relation

less than 1 minute read

Introduction to Lo phases, cholesterol induction of Lo phase and modulating APP-C99, and the role of Lo phase and subcellular compartments in Aβ generation.

Writing a Subset of Atom Coordinates in OpenMM

2 minute read

Often times in MD there are cases where we would like to write the coordinates of a system at a much higher frequency than is typical.

MolPainter and MolSolvator

1 minute read

Tools for building and solvating complex, planar molecular systems of arbitrary molecular composition and placement via painting.

OpenMM Tutorial

less than 1 minute read

I post the slides and tutorial scripts for an introductory OpenMM tutorial intended to showcase OpenMM’s features (and, by necessity, complexity).

George A. Pantelopulos

Recent Posts

Extramembrane β-strands control homodimerization of C99

An Introduction to Bilayer Phases, Cholesterol, Amyloid Precursor Protein, and their Relation

Writing a Subset of Atom Coordinates in OpenMM

MolPainter and MolSolvator

OpenMM Tutorial