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.

2D Bond-Orientational Order for Lipid Membranes

4 minute read

I discuss the use of 2D Bond-Orientational Order to describe lipid phase in membrane and the use of projections to address membrane undulation when measuring.

Measuring Structural Order Parameters in Intra- and Interleaflet Lipid Clusters

4 minute read

I discuss use of hierarchical clustering to identify intra- and inter-leaflet clusters of lipids and analysis using MDAnalysis, scipy, and multiprocessing.

Mass-Scaling Simulated Tempering for Optimizing Time-steps

4 minute read

The simulated and parallel tempering are briefly discussed. I explain the MSST method and present its implementation in OpenMM.

George A. Pantelopulos

Recent Posts

2D Bond-Orientational Order for Lipid Membranes

Measuring Structural Order Parameters in Intra- and Interleaflet Lipid Clusters

Mass-Scaling Simulated Tempering for Optimizing Time-steps