Physics Dept Seminar

March 9, Monday

From Atomistic Detail to Mesoscopic Complexity:

A Coarse-Grained Journey in Biomolecular Simulation

Dr. Peter Park

Lehigh Univ.

(Biophysics: Host: Dias)

Time: 11:45 am - 12:45 pm with 11:30 am teatime

Room: ECE 202

Molecular dynamics (MD) simulations connect microscopic interactions to emergent biological functions. My research began with atomistic MD simulations of membrane-active peptides interacting with lipid bilayers, where chemical detail enables mechanistic insight. As the scientific questions evolved toward larger peptide concentrations, atomistic resolution became computationally prohibitive.

To access larger systems — including multi-peptide assemblies and full lipid vesicles — I transitioned from all-atom to coarse-grained (CG) modeling using the Martini force field. By reducing chemical resolution while preserving essential thermodynamic properties, Martini enabled the simulation of mesoscale peptide–membrane phenomena inaccessible at the atomistic level. I applied Martini to peptide/vesicle systems to investigate curvature induction, aggregation, and membrane disruption mechanisms.

Subsequently, my work needed force field development and validation, including systematic testing of GoMartini3 for structure-biased protein modeling. More recently, I have focused on lipid nanoparticles (LNPs), particularly the parameterization of ionizable lipids critical for nucleic acid delivery systems. My scientific pathway required required bridging physical chemistry, statistical mechanics, and model calibration against experimental observables.

This seminar will present both scientific results and methodological insights, illustrating how coarse-graining serves not merely as a computational shortcut, but as a framework for exploring emergent biophysical phenomena across scales.