R-CCS Cafe第255回（2023年11月6日）

Title:
Coarse-grained modeling and simulation of protein and lipid dynamics
Abstract:
Computational modeling and simulations are powerful approaches to examine the structure-dynamics-function relationships of biomolecules. Due to the computational limitations, molecular dynamics simulations with atomistic models cannot describe slow biological processes. Here, we apply residue-level coarse-grained models for proteins and lipid molecules to study conformational dynamics of biomolecules in the cell. Structure-based approaches, such as the Go-model, are mainly employed for simulating protein dynamics, while physics-based approaches are partially used. We have also developed a heterogeneous domain-decomposition scheme for coarse-grained molecular dynamics simulations and carried out large-scale biological simulations on Fugaku. We have also developed new coarse-grained models of lipid molecules treating their electrostatic interactions explicitly. We plan to integrate the coarse-grained lipid models with the residue-level coarse-grained models for proteins and simulate large biological membranes or other slow biological processes near the membrane interfaces.