Toward Grid-Based Models for Molecular Association.

ABSTRACT: This paper presents a grid-based approach to model molecular association processes as an alternative to sampling-based Markov models. Our method discretizes the six-dimensional space of relative translation and orientation into grid cells. By discretizing the Fokker-Planck operator governing the system dynamics via the square-root approximation, we derive analytical expressions for the transition rate constants between grid cells. These expressions depend on geometric properties of the grid, such as the cell surface area and volume, which we provide. In addition, one needs only the molecular energy at the grid cell center, circumventing the need for extensive MD simulations and reducing the number of energy evaluations to the number of grid cells. The resulting rate matrix is closely relat

SUBMITTER: Zupan H 

PROVIDER: S-EPMC11780749 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature