Programmable Potentials: Approximate N-body potentials from coarse-level logic

TL;DR

This paper introduces a systematic method to construct approximate N-body potentials using logic-based pairwise potentials, enabling accurate meso-scale modeling of complex chemical and biological systems.

Contribution

It presents a novel formalism that combines logic rules with pairwise potentials to create coarse-grained N-body models for diverse molecular systems.

Findings

Successfully applied to inhibitor molecules, chemical bond breaking, and DNA transcription.

Provides a low-dimensional yet accurate representation of meso-scale behavior.

Potential for reverse design of molecular processes.

Abstract

This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from experimental data or ab initio methods. The meso-scale behavior is translated into logic rules for the dynamics. Each pairwise potential has an associated logic function that is constructed using the logic rules, a class of elementary logic functions, and AND, OR, and NOT gates. The effect of each logic function is to turn its associated potential on and off. The N-body potential is constructed as linear combination of the pairwise potentials, where the "coefficients" of the potentials are smoothed versions of the associated logic functions. These potentials allow a potentially low-dimensional description of complex processes while still accurately capturing the relevant physics at the meso-scale. We present the proposed formalism to construct coarse-grained potential models for three examples: an inhibitor molecular system, bond breaking in chemical reactions, and DNA transcription from biology. The method can potentially be used in reverse for design of molecular processes by specifying properties of molecules that can carry them out.