Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

Abstract

The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, we provide several illustrative case studies where dynamical topology is necessary. In particular, it is shown that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems.

12 pages, 10 figures, accepted for publication in Eur. Phys. J. D

References in corpus (4)

• Physics of ion beam cancer therapy: a multi-scale approach
• Molecular dynamics study of the stability of a carbon nanotube atop a catalytic nanoparticle
• Alpha helix-coil phase transition: analysis of ab initio theory predictions
• A Rational Method for Probing Macromolecules Dissociation: The Antibody-Hapten System

Cited by in corpus (20)

• Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment
• Multiscale simulation of the focused electron beam induced deposition process
• Molecular dynamics study of accelerated ion-induced shock waves in biological media
• The effect of ion-induced shock waves on the transport of reacting species around energetic ion tracks
• Lethal DNA damages caused by ion-induced shock waves in cells
• Reactive molecular dynamics simulations of organometallic compound W(CO)6 fragmentation
• Classical molecular dynamics simulations of fusion and fragmentation in fullerene-fullerene collisions
• Phenomenon-based prediction of relative biological effectiveness of ion beams by means of the MultiScale Approach
• Modeling the effect of ion-induced shock waves and DNA breakage with the reactive CHARMM force field
• Irradiation driven molecular dynamics: A review
• Cell survival probability in a spread-out Bragg peak for novel treatment planning
• Ion-impact-induced multifragmentation of liquid droplets
• Atomistic simulation of the FEBID-driven growth of iron-based nanostructures
• Irradiation driven molecular dynamics simulation of the FEBID process for Pt(PF${}_3$)${}_4$
• Atomistic modeling of thermal effects in focused electron beam induced deposition of Me${}_2$Au(tfac)
• Role of the molecular environment in quenching the irradiation-driven fragmentation of Fe(CO)${}_5$: a reactive molecular dynamics study
• Calculation of survival probabilities for cells exposed to high ion fluences
• Advances in multiscale modeling for novel and emerging technologies
• Atomistic modelling of the channeling process with radiation reaction force included
• A molecular dynamics simulation of the abrupt changes in the thermodynamic properties of water after formation of nano-bubbles / nano-cavities induced by passage of charged particles