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

  • Gennady B. Sushko
  • Ilia A. Solov’yov
  • Alexey V. Verkhovtsev
  • Sergey N. Volkov
  • Andrey V. Solov’yov
Regular Article
Part of the following topical collections:
  1. Topical Issue: COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy

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.

Graphical abstract

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Copyright information

© EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Gennady B. Sushko
    • 1
    • 2
  • Ilia A. Solov’yov
    • 3
    • 4
  • Alexey V. Verkhovtsev
    • 1
    • 2
    • 4
  • Sergey N. Volkov
    • 5
  • Andrey V. Solov’yov
    • 2
    • 4
  1. 1.Goethe-Universität Frankfurt am MainFrankfurt am MainGermany
  2. 2.MBN Research Center, Altenhöferallee 3Frankfurt am MainGermany
  3. 3.University of Southern Denmark (SDU)Odense MDenmark
  4. 4.A.F. Ioffe Physical-Technical InstituteSt. PetersburgRussia
  5. 5.Bogolyubov Institute for Theoretical PhysicsKievUkraine

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