Studying DNA damage and nanofragmentation
processes with MBN Explorer
www.fias.uni-frankfurt.de/mbn
G.B. Sushko1,2, M.A. Panshenskov1,2, S.S. Kazenyuk1,3, A.V. Yakubovich1,2, I.A. Solov’yov1,4, A.V. Solov’yov1,2
1) Virtual Institute on Nano Films, Allee des Noisetiers, 2 bte 30 Angleur, Belgium
2) Frankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Germany
3) Saint Petersburg Academic University of the Russian Academy of Sciences, 8/3 Khlopina str., 194021, Saint-Petersburg, Russia.
4) Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N. Mathews Ave, Urbana, Illinois 61801.
E-mail: ilia@mbnexplorer.com
Johann WolfgangGoethe
Goethe University
University
Introduction
Computational features
MBN Explorer [1,2] is a multi-purpose software
package designed to study molecular systems of
various degrees of complexity. A broad
variety of interatomic potentials implemented
in the MBN Explorer allows to simulate the
www.mbnexplorer.com
structure and dynamics of different molecular
systems, such as atomic clusters, fullerenes, nanotubes, proteins, DNA [3],
composite systems, nanofractals, etc. A distinct feature of the program is its
universality and applicability to a broad range of problems and molecular
systems. MBN Explorer is free of charge for academic institutions and can be
downloaded from the website www.mbnexplorer.com.
After registration on the website users get access to a detailed documentation on
the program as well to the extended library of examples of calculations covering
all features of MBN Explorer. One can use these examples as templates for
quick and convenient configuration of own tasks.
Possibilities
Parallel computing
MBN Explorer can perform the following
computations:
•Calculation of potential and kinetic energy
•Classical molecular dynamics simulation
•Structure optimization
•Monte-Carlo-based modeling of kinetic
processes
In order to reduce the time of computations, MBN Explorer
1.1 can use advantage of multiple processor cores using
OpenMP technology if executed on a multicore workstation.
Upcoming version will include support for MPI technology for
execution on clusters. Figure shows parallel speedup of
calculations for different systems.
Computational efficiency
Despite
the
universality,
the
computational efficiency of MBN
Explorer is comparable (and in
some cases even higher) than the
computational efficiency of the
existing programs.
Case studies
DNA damage by a shock wave caused by heavy ion propagation
DNA and Proteins – the elementary machines of life. With MBN
Explorer one can investigate the dynamics of Bio-Nano Systems of
varied level of complexity.
Full-atom MD simulation of a shock wave
propagating through a water medium with
nucleosome (~7･105 atoms). The simulations are
done with extended version of CHARMM
forcefields allowing for covalent bonds of DNA
backbone disintegration. Linear energy transfer of
heavy ion is ~7 keV/nm, which corresponds to
iron in the vicinity of its Bragg peak [3]. Strengths
of DNA backbone covalent bonds was chosen to
be equal to 19-21.5 kcal/mole. Long-range
electrostatic interactions were treated using
smooth particle mesh Ewald method via cardinal
B-splines [9].
Alteration of the properties of a surface by
deposition of metal clusters is of crucial
importance for the development of novel
coatings and catalysts. During the last years
the formation of silver fractals on graphite
substrate was extensively studied
both
experimentally [4-6] and theoretically [7,8].
Structure of the modeled systems
Molecular
Mechanics
potentials
Many-body
potentials
Pair potentials
Potentials of interatomic interactions implemented in the MBN Explorer
Lennard-Jones
Exponential
Power
Coulomb
Dzugutov
Girifalco
Morse
Sutton-Chen
Finnis-Sinclair
Gupta
Brenner
Tersoff
Nanoindentation of NiTi alloy
As a result of simulation we observe DNA
backbone fragmentation and breakage of P-O
bonds. The figure on the left represents the
structure of the system at 1.8 ps after heavy ion
propagation.
c)
The Lennard-Jones potential is a
mathematically simple model that
describes the van der Waals interaction.
The Dzugutov pair potential can be
applied for modeling of glass-forming
liquid metals.
Sutton-Chen potential is an example of a many-body potential. It is
usually used for the description of interaction of atoms in metallic
clusters and nanoparticles. Many-body potential can not be represented
as a linear combination of pair potentials.
Bond
Angle
Dihedral
Improper
Molecular simulation of nanoindentation process [10] of block of NiTi alloy. Calculations were performed
using MBN Explorer 1.1. Finnis-Sinclair potential was used in order to describe interaction between Ni and
Ti atoms. Rigid carbon indenter was moving with the speed 40 m/s. Sample cube's side is 26nm, it
consisted of 1 million of atoms. Figure illustrates a) isometric view of the system, b) side view of the
system, and c) stress distribution in the system.
Fractal growth and fragmentation on a surface
, where
The basic idea of the
molecular
mechanics
potential is to introduce
a simple parametric
form of the potential for
all physically important
interactions
in
a
molecular system.
Extended Molecular Mechanics potentials
a) Original and Extended bond potentials, b) Switching function for angular, dihedral and improper dihedral terms, c)
dependence of the angular term at various interactomic distances, d) dependence of the dihedral term at various
interatomic distances
In upcoming version of MBN Explorer molecular mechanics potentials were extended for
investigation the processes of covalent bonds breakage under mechanical stresses. User can define
the dissociation energy of the covalent bond and the bond breakage distance. The energy terms
corresponding to the variation of distances are modified with Morse potential (see figure a) having the
same equilibrium distance and steepness of the harmonic well at minimum as that defined by original
CHARMM molecular mechanics forcefield. Angular and dihedral angular terms associated with the
breaking bond are modified using smooth arctangent functions (see figures b, c, d).
(a) The fractal structure obtained by the diffusion
limited aggregation (DLA) method implemented in
MBN Explorer [7,8]; (b) Three dimensional structure
of a silver fractal grown on a graphite surface. The
simulations were conducted using Kinetic MonteCarlo method.
Time evolution of the number of fragments
calculated for the fragmentation of a fractal shown
in the left figure (black curve), and during the
nucleation process of randomly distributed
particles on surface (red curve). (a) weak binding
energy (b) enhanced binding energy.
References
1. I. A. Solov'yov, A. V. Yakubovich, P. V. Nikolaev, I. Volkovets, A. V. Solov'yov, "MesoBioNano explorer—A universal program for
multiscale computer simulations of complex molecular structure and dynamics." Journal Comp. Chem. 33, 30 (2012).
2. I.A. Solov'yov, A. Koshelev, A. Shutovich, A.V. Solov'yov, W.Greiner, Phys. Rev. Lett. 90, 053401 (2003).
3. E. Surdutovich, A.V. Yakubovich, A.V. Solovyov, Sci. Rep., 3, 1289 (2013).
4. A. Lando, N. Kébaïli, P. Cahuzac, A. Masson, C. Bréchignac, Phys. Rev. Lett. 97, 133402 (2006).
5. A. Lando, N. Kébaïli, P. Cahuzac, C. Colliex, M. Couillard, A. Masson, M. Schmidt, C. Bréchignac, EPJD 43, 151 (2007).
6. C. Bréchignac et al., Eur. Phys. J. D 24, 265 (2003).
7. V.V. Dick, I.A. Solov'yov, A.V. Solov'yov, arXiv:1001.3992v1, (2010), submitted to Phys. Rev. B.
8. V.V. Dick, I.A. Solov'yov, and A.V. Solov'yov, AIP Conf. Proc. 1197, 76 (2009).
9. U. Essmann, L. Perera, M. Berkowitz. J. Chem. Phys. 103, (1995).
10. A.V. Verkhovtsev, A.V. Yakubovich, G.B. Sushko, M. Hanauske, A.V. Solov’yov, Comp. Mat. Sci., in press (2013).