MBN Explorer [ 1,2] is a multi-purpose software package designed to study molecular systems of

1. Studying DNA damage and nanofragmentation processes with MBN Explorer 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 Goethe 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 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. Parallel computing Possibilities • 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. www.mbnexplorer.com 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 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]. 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. 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]. 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. Structure of the modeled systems Potentials of interatomic interactions implemented in the MBN Explorer Lennard-Jones Exponential Power Coulomb Dzugutov Girifalco Morse Nanoindentation of NiTi alloy c) Pair potentials 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. Molecular simulation of nanoindentationprocess [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. 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. Sutton-Chen Finnis-Sinclair Gupta Brenner Tersoff Many-body potentials 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. Bond Angle Dihedral Improper Molecular Mechanics potentials 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. (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 Monte-Carlo method. Extended Molecular Mechanics potentials References 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 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). I.A. Solov'yov, A. Koshelev, A. Shutovich, A.V. Solov'yov, W.Greiner, Phys. Rev. Lett. 90, 053401 (2003). E. Surdutovich, A.V. Yakubovich, A.V. Solovyov, Sci. Rep., 3, 1289 (2013). A. Lando, N. Kébaïli, P. Cahuzac, A. Masson, C. Bréchignac, Phys. Rev. Lett. 97, 133402 (2006). A. Lando, N. Kébaïli, P. Cahuzac, C. Colliex, M. Couillard, A. Masson, M. Schmidt, C. Bréchignac, EPJD 43, 151 (2007). C. Bréchignacet al., Eur. Phys. J. D 24, 265 (2003). V.V. Dick, I.A. Solov'yov, A.V. Solov'yov, arXiv:1001.3992v1, (2010), submitted to Phys. Rev. B. V.V. Dick, I.A. Solov'yov, and A.V. Solov'yov,AIP Conf. Proc. 1197, 76 (2009). U. Essmann, L. Perera, M. Berkowitz. J. Chem. Phys. 103, (1995). A.V. Verkhovtsev, A.V. Yakubovich, G.B. Sushko, M. Hanauske, A.V. Solov’yov, Comp. Mat. Sci., in press(2013). 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).