MBN Explorer

MesoBioNano Explorer (MBN Explorer) is a multi-purpose computer software package aimed to model molecular systems of varied level of complexity. The program is developed jointly with Prof. Andrey V. Solov'yov and his colleagues. MBN Explorer for academic institutions is distributed free of charge and includes precompiled binaries for Linux, Windows and MacOSX platforms on the MBN Explorer official website www.mbnexplorer.com.

mbn-explorer-systems.jpg
Figure 1. Variety of molecular systems which can be simulated using MBN Explorer: encapsulated clusters, deposited nanoparticles, nanofractals, composite nanowires, proteins, biomolecules, e.g., DNA, in solution. Structure and properties of any of these objects or any of their combinations can be studied using MBN Explorer.

 

MBN Explorer allows to model molecular systems of varied level of complexity. In particular, MBN Explorer is suited to compute system's energy, to optimize molecular structure, as well as to consider the molecular and random walk dynamics. MBN Explorer allows to use a broad variety of interatomic potentials, to model different molecular systems, such as atomic clusters, fullerenes, nanotubes, polypeptides, proteins, DNA, composite systems, nanofractals, etc. On demand, MBN Explorer allows to group particles in the system into rigid fragments, thereby significantly reducing the number of dynamical degrees of freedom. Despite the universality, the computational efficiency of MBN Explorer is comparable (and in some cases even higher) than the computational efficiency of other software packages, making MBN Explorer a possible alternative to the available codes.

Computational tasks

-- Single point energy calculation;
-- Molecular structure optimization;
-- Classical molecular dynamics simulation;
-- Random walk dynamics

Interaction potentials

-- Power potential;
-- Exponential potential;
-- Coulomb potential;
-- Lennard-Jones potential;
-- Morse potential;
-- Girifalco potential;
-- Dzugutov potential;
-- Quasi Sutton-Chen potential;
-- Sutton-Chen potential;
-- Gupta potential;
-- Brenner potential;
-- Tersoff potential;
-- Finnis-Sinclair potential;
-- CHARMM molecular mechanics potential;
-- External electric fields;
-- External viscous fields;

Implemented algorithms

-- OpenMP parallelization for shared memory computers;
-- Velocity Verlet and Leapfrog integrators;
-- Velocity quenching and conjugate gradient optimization methods;
-- Linked Cell algorithm;
-- Periodic and reflective boundary conditions;
-- Langevin and Berendsen thermostats;
-- Ewald summation for long-range interactions;
-- Rigid body Euler dynamics;
-- External forces and user-defined particle manipulation;
-- Momentum and angular momentum control;

Input and output formats

-- Cartesian XYZ;
-- Binary DCD;
-- Protein data bank, PDB;
-- X-PLOR PSF;

Recent Publications

Advances in multiscale modeling for novel and emerging technologies, Alexey V. Verkhovtsev, Ilia A. Solov'yov, Andrey V. Solov'yov, European Physical Journal D, 75, 217-(1-18), (2021)
Irradiation-driven molecular dynamics: a review, Alexey V. Verkhovtsev, Ilia A. Solov'yov, Andrey V. Solov'yov, European Physical Journal D, 75, 213-(1-12), (2021)
Lethal DNA damage caused by ion-induced shock waves in cells, Ida Friis, Alexey Verkhovtsev, Ilia A. Solov'yov, Andrey V. Solov'yov, Physical Review E, 104, 054408, (2021)
Multiscale modeling with MBN Explorer and MBN Studio, Alexey V. Verkhovtsev, Ilia A. Solov'yov, Andrey V. Solov'yov, in: Tools for investigating electronic excitation: experiment and multi-scale modelling, edited by: T. Apostolova and J. Kohanoff and N. Medvedev and E. Oliva and A. Rivera, 295-323, Instituto de Fusión Nuclear "Guillermo Velarde" Universidad Politécnica de Madrid, (2021)
Irradiation driven molecular dynamics with reactive CHARMM force field, Alexey V. Verkhovtsev, Ilia A. Solov'yov, Andrey V. Solov'yov, in: Tools for investigating electronic excitation: experiment and multi-scale modelling, edited by: T. Apostolova and J. Kohanoff and N. Medvedev and E. Oliva and A. Rivera, 325-3244, Instituto de Fusión Nuclear "Guillermo Velarde" Universidad Politécnica de Madrid, (2021)