MBN Explorer: Difference between revisions

Revision as of 12:12, 24 April 2020

Revision as of 10:30, 29 September 2020

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== History ==

MBN Explorer inherited the experience obtained on the development of the software package Cluster Searcher. It started around 2000 as a classical molecular dynamics code for simulating many-body systems interacting via the Morse and the Lennard-Jones potentials.<ref>{{cite web|title=MBN Explorer: A decade development now available for the community|url=http://www.vinf.eu/news/mbn-explorer-decade-development-now-available-community|publisher=Virtual Institute of Nano Films|accessdate=31 August 2017}}</ref> A variety of interatomic potentials and the possibility to combine a group of atoms into rigid blocks were introduced in 2005-2007. The first version of MBN Explorer was released in 2012 as a multipurpose computer code allowing to model different molecular systems of varied level of complexity.<ref>{{cite journal |authors=I.A. Solov'yov, A.V. Yakubovich, P.V. Nikolaev, I. Volkovets, A.V. Solov'yov |title= MesoBioNano Explorer - A universal program for multiscale computer simulations of complex molecular structure and dynamics |journal= J. Comput. Chem. |volume= 33 |issue= 30 |pages= 2412–2439 |year= 2012 |pmid= 22965786 |doi= 10.1002/jcc.23086|s2cid= 22553279 }}</ref>

== Features ==

MBN Explorer allows for the multiscale description of molecular systems by means of kinetic Monte Carlo approach<ref>{{cite journal |authors=M. Panshenskov, I.A. Solov'yov, A.V. Solov'yov |title= Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics |journal= J. Comput. Chem. |volume= 35 |issue= 17 |pages= 1317–1329 |year= 2014 |pmid= 24752427 |doi= 10.1002/jcc.23613|s2cid= 8788528 }}</ref> and the irradiation-driven molecular dynamics<ref name="IDMD_EPJD_paper">{{cite journal |authors=G.B. Sushko, I.A. Solov'yov, A.V. Solov'yov |title= Molecular dynamics for irradiation driven chemistry: application to the FEBID process |journal= Eur. Phys. J. D |volume= 70 |issue= 10 |pages= 217 |year= 2016 |doi=10.1140/epjd/e2016-70283-5|s2cid= 54844470 |url= https://portal.findresearcher.sdu.dk/da/publications/52cb3c8a-5c82-4686-be64-b541107227b9 }}</ref>. By means of the Monte Carlo approach, the software allows to simulate diffusion-drive processes involving molecular systems on much larger time scales that can be reached in conventional molecular dynamics simulations<ref name="MBN_Springer_2017">{{cite book |title= Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer|author1=I.A. Solov'yov |author2=A.V. Korol |author3=A.V. Solov'yov |year= 2017 |publisher=Springer International Publishing |isbn= 978-3-319-56085-4 }}</ref>. The software allows to combine different types of [[Interatomic_potential|interatomic potentials]] to specify more than one interaction to a particular atom or a group of atoms.

MBN Explorer supports several standard atomic trajectory formats, such as XYZ (text format), DCD<ref>{{cite web|title=DCD Trajectory I/O|url=http://www.mdanalysis.org/mdanalysis/documentation_pages/coordinates/DCD.html}}</ref> (binary format) and DCD+XYZ (hybrid format). It also supports the [[Protein_Data_Bank_(file_format)|Protein Data Bank]]<ref>{{cite web|title=Protein Data Bank|url=https://www.rcsb.org/pdb/home/home.do}}</ref> (pdb) file format for describing the three-dimensional structures of biomolecules.

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Advanced features of the program include:

* flexible [[Coarse-grained_modeling|coarse graining]] and the possibility to simulate [[Euler%27s_equations_(rigid_body_dynamics)|dynamics of rigid bodies]],

* the possibility to perform relativistic molecular dynamics simulations<ref>{{cite journal |authors=G.B. Sushko, V.G. Bezchastnov, I.A. Solov'yov, A.V. Korol, W. Greiner, A.V. Solov'yov |title= Simulation of ultra-relativistic electrons and positrons channeling in crystals with MBN Explorer |journal= J. Comput. Phys. |volume= 252 |pages= 404–418 |year= 2013 |doi=10.1016/j.jcp.2013.06.028|arxiv=1307.6771 |s2cid= 2157486 }}</ref> of [[Ultrarelativistic_limit|ultra-relativistic]] particles in crystalline media,

* simulation of irradiation-induced chemical transformations by means of irradiation-driven molecular dynamics<ref name="IDMD_EPJD_paper" />.