# MBN Explorer > Mediated Wiki article. Canonical URL: https://mediated.wiki/source/MBN_Explorer > Markdown URL: https://mediated.wiki/source/MBN_Explorer.md > Source: https://en.wikipedia.org/wiki/MBN_Explorer > Source revision: 1280775038 > License: Creative Commons Attribution-ShareAlike 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) {{Short description|Chemistry simulation software}} {{Infobox software | name = MesoBioNano Explorer | developer = MBN Research Center | released = {{Start date and age|2012}} | latest release version = 3.0 | latest release date = {{Start date and age|2017|03|31}} | programming language = [C++](/source/C%2B%2B) | operating system = [Cross-platform](/source/Cross-platform): [Windows](/source/Microsoft_Windows), [Linux](/source/Linux), [macOS](/source/macOS) | platform = [x86](/source/x86), [x86-64](/source/x86-64) | size = | language = English | genre = [Molecular dynamics](/source/Molecular_dynamics), [kinetic Monte Carlo](/source/kinetic_Monte_Carlo) simulations | license = [Proprietary](/source/Proprietary_software); free trial | website = {{URL|www.mbnexplorer.com}} }} '''MBN Explorer''' ('''MesoBioNano Explorer''') is a software package for [molecular dynamics](/source/molecular_dynamics) simulations, [structure optimization](/source/Energy_minimization) and [kinetic Monte Carlo](/source/kinetic_Monte_Carlo) simulations. It is designed for [multiscale computational analysis](/source/Multiscale_modeling) of structure and dynamics of [atomic clusters](/source/Cluster_(physics)) and [nanoparticle](/source/nanoparticle)s, [biomolecule](/source/biomolecule)s and nanosystems, nanostructured materials, different states of matter and various interfaces.{{cite web|title=About MBN Explorer|url=http://www.mbnresearch.com/get-mbn-explorer-software|publisher=mbnresearch.com|access-date=31 August 2017}} The software has been developed by MBN Research Center. == 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.{{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|access-date=31 August 2017}} 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.{{cite journal |author=I.A. Solov'yov |author2=A.V. Yakubovich |author3=P.V. Nikolaev |author4=I. Volkovets |author5=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 }} == Features == MBN Explorer allows for the multiscale description of molecular systems by means of kinetic Monte Carlo approach{{cite journal |author=M. Panshenskov |author2=I.A. Solov'yov |author3=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 }} and the irradiation-driven molecular dynamics.{{cite journal |author=G.B. Sushko |author2=I.A. Solov'yov |author3=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 |page= 217 |year= 2016 |doi=10.1140/epjd/e2016-70283-5|bibcode= 2016EPJD...70..217S |s2cid= 54844470 |url= https://portal.findresearcher.sdu.dk/da/publications/52cb3c8a-5c82-4686-be64-b541107227b9 }} 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.{{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 }} The software allows to combine different types of [interatomic potential](/source/interatomic_potential)s 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{{cite web|title=DCD Trajectory I/O|url=http://www.mdanalysis.org/mdanalysis/documentation_pages/coordinates/DCD.html}} (binary format) and DCD+XYZ (hybrid format). It also supports the [Protein Data Bank](/source/Protein_Data_Bank_(file_format)){{cite web|title=Protein Data Bank|url=https://www.rcsb.org/pdb/home/home.do}} (pdb) file format for describing the three-dimensional structures of biomolecules. Advanced features of the program include: * flexible [coarse graining](/source/Coarse-grained_modeling) and the possibility to simulate [dynamics of rigid bodies](/source/Euler's_equations_(rigid_body_dynamics)), * the possibility to perform relativistic molecular dynamics simulations{{cite journal |author=G.B. Sushko |author2=V.G. Bezchastnov |author3=I.A. Solov'yov |author4=A.V. Korol |author5=W. Greiner |author6=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 |bibcode= 2013JCoPh.252..404S |s2cid= 2157486 }} of [ultra-relativistic](/source/Ultrarelativistic_limit) particles in crystalline media, * simulation of irradiation-induced chemical transformations by means of irradiation-driven molecular dynamics. == MBN Studio == MBN Explorer is complemented with MBN Studio{{cite web|title=About MBN Studio|url=http://www.mbnresearch.com/mbn-studio|publisher=mbnresearch.com|access-date=31 August 2017}} - a multi-task program for molecular modeling and design, as well as for visualization and analysis of results of the simulations performed with MBN Explorer. The built-in molecular modeler can be used to construct isolated and solvated biomolecules, condensed molecular materials, carbon nanotubes and graphene sheets, nanoparticles and crystalline samples. == Projects and collaborations == MBN Explorer has been utilized in different research projects in the fields of materials science, nanotechnology and radiation damage: * ARGENT - Advanced Radiotherapy, Generated by Exploiting Nanoprocesses and Technologies{{cite web|title=FP7 ITN ARGENT Project|url=http://www.itn-argent.eu}}
This is a multidisciplinary network project involving different research groups, academic and industrial partners. It is financed by the Seventh Framework Programme (FP7) of the EU. * PEARL - Periodically Bent Crystals for Crystalline Undulators{{cite web|title=PEARL Project|url=http://cordis.europa.eu/project/rcn/200088_en.html}}
This is an international project supported by the Horizon 2020 Programme (H2020) of the EU. * Nano-IBCT - Nanoscale Insights into Ion-Beam Cancer Therapy{{cite web|title=COST Action Nano-IBCT|url=http://www.cost.eu/COST_Actions/mpns/nano-ibct/}} * VINAT - Theoretical analysis, design and virtual testing of biocompatibility and mechanical properties of titanium-based nanomaterials{{cite web|title=VINAT Project|url=http://cordis.europa.eu/project/rcn/101137_en.html}} == See also == * [Comparison of software for molecular mechanics modeling](/source/Comparison_of_software_for_molecular_mechanics_modeling) * [List of software for nanostructures modeling](/source/List_of_software_for_nanostructures_modeling) * [NAMD](/source/NAMD) * [GROMACS](/source/GROMACS) * [LAMMPS](/source/LAMMPS) == References == {{Reflist|2}} == External links == * [http://www.mbnresearch.com/ MBN Research Center website] Category:Molecular dynamics software Category:Computational chemistry Category:Molecular modelling software Category:Physics software --- Adapted from the Wikipedia article [MBN Explorer](https://en.wikipedia.org/wiki/MBN_Explorer) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/MBN_Explorer?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.