MBN Explorer: Difference between revisions

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{{Short description|Chemistry simulation software}}

{{Infobox software

| name = MesoBioNano Explorer

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| released = {{Start date and age|2012}}

| latest release version = 3.0

| latest release date = {{Start date and age|2017|03|31|}}

| status = Active

| programming language = [[C++]]

| operating system = [[Cross-platform]]: [[Microsoft Windows|Windows]], [[Linux]], [[macOS]]

| platform = [[x86]], [[x86-64]]
| size =

| language = English

| genre = [[Molecular dynamics]], [[Kinetic_Monte_Carlo|kinetic Monte Carlo]] simulations

| license = [[Proprietary software|Proprietary]]; free trial

| website = {{URL|www.mbnexplorer.com}}

}}

'''MBN Explorer''' ('''MesoBioNano Explorer''') is a software package for [[Molecular dynamics|molecular dynamics]] simulations, [[Energy_minimizationEnergy minimization|structure optimization]] and [[Kinetic_Monte_Carlo|kinetic Monte Carlo]] simulations. It is designed for [[Multiscale_modelingMultiscale modeling|multiscale computational analysis]] of structure and dynamics of [[Cluster_Cluster (physics)|atomic clusters]] and [[Nanoparticle|nanoparticlesnanoparticle]]s, [[Biomolecule|biomoleculesbiomolecule]]s and nanosystems, nanostructured materials, different states of matter and various interfaces.<ref>{{cite web|title=About MBN Explorer|url=http://www.mbnresearch.com/get-mbn-explorer-software|publisher=mbnresearch.com|accessdateaccess-date=31 August 2017}}</ref> 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.<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|accessdateaccess-date=31 August 2017}}</ref> A variety of interatomic potentials and the possibility to combine a group of atoms into rigid blocks were introduced in 2005-20072005–2007. 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 |authorsauthor=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= 2412-24392412–2439 |year= 2012 |pmid= 22965786 |doi= 10.1002/jcc.23086|s2cid= 22553279 }}</ref>

== Features ==

MBN Explorer adoptsallows afor the [[Multiscale_modeling|multiscale modeling]]description of molecular systems by means of kinetic Monte Carlo approach<ref>{{cite journal |author=M. ItPanshenskov allows|author2=I.A. toSolov'yov study|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 }}</ref> and the irradiation-driven molecular dynamics.<ref name="IDMD_EPJD_paper">{{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 }}</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 potentialspotential]]s to specify more than one interaction to a particular atom or a group of atoms. Advanced features of the program include:

* flexible [[Coarse-grained_modeling|coarse graining]],

* 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}}</ref> of [[Ultrarelativistic_limit|ultra-relativistic]] particles in crystalline media,

* simulation of irradiation-induced chemical transformations by means of irradiation-driven molecular dynamics.<ref>{{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 |pages= 217 |year= 2016 |doi=10.1140/epjd/e2016-70283-5}}</ref>.

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.

The software is complemented with MBN Studio<ref name="MBN_Springer_2017" /><ref>{{cite web|title=About MBN Studio|url=http://www.mbnresearch.com/mbn-studio|publisher=mbnresearch.com|accessdate=31 August 2017}}</ref> - a graphical user interface that is used to set up calculations, construct various molecular systems, and analyze results of the simulations.

Advanced features of the program include:

* flexible [[Coarse-grained modeling|coarse graining]] and the possibility to simulate [[Euler's equations (rigid body dynamics)|dynamics of rigid bodies]],

* the possibility to perform relativistic molecular dynamics simulations<ref>{{cite journal |authorsauthor=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= 404-418404–418 |year= 2013 |doi=10.1016/j.jcp.2013.06.028|arxiv=1307.6771 |bibcode= 2013JCoPh.252..404S |s2cid= 2157486 }}</ref> of [[Ultrarelativistic_limitUltrarelativistic 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" />

== MBN Studio ==

TheMBN softwareExplorer is complemented with MBN Studio<ref name="MBN_Springer_2017" /><ref>{{cite web|title=About MBN Studio|url=http://www.mbnresearch.com/mbn-studio|publisher=mbnresearch.com|accessdateaccess-date=31 August 2017}}</ref> - a graphicalmulti-task userprogram interfacefor thatmolecular ismodeling 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 setconstruct upisolated calculations,and constructsolvated biomolecules, variouscondensed molecular systemsmaterials, carbon nanotubes and analyzegraphene resultssheets, ofnanoparticles theand simulations.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<ref>{{cite web|title=FP7 ITN ARGENT Project|url=http://www.itn-argent.eu}}</ref><br />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.

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== See also ==

* [[Comparison_of_software_for_molecular_mechanics_modeling|Comparison of software for molecular mechanics modeling]]

* [[List_of_software_for_nanostructures_modeling|List of software for nanostructures modeling]]

* [[NAMD]]

* [[GROMACS]]

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[[Category:Molecular dynamics software]]

[[Category:MolecularComputational modelling softwarechemistry]]

[[Category:Molecular modelling software]]

[[Category:Physics software]]