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 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 allows tofor combinethe differentmultiscale typesdescription of [[Interatomic_potential|interatomicmolecular potentials]]systems toby specify more than one interaction to a particular atom or a groupmeans of atoms.kinetic AdvancedMonte featuresCarlo of the program include flexible [[Coarse-grained_modeling|coarse graining]], the possibility to perform relativistic molecular dynamics simulationsapproach<ref>{{cite journal |authorsauthor=G.BM. Sushko, V.G. Bezchastnov,Panshenskov |author2=I.A. Solov'yov, A.V. Korol, W. Greiner, |author3=A.V. Solov'yov |title= SimulationEfficient of3D ultra-relativistickinetic electronsmonte andcarlo positronsmethod channelingfor inmodeling crystalsof withmolecular MBNstructure Explorerand dynamics |journal= J. Comput. PhysChem. |volume= 25235 |issue= 17 |pages= 404-4181317–1329 |year= 20132014 |pmid= 24752427 |doi= 10.10161002/jjcc.jcp.2013.06.02823613|s2cid= 8788528 }}</ref> of [[Ultrarelativistic_limit|ultra-relativistic]] particles in crystalline media, and simulation of irradiation-induced chemical transformations by means ofthe irradiation-driven molecular dynamics.<ref name="IDMD_EPJD_paper">{{cite journal |authorsauthor=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 |pagesissue= 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]]s to specify more than one interaction to a particular atom or a group of atoms.

The software is complemented with MBN Studio<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.

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.

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 |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 }}</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" />

== MBN Studio ==

MBN Explorer 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|access-date=31 August 2017}}</ref> - 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<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]]

* [[NAMD]]

* [[GROMACS]]

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[[Category:Molecular dynamics software]]

[[Category:MolecularComputational modelling softwarechemistry]]

[[Category:Molecular modelling software]]

[[Category:Physics software]]