| 词条 | MBN Explorer |
| 释义 |
| 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|}} | status = Active | programming language = C++ | operating system = Cross-platform: Windows, Linux, macOS | platform = x86, x86-64| size = | language = English | genre = Molecular dynamics, kinetic Monte Carlo simulations | license = Proprietary; free trial | website = {{URL|www.mbnexplorer.com}} }} MBN Explorer (MesoBioNano Explorer) is a software package for molecular dynamics simulations, structure optimization and kinetic Monte Carlo simulations. It is designed for multiscale computational analysis of structure and dynamics of atomic clusters and nanoparticles, biomolecules and nanosystems, nanostructured materials, different states of matter and various interfaces.[1] The software has been developed by MBN Research Center. HistoryMBN 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.[2] 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.[3] FeaturesMBN Explorer allows for the multiscale description of molecular systems by means of kinetic Monte Carlo approach[4] and the irradiation-driven molecular dynamics[5]. 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[6]. The software allows to combine different types of 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[7] (binary format) and DCD+XYZ (hybrid format). It also supports the Protein Data Bank[8] (pdb) file format for describing the three-dimensional structures of biomolecules. Advanced features of the program include:
MBN StudioMBN Explorer is complemented with MBN Studio[6][10] - 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 collaborationsMBN Explorer has been utilized in different research projects in the fields of materials science, nanotechnology and radiation damage:
See also
References1. ^{{cite web|title=About MBN Explorer|url=http://www.mbnresearch.com/get-mbn-explorer-software|publisher=mbnresearch.com|accessdate=31 August 2017}} 2. ^{{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}} 3. ^{{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}} 4. ^{{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}} 5. ^1 {{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}} 6. ^1 {{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 }} 7. ^{{cite web|title=DCD Trajectory I/O|url=http://www.mdanalysis.org/mdanalysis/documentation_pages/coordinates/DCD.html}} 8. ^{{cite web|title=Protein Data Bank|url=https://www.rcsb.org/pdb/home/home.do}} 9. ^{{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 }} 10. ^{{cite web|title=About MBN Studio|url=http://www.mbnresearch.com/mbn-studio|publisher=mbnresearch.com|accessdate=31 August 2017}} 11. ^{{cite web|title=FP7 ITN ARGENT Project|url=http://www.itn-argent.eu}} 12. ^{{cite web|title=PEARL Project|url=http://cordis.europa.eu/project/rcn/200088_en.html}} 13. ^{{cite web|title=COST Action Nano-IBCT|url=http://www.cost.eu/COST_Actions/mpns/nano-ibct/}} 14. ^{{cite web|title=VINAT Project|url=http://cordis.europa.eu/project/rcn/101137_en.html}} External links
3 : Molecular dynamics software|Molecular modelling software|Physics software |
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