MBN Explorer

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 }}

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 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{{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{{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 and the possibility to simulate dynamics of rigid bodies,
• 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 particles in crystalline media,
• simulation of irradiation-induced chemical transformations by means of irradiation-driven molecular dynamics.

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.

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}}

• Comparison of software for molecular mechanics modeling
• List of software for nanostructures modeling
• NAMD
• GROMACS
• LAMMPS

{{Reflist|2}}

• [http://www.mbnresearch.com/ MBN Research Center website]

Category:Molecular dynamics software

Category:Computational chemistry

Category:Molecular modelling software

Category:Physics software