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Abstract This chapter introduces MesoBioNano Explorer (MBN Explorer) (Solov’yov et al. J Comput Chem 33:2412–2439, (2012), [1]), a software package for the advanced multiscale simulations of complex molecular structure and dynamics and highlights some of its biomedical and nanotechnology applications. MBN Explorer has many unique features, a wide range of applications in Physics, Chemistry, Biology, Material Science, and in related Industries. It is suitable for classical molecular dynamics, Monte Carlo and relativistic dynamics simulations of a large range of molecular systems of different kind, such as nano- and biological systems, nanostructured materials, composite/hybrid materials, gases, liquids, solids and various interfaces, with the sizes ranging from atomic to mesoscopic. MBN Explorer can be exploited together with MBN Studio (Solov’yov et al. MBN Studio, (2015), [2]), a specially developed graphical user interface.

1 Introduction The Meso-Bio-Nano (MBN) Science is the interdisciplinary field of research studying structure-formation and dynamics of animate and inanimate matter on the nano- and the mesoscales. It bundles up several traditional topics in theoretical physics under a common theme. The range of open challenging scientific problems in this field is rather broad. They may include: structure and dynamics of clusters, nanoparticles and biomolecules; clustering, self-organization, growth and structure-formation processes, their multiscale nature and scaling laws; assemblies of clusters/nanoparticles and bio-macromolecules, hybrid bio-nano systems, nanostructured materials; surface phenomena; nanoscale phase transitions; thermal, optical and A.V. Solov’yov (B) MBN Research Center at Frankfurter Innovationszentrum Biotechnologie, Altenhöferallee 3, 60438 Frankfurt am Main, Germany e-mail: [email protected] A.V. Solov’yov A.F. Ioffe Physical-Technical Institute, Polytekhnicheskaya Ul. 26, 194021 Saint Petersburg, Russia © Springer International Publishing Switzerland 2017 A.V. Solov’yov (ed.), Nanoscale Insights into Ion-Beam Cancer Therapy, DOI 10.1007/978-3-319-43030-0_9

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magnetic properties; collective phenomena; electron/spin transport and molecular electronics; nuclear magnetic resonance; collision, fusion, fission and fragmentation processes; channeling effects; radiation effects; radiobiological effects and many more. There are many important applications closely linked to the field. One of such important applications is the Ion-Beam Cancer Therapy (IBCT). Understanding the processes behind IBCT on the molecular, nano- and meso- scales is an open area of intensive current research, which is widely discussed in this book. The list of topical areas in the field grows rather rapidly facilitating also the development of the relevant theoretical and computational methods. In many areas the future of many industrial products is associated with the creation of an integrated environment for numerical design and modeling. This encompasses a wide range of end-products and