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MBN Explorer and MBN Studio Tutorials: Version 5.0 (can be ordered here) A. Verkhovtsev, I.A. Solov'yov, A.V. Korol, G.B. Sushko, A.V. Solov'yov, MBN Explorer and MBN Studio Tutorials: Version 5.0, MesoBioNano Science Publishing, Frankfurt am Main (2024), 597 p.

MBN Explorer and MBN Studio Tutorials: Version 5.0

The book describes the practical exercises with the MBN Explorer and MBN Studio software packages introducing and illustrating a wide range of applications of the software in different fields. The standard and unique algorithms for classical, Euler, reactive, irradiation-driven, relativistic molecular dynamics and stochastic dynamics and for the structure optimisation of complex molecular systems are introduced and explained in detail using illustrative case studies.

see Table of Contents
MBN Explorer Users' Guide: Version 3.0 (can be ordered here) I.A. Solov'yov, G.B. Sushko, A.V. Solov'yov, MBN Explorer Users' Guide: Version 3.0, MesoBioNano Science Publishing, Frankfurt am Main (2017), 264 p.

MBN Explorer Users' Guide: Version 3.0

The MBN Explorer Users' Guide describes how to install and to run MBN Explorer, the software package for advanced multiscale simulations of complex molecular structure and dynamics.
This guide includes the description of the main features and the algorithms of the program, the manual how to use the program for specific tasks, the description of all the program commands and keywords, the specification of input information, parameters, files and formats, and instructions on how to handle the program on Windows, Linux/Unix and macOS platforms.

see Table of Contents
MBN Explorer and MBN Studio Tutorials: Version 3.0 (can be ordered here) I.A. Solov'yov, G.B. Sushko, A.V. Verkhovtsev, A.V. Korol, A.V. Solov'yov, MBN Explorer and MBN Studio Tutorials: Version 3.0, MesoBioNano Science Publishing, Frankfurt am Main (2017), 288 p.

MBN Explorer and MBN Studio Tutorials: Version 3.0

This book describes the practical exercises with MBN Explorer and MBN Studio software packages introducing and illustrating a broad range of applications of the software in various fields. The standard and unique algorithms for molecular and Monte Carlo dynamics and for optimization of complex molecular systems are introduced and explained in details invoking illustrative case studies.
MBN Explorer is a multi-purpose software package for advanced multiscale simulations of complex molecular structure and dynamics. It has many unique features and a wide range of applications in Physics, Chemistry, Biology, Materials Science, and Industry. A broad variety of algorithms and interatomic potentials implemented in the program allow simulations of structure and dynamics of a broad range of systems with the sizes from the atomic up to the mesoscopic scales. MBN Explorer is available for Windows, Linux, and macOS. It is fully parallelized and can be exploited on computer clusters and supercomputers.
MBN Studio is a special multi-task software toolkit with a graphical user interface for MBN Explorer. It helps setting up calculations with MBN Explorer, monitoring their progress and examining the calculation results. The graphical utility enables to visualize selected inputs and outputs. A number of built-in tools allow for the calculation and analysis of specific systems' characteristics. A special modelling plug-in allows constructing a large variety of molecular systems built of arbitrary atomic and molecular constituents.

see Table of Contents
Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer I.A. Solov’yov, A.V. Korol, A.V. Solov’yov, Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer, Springer International Publishing (2017), 447 p., ISBN: 978-3-319-56085-4 (hardcover), ISBN: 978-3-319-56087-8 (e-book)

Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer

This book introduces readers to MesoBioNano (MBN) Explorer – a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface – the MBN Studio – which enables the set-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science – ranging from the nano- to the mesoscale.
The book is aimed at scientists, post-graduate and graduate students specializing in the field of theoretical physics, computational physics, molecular and nanophysics, and materials science.

see more information about this book on the dedicated webpage of Springer
MBN Explorer: Simulations of Nanomaterials Structure and Dynamics I.A. Solov'yov, G.B. Sushko, A.V. Verkhovtsev, A.V. Korol, A.V. Solov'yov, MBN Explorer: Simulations of Nanomaterials Structure and Dynamics, Polytechnic University Publishing House, St. Petersburg State Polytechnic University, St. Petersburg (2015), 102 p.

MBN Explorer: Simulations of Nanomaterials Structure and Dynamics

The book is a tutorial on the practical use of the software package MBN Explorer suitable for the multiscale modelling of structure and dynamics of complex molecular systems. The standard algorithms of molecular dynamics and optimisation are introduced and explained in details invoking illustrative case studies. The original algorithms implemented in the code are described in a similar fashion. Many different problems arising in studies of nanoscale systems and materials as well as the processes with their involvement are analysed through numerical calculations of the system energy, optimisation of molecular structure accounting for all the atoms in the system. Particular attention is paid to the studies of mechanical properties of nanostructured materials and propagation of particles in a medium by means of modern methods of molecular dynamics.
The book is aimed at scientists, post-graduate and graduate students specializing in the field of theoretical physics, computational physics, molecular and nanophysics, materials science, as well as for teaching these disciplines in English.

see Table of Contents
MBN Explorer: Dynamics of Biomolecular Systems and Self-organization I.A. Solov'yov, G.B. Sushko, A.V. Verkhovtsev, A.V. Korol, A.V. Solov'yov, MBN Explorer: Dynamics of Biomolecular Systems and Self-organization, Polytechnic University Publishing House, St. Petersburg State Polytechnic University, St. Petersburg (2015), 112 p.

MBN Explorer: Dynamics of Biomolecular Systems and Self-organization

The book is a tutorial on the practical use of the software package MBN Explorer suitable for the multiscale modelling of structure and dynamics of complex molecular systems. The standard algorithms of molecular dynamics and optimisation are introduced in the book and explained in details invoking illustrative case studies. The original algorithms implemented in the code are described in a similar fashion. Many different problems arising in the studies of physical, chemical and biological systems and the processes occurring therein are analysed through numerical calculations of the system energy, optimisation of molecular structure accounting for dynamics of all the atoms in the system. The Monte Carlo approach is also introduced and applied to a number of case studies. Particular attention is paid to the problem of self-organisation in bio- and nanosystems and to the modelling of formation, growth and fragmentation of nanosystems, and in particular nanofractals and nanowires.
The book is aimed at scientists, post-graduate and graduate students specializing in the field of theoretical physics, computational physics, molecular, bio- and nanophysics, materials science, as well as for teaching these disciplines in English.

see Table of Contents
MesoBioNano Explorer - a universal program for multiscale computer simulations of complex molecular structure and dynamics the key reference publication on MBN Explorer, its main features and capabilities Reference: I.A. Solov'yov, A.V. Yakubovich, P.V. Nikolaev, I. Volkovets, and A.V. Solov'yov, MesoBioNano Explorer - a universal program for multiscale computer simulations of complex molecular structure and dynamics, J. Comput. Chem., vol. 33, pp. 2412-2439 (2012) read more...
Modeling MesoBioNano systems with MBN Studio made easy the key reference publication on MBN Studio, its main features and capabilities Reference: G.B. Sushko, I.A. Solov'yov, and A.V. Solov'yov, Modeling MesoBioNano systems with MBN Studio made easy, J. Mol. Graph. Model., vol. 88, pp. 247-260 (2019) read more...
Simulation of ultra-relativistic electrons and positrons channeling in crystals with MBN Explorer the key reference publication on the implementation of relativistic molecular dynamics module in MBN Explorer Reference: G.B. Sushko, V.G. Bezchastnov, I.A. Solov'yov, A.V. Korol, W. Greiner, and A.V. Solov'yov, Simulation of ultra-relativistic electrons and positrons channeling in crystals with MBN Explorer, J. Comput. Phys., vol. 252, pp. 404–418 (2013) read more...
Efficient 3D kinetic Monte Carlo method for modeling of molecular structure and dynamics the key reference publication on the implementation of 3D kinetic Monte Carlo module in MBN Explorer Reference: M. Panshenskov, I.A. Solov'yov, and A.V. Solov'yov, Efficient 3D kinetic Monte Carlo method for modeling of molecular structure and dynamics, J. Comput. Chem., vol. 35, pp. 1317-1329 (2014) read more...
Molecular dynamics for irradiation driven chemistry: application to the FEBID process the paper introducing the Irradiation Driven Molecular Dynamics (IDMD) methodology Reference: G.B. Sushko, I.A. Solov'yov, and A.V. Solov'yov, Molecular dynamics for irradiation driven chemistry: application to the FEBID process, Eur. Phys. J. D, vol. 70, 217 (2016) read more...
Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology the paper introducing molecular mechanics with dynamical topology and the reactive CHARMM force field Reference: G.B. Sushko, I.A. Solov'yov, A.V. Verkhovtsev, S.N. Volkov, and A.V. Solov'yov, Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology, Eur. Phys. J. D, vol. 70, 12 (2016) read more...