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Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer

Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer
Author: Ilia A. Solov’yov
Publisher: Springer
Total Pages: 451
Release: 2017-05-16
Genre: Science
ISBN: 3319560875
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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. MBN Explorer is particularly suited to computing the system’s energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational efficiency of MBN Explorer is comparable to that of other, more specialized software packages, making it a viable multi-purpose alternative for the computational modeling of complex molecular systems. A number of detailed case studies presented in the second part of this book demonstrate MBN Explorer’s usefulness and efficiency in the fields of atomic clusters and nanoparticles, biomolecular systems, nanostructured materials, composite materials and hybrid systems, crystals, liquids and gases, as well as in providing modeling support for novel and emerging technologies. Last but not least, with the release of the 3rd edition of MBN Explorer in spring 2017, a free trial version will be available from the MBN Research Center website (mbnresearch.com).

Mbn Explorer Users' Guide

Mbn Explorer Users' Guide
Author: Ilia Solov'yov
Publisher: Createspace Independent Publishing Platform
Total Pages: 264
Release: 2017-09-26
Genre:
ISBN: 9781975639044
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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 Macintosh platforms. MBN Explorer is being developed and distributed by MBN Research Center, www.mbnresearch.com. The use of MBN Explorer for non-commercial purpose is granted through low price academic licenses. This licensing agreement is restricted to Universities and Research Centers aiming for scientific publication of their results. Reference to MBN Explorer in reports, publications, or communication mentioning research results obtained with the use of MBN Explorer is required. All details about terms and conditions are available on the website: www.mbnresearch.com Accessible individual and multi-users license agreements are also offered for commercial exploitation of MBN Explorer. Purchased license rights provide access to (i) MBN Explorer software and its updates, (ii) MBN Explorer documentation package, (iii) MBN Explorer user's workshops. Special packages including education, dedicated hands-on training and helpdesk are also available. Contact us or visit our website www.mbnresearch.com for more details.

Dynamics of Systems on the Nanoscale

Dynamics of Systems on the Nanoscale
Author: Ilia A. Solov'yov
Publisher: Springer Nature
Total Pages: 554
Release: 2022-06-03
Genre: Science
ISBN: 3030992918
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This book presents the structure formation and dynamics of animate and inanimate matter on the nanometre scale. This is a new interdisciplinary field known as Meso-Bio-Nano (MBN) science that lies at the intersection of physics, chemistry, biology and material science. Special attention in the book is devoted to investigations of the structure, properties and dynamics of complex MBN systems by means of photonic, electronic, heavy particle and atomic collisions. This includes problems of fusion and fission, fragmentation, surfaces and interfaces, reactivity, nanoscale phase and morphological transitions, irradiation-driven transformations of complex molecular systems, collective electron excitations, radiation damage and biodamage, channeling phenomena and many more. Emphasis in the book is placed on the theoretical and computational physics research advances in these areas and related state-of-the-art experiments. Particular attention in the book is devoted to the utilization of advanced computational techniques and high-performance computing in studies of the dynamics of systems.

Mbn Explorer and Mbn Studio Tutorials

Mbn Explorer and Mbn Studio Tutorials
Author: Ilia Solov'yov
Publisher: Createspace Independent Publishing Platform
Total Pages: 288
Release: 2017-10-20
Genre:
ISBN: 9781976460920
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This book describes the practical exercises with MesoBioNano (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 optimisation 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 parallelised 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 visualise 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. MBN Explorer and MBN Studio are being developed and distributed by MBN Research Center. For more details visit the MBN Research Center website: www.mbnresearch.com

Molecular Modeling and Multiscaling Issues for Electronic Material Applications

Molecular Modeling and Multiscaling Issues for Electronic Material Applications
Author: Artur Wymyslowski
Publisher: Springer
Total Pages: 203
Release: 2014-11-20
Genre: Technology & Engineering
ISBN: 3319128620
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This book offers readers a snapshot of the progression of molecular modeling in the electronics industry and how molecular modeling is currently being used to understand materials to solve relevant issues in this field. The reader is introduced to the evolving role of molecular modeling, especially seen from the perspective of the IEEE community and modeling in electronics. This book also covers the aspects of molecular modeling needed to understand the relationship between structures and mechanical performance of materials. The authors also discuss the transitional topic of multiscale modeling and recent developments on the atomistic scale and current attempts to reach the submicron scale, as well as the role that quantum mechanics can play in performance prediction.

Nanoscale Insights into Ion-Beam Cancer Therapy

Nanoscale Insights into Ion-Beam Cancer Therapy
Author: Andrey V. Solov’yov
Publisher: Springer
Total Pages: 498
Release: 2016-12-07
Genre: Science
ISBN: 3319430300
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This book provides a unique and comprehensive overview of state-of-the-art understanding of the molecular and nano-scale processes that play significant roles in ion-beam cancer therapy. It covers experimental design and methodology, and reviews the theoretical understanding of the processes involved. It offers the reader an opportunity to learn from a coherent approach about the physics, chemistry and biology relevant to ion-beam cancer therapy, a growing field of important medical application worldwide. The book describes phenomena occurring on different time and energy scales relevant to the radiation damage of biological targets and ion-beam cancer therapy from the molecular (nano) scale up to the macroscopic level. It illustrates how ion-beam therapy offers the possibility of excellent dose localization for treatment of malignant tumours, minimizing radiation damage in normal tissue whilst maximizing cell-killing within the tumour, offering a significant development in cancer therapy. The full potential of such therapy can only be realized by better understanding the physical, chemical and biological mechanisms, on a range of time and space scales that lead to cell death under ion irradiation. This book describes how, using a multiscale approach, experimental and theoretical expertise available can lead to greater insight at the nanoscopic and molecular level into radiation damage of biological targets induced by ion impact. The book is intended for advanced students and specialists in the areas of physics, chemistry, biology and medicine related to ion-beam therapy, radiation protection, biophysics, radiation nanophysics and chemistry, atomic and molecular physics, condensed matter physics, and the physics of interaction of charged particles with matter. One of the most important features of the book is the inclusive multiscale approach to the understanding of complex and highly interdisciplinary processes behind ion-beam cancer therapy, which stretches from the atomistic level up to the biological scale and is demonstrated to be in excellent agreement with experimental observations.

Novel Lights Sources Beyond Free Electron Lasers

Novel Lights Sources Beyond Free Electron Lasers
Author: Andrei Korol
Publisher: Springer Nature
Total Pages: 221
Release: 2022-06-09
Genre: Science
ISBN: 3031042824
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This book discusses possibilities and perspectives for designing and practical realization of novel intensive gamma-ray crystal-based light sources that can be constructed through exposure of oriented crystals—linear, bent and periodically bent, to beams of ultrarelativistic positrons and electrons. The book shows case studies like the tunable light sources based on periodically bent crystals that can be designed with the state-of-the-art beam facilities. A special focus is given to the analysis of generation of the gamma rays because the current technologies based on particle motion in the magnetic field become inefficient or incapable to achieve the desired gamma rays’ intensities. It is demonstrated that the intensity of radiation from crystal-based light sources can be made comparable to or even higher than what is achievable in conventional synchrotrons and undulators operating although in the much lower photon energy range. By exploring the coherence effects, the intensity can be boosted by orders of magnitude. The practical realization of such novel light sources will lead to the significant technological breakthroughs and societal impacts similar to those created earlier by the developments of lasers, synchrotrons and X-rays free-electron lasers. Readers learn about the underlying fundamental physics and familiarize with the theoretical, experimental and technological advances made during last two decades in exploring various features of investigations into crystal-based light sources. This research draws upon knowledge from many research fields, such as material science, beam physics, physics of radiation, solid-state physics and acoustics, to name but a few. The authors provide a useful introduction in this emerging field to a broad readership of researchers and scientists with various backgrounds and, accordingly, make the book as self-contained as possible.

Molecular Modeling and Multiscaling Issues for Electronic Material Applications

Molecular Modeling and Multiscaling Issues for Electronic Material Applications
Author: Nancy Iwamoto
Publisher: Springer
Total Pages: 260
Release: 2014-03-03
Genre: Technology & Engineering
ISBN: 9781489988379
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Molecular Modeling and Multiscaling Issues for Electronic Material Applications provides a snapshot on the progression of molecular modeling in the electronics industry and how molecular modeling is currently being used to understand material performance to solve relevant issues in this field. This book is intended to introduce the reader to the evolving role of molecular modeling, especially seen through the eyes of the IEEE community involved in material modeling for electronic applications. Part I presents the role that quantum mechanics can play in performance prediction, such as properties dependent upon electronic structure, but also shows examples how molecular models may be used in performance diagnostics, especially when chemistry is part of the performance issue. Part II gives examples of large-scale atomistic methods in material failure and shows several examples of transitioning between grain boundary simulations (on the atomistic level)and large-scale models including an example of the use of quasi-continuum methods that are being used to address multiscaling issues. Part III is a more specific look at molecular dynamics in the determination of the thermal conductivity of carbon-nanotubes. Part IV covers the many aspects of molecular modeling needed to understand the relationship between the molecular structure and mechanical performance of materials. Finally, Part V discusses the transitional topic of multiscale modeling and recent developments to reach the submicronscale using mesoscale models, including examples of direct scaling and parameterization from the atomistic to the coarse-grained particle level.

Multiscale Modeling of Particle Interactions

Multiscale Modeling of Particle Interactions
Author: Michael King
Publisher: John Wiley & Sons
Total Pages: 398
Release: 2010-03-30
Genre: Science
ISBN: 047057982X
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Discover how the latest computational tools are building our understanding of particle interactions and leading to new applications With this book as their guide, readers will gain a new appreciation of the critical role that particle interactions play in advancing research and developing new applications in the biological sciences, chemical engineering, toxicology, medicine, and manufacturing technology The book explores particles ranging in size from cations to whole cells to tissues and processed materials. A focus on recreating complex, real-world dynamical systems helps readers gain a deeper understanding of cell and tissue mechanics, theoretical aspects of multiscale modeling, and the latest applications in biology and nanotechnology. Following an introductory chapter, Multiscale Modeling of Particle Interactions is divided into two parts: Part I, Applications in Nanotechnology, covers: Multiscale modeling of nanoscale aggregation phenomena: applications in semiconductor materials processing Multiscale modeling of rare events in self-assembled systems Continuum description of atomic sheets Coulombic dragging and mechanical propelling of molecules in nanofluidic systems Molecular dynamics modeling of nanodroplets and nanoparticles Modeling the interactions between compliant microcapsules and patterned surfaces Part II, Applications in Biology, covers: Coarse-grained and multiscale simulations of lipid bilayers Stochastic approach to biochemical kinetics In silico modeling of angiogenesis at multiple scales Large-scale simulation of blood flow in microvessels Molecular to multicellular deformation during adhesion of immune cells under flow Each article was contributed by one or more leading experts and pioneers in the field. All readers, from chemists and biologists to engineers and students, will gain new insights into how the latest tools in computational science can improve our understanding of particle interactions and support the development of novel applications across the broad spectrum of disciplines in biology and nanotechnology.

Multiscale Materials Modeling for Nanomechanics

Multiscale Materials Modeling for Nanomechanics
Author: Christopher R. Weinberger
Publisher: Springer
Total Pages: 547
Release: 2016-08-30
Genre: Technology & Engineering
ISBN: 3319334808
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This book presents a unique combination of chapters that together provide a practical introduction to multiscale modeling applied to nanoscale materials mechanics. The goal of this book is to present a balanced treatment of both the theory of the methodology, as well as some practical aspects of conducting the simulations and models. The first half of the book covers some fundamental modeling and simulation techniques ranging from ab-inito methods to the continuum scale. Included in this set of methods are several different concurrent multiscale methods for bridging time and length scales applicable to mechanics at the nanoscale regime. The second half of the book presents a range of case studies from a varied selection of research groups focusing either on a the application of multiscale modeling to a specific nanomaterial, or novel analysis techniques aimed at exploring nanomechanics. Readers are also directed to helpful sites and other resources throughout the book where the simulation codes and methodologies discussed herein can be accessed. Emphasis on the practicality of the detailed techniques is especially felt in the latter half of the book, which is dedicated to specific examples to study nanomechanics and multiscale materials behavior. An instructive avenue for learning how to effectively apply these simulation tools to solve nanomechanics problems is to study previous endeavors. Therefore, each chapter is written by a unique team of experts who have used multiscale materials modeling to solve a practical nanomechanics problem. These chapters provide an extensive picture of the multiscale materials landscape from problem statement through the final results and outlook, providing readers with a roadmap for incorporating these techniques into their own research.