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).

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.

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.

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.

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.

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.

This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.

This book explores novel computational strategies for simulating excess energy dissipation alongside transient structural changes in photoexcited molecules, and accompanying solvent rearrangements. It also demonstrates in detail the synergy between theoretical modelling and ultrafast experiments in unravelling various aspects of the reaction dynamics of solvated photocatalytic metal complexes. Transition metal complexes play an important role as photocatalysts in solar energy conversion, and the rational design of metal-based photocatalytic systems with improved efficiency hinges on the fundamental understanding of the mechanisms behind light-induced chemical reactions in solution. Theory and atomistic modelling hold the key to uncovering these ultrafast processes. Linking atomistic simulations and modern X-ray scattering experiments with femtosecond time resolution, the book highlights previously unexplored dynamical changes in molecules, and discusses the development of theoretical and computational frameworks capable of interpreting the underlying ultrafast phenomena.

This book collects the slides prepared for the course of Advanced Engineering Thermodynamics (Master of Science in Mechanical Engineering) and those for the course of Multiscale Modelling and Simulation of Molecular and Mesoscopic Dynamics (PhD Program in Energetics), taught in English at Turin Polytechnic. Here, we provide a broad overview on the different topics taught in our classes. Even though not all topics are presented in the same class, students should be able to more easily reconstruct the connections among different phenomena (and scales), build their own mind map and, eventually, find their own way of deepening the subjects they are more interested in. Several engineering applications have been included. This helps in stressing that very different phenomena are described by transport theory and obey the same underlying fundamental laws of engineering thermodynamics. Detailed tutorials are reported, based on open-source codes for the laboratories (Gromacs, Palabos, OpenFoam and Cantera).

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.