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 addresses a wide range of topics relating to the properties and behavior of condensed matter under extreme conditions such as intense magnetic and electric fields, high pressures, heat and cold, and mechanical stresses. It is divided into four sections devoted to condensed matter theory, molecular chemistry, theoretical physics, and the philosophy and history of science. The main themes include electronic correlations in material systems under extreme pressure and temperature conditions, surface physics, the transport properties of low-dimensional electronic systems, applications of the density functional theory in molecular systems, and graphene. The book is the outcome of a workshop held at the University of Catania, Italy, in honor of Professor Renato Pucci on the occasion of his 70th birthday. It includes selected invited contributions from collaborators and co-authors of Professor Pucci during his long and successful career, as well as from other distinguished guest authors.

This book presents recent research on Advanced Computing in Industrial Mathematics, which is one of the most prominent interdisciplinary areas and combines mathematics, computer science, scientific computations, engineering, physics, chemistry, medicine, etc. Further, the book presents the tools of Industrial Mathematics, which are based on mathematical models, and the corresponding computer codes, which are used to perform virtual experiments to obtain new data or to better understand the existing experimental results. The book gathers the peer-reviewed papers presented during the 10th Annual Meeting of the Bulgarian Section of SIAM (BGSIAM) from December 21 to 22, 2015 in Sofia, Bulgaria.

This book is a collection of problems that are intended to aid students in graduate and undergraduate courses in Classical and Quantum Physics. It is also intended to be a study aid for students that are preparing for the PhD qualifying exam. Many of the included problems are of a type that could be on a qualifying exam. Others are meant to elucidate important concepts. Unlike other compilations of problems, the detailed solutions are often accompanied by discussions that reach beyond the specific problem.The solution of the problem is only the beginning of the learning process--it is by manipulation of the solution and changing of the parameters that a great deal of insight can be gleaned. The authors refer to this technique as "massaging the problem," and it is an approach that the authors feel increases the pedagogical value of any problem.

This thesis provides a comprehensive description of methods used to compute the vibrational spectra of liquid systems by molecular dynamics simulations. The author systematically introduces theoretical basics and discusses the implications of approximating the atomic nuclei as classical particles. The strengths of the methodology are demonstrated through several different examples. Of particular interest are ionic liquids, since their properties are governed by strong and diverse intermolecular interactions in the liquid state. As a novel contribution to the field, the author presents an alternative route toward infrared and Raman intensities on the basis of a Voronoi tessellation of the electron density. This technique is superior to existing approaches regarding the computational resources needed. Moreover, this book presents an innovative approach to obtaining the magnetic moments and vibrational circular dichroism spectra of liquids, and demonstrates its excellent agreement with experimental reference data.

This thesis presents the latest developments in new catalytic C-C bond formation methods using easily accessible carboxylate salts through catalytic decarboxylation with good atom economy, and employing the sustainable element iron as the catalyst to directly activate C-H bonds with high step efficiency. In this regard, it explores a mechanistic understanding of the newly discovered decarboxylative couplings and the catalytic reactivity of the iron catalyst with the help of density functional theory calculation. The thesis is divided into two parts, the first of which focuses on the development of a series of previously unexplored, inexpensive carboxylate salts as useful building blocks for the formation of various C-C bonds to access valuable chemicals. In turn, the second part is devoted to several new C-C bond formation methodologies using the most ubiquitous transition metal, iron, as a catalyst, and using the ubiquitous C-H bond as the coupling partner.

Kinetic Monte Carlo (kMC) simulations still represent a quite new area of research, with a rapidly growing number of publications. Broadly speaking, kMC can be applied to any system describable as a set of minima of a potential-energy surface, the evolution of which will then be regarded as hops from one minimum to a neighboring one. The hops in kMC are modeled as stochastic processes and the algorithms use random numbers to determine at which times the hops occur and to which neighboring minimum they go. Sometimes this approach is also called dynamic MC or Stochastic Simulation Algorithm, in particular when it is applied to solving macroscopic rate equations. This book has two objectives. First, it is a primer on the kMC method (predominantly using the lattice-gas model) and thus much of the book will also be useful for applications other than to surface reactions. Second, it is intended to teach the reader what can be learned from kMC simulations of surface reaction kinetics. With these goals in mind, the present text is conceived as a self-contained introduction for students and non-specialist researchers alike who are interested in entering the field and learning about the topic from scratch.

Chemical structure and bonding. The scope of the series spans the entire Periodic Table and addresses structure and bonding issues associated with all of the elements. It also focuses attention on new and developing areas of modern structural and theoretical chemistry such as nanostructures, molecular electronics, designed molecular solids, surfaces, metal clusters and supramolecular structures. Physical and spectroscopic techniques used to determine, examine and model structures fall within the purview of Structure and Bonding to the extent that the focus is on the scientific results obtained and not on specialist information concerning the techniques themselves. Issues associated with the development of bonding models and generalizations that illuminate the reactivity pathways and rates of chemical processes are also relevant. The individual volumes in the series are thematic. The goal of each volume is to give the reader, whether at a university or in industry, a comprehensive overview of an area where new insights are emerging that are of interest to a larger scientific audience. Thus each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years should be presented using selected examples to illustrate the principles discussed. A description of the physical basis of the experimental techniques that have been used to provide the primary data may also be appropriate, if it has not been covered in detail elsewhere. The coverage need not be exhaustive in data, but should rather be conceptual, concentrating on the new principles being developed that will allow the reader, who is not a specialist in the area covered, to understand the data presented. Discussion of possible future research directions in the area is welcomed. Review articles for the individual volumes are invited by the volume editors.

This book has developed over the past fifteen years from a modern course on stochastic chemical kinetics for graduate students in physics, chemistry and biology. The first part presents a systematic collection of the mathematical background material needed to understand probability, statistics, and stochastic processes as a prerequisite for the increasingly challenging practical applications in chemistry and the life sciences examined in the second part. Recent advances in the development of new techniques and in the resolution of conventional experiments at nano-scales have been tremendous: today molecular spectroscopy can provide insights into processes down to scales at which current theories at the interface of physics, chemistry and the life sciences cannot be successful without a firm grasp of randomness and its sources. Routinely measured data is now sufficiently accurate to allow the direct recording of fluctuations. As a result, the sampling of data and the modeling of relevant processes are doomed to produce artifacts in interpretation unless the observer has a solid background in the mathematics of limited reproducibility. The material covered is presented in a modular approach, allowing more advanced sections to be skipped if the reader is primarily interested in applications. At the same time, most derivations of analytical solutions for the selected examples are provided in full length to guide more advanced readers in their attempts to derive solutions on their own. The book employs uniform notation throughout, and a glossary has been added to define the most important notions discussed.

The field of atomic clusters continues to attract great interest amongst physicists and chemists alike. This is in part due to their intrinsic properties and potential industrial applications. The first part of Binary Clusters is devoted to recent developments in experimental techniques, the second part covers a variety of theoretical approaches. Different theoretical methods based on group/graph theories and quantum chemical computational methods as well as various spectroscopy techniques (such as mass, laser, infrared, photoelectron etc.) are applied to the determination of the existence of geometrical and electronic structures, chemical bonding phenomena, and the thermodynamic stabilities of several classes of binary clusters. All chapters within this review volume have been contributed by experts in chemistry, physics, and material sciences based at the University of Leuven, Belgium. This book is aimed at professionals and students working in cluster science.

This thesis demonstrates how molecular modeling techniques can be used to gain significant insights into numerous applications that are increasingly attracting research interest because of their societal importance. It presents innovative ideas that, by altering the fundamental physical phenomena occurring at the solid/liquid interface, allow the fluid transport in nanochannels to be manipulated so as to improve the performance of the practical applications. The applications explicitly considered in this thesis are the design of drag-reducing and self-cleaning surfaces; water desalination; and shale gas exploration - all of which are, to some extent, governed by nanoscale fluid transport. Overall, this thesis is useful for students and researchers entering the field who wish to understand how molecular modeling can improve the performance in a wide range of applications.

This book offers an easy-to-understand introduction to the computational mass transfer (CMT) method. On the basis of the contents of the first edition, this new edition is characterized by the following additional materials. It describes the successful application of this method to the simulation of the mass transfer process in a fluidized bed, as well as recent investigations and computing methods for predictions for the multi-component mass transfer process. It also demonstrates the general issues concerning computational methods for simulating the mass transfer of the rising bubble process. This new edition has been reorganized by moving the preparatory materials for Computational Fluid Dynamics (CFD) and Computational Heat Transfer into appendices, additions of new chapters, and including three new appendices on, respectively, generalized representation of the two-equation model for the CMT, derivation of the equilibrium distribution function in the lattice-Boltzmann method, and derivation of the Navier-Stokes equation using the lattice-Boltzmann model. This book is a valuable resource for researchers and graduate students in the fields of computational methodologies for the numerical simulation of fluid dynamics, mass and/or heat transfer involved in separation processes (distillation, absorption, extraction, adsorption etc.), chemical/biochemical reactions, and other related processes.

The series Structure and Bonding publishes critical reviews on topics of research concerned with chemical structure and bonding. The scope of the series spans the entire Periodic Table and addresses structure and bonding issues associated with all of the elements. It also focuses attention on new and developing areas of modern structural and theoretical chemistry such as nanostructures, molecular electronics, designed molecular solids, surfaces, metal clusters and supramolecular structures. Physical and spectroscopic techniques used to determine, examine and model structures fall within the purview of Structure and Bonding to the extent that the focus is on the scientific results obtained and not on specialist information concerning the techniques themselves. Issues associated with the development of bonding models and generalizations that illuminate the reactivity pathways and rates of chemical processes are also relevant. The individual volumes in the series are thematic. The goal of each volume is to give the reader, whether at a university or in industry, a comprehensive overview of an area where new insights are emerging that are of interest to a larger scientific audience. Thus each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years should be presented using selected examples to illustrate the principles discussed. A description of the physical basis of the experimental techniques that have been used to provide the primary data may also be appropriate, if it has not been covered in detail elsewhere. The coverage need not be exhaustive in data, but should rather be conceptual, concentrating on the new principles being developed that will allow the reader, who is not a specialist in the area covered, to understand the data presented. Discussion of possible future research directions in the area is welcomed. Review articles for the individual volumes are invited by the volume editors

The series Structure and Bonding publishes critical reviews on topics of research concerned with chemical structure and bonding. The scope of the series spans the entire Periodic Table and addresses structure and bonding issues associated with all of the elements. It also focuses attention on new and developing areas of modern structural and theoretical chemistry such as nanostructures, molecular electronics, designed molecular solids, surfaces, metal clusters and supramolecular structures. Physical and spectroscopic techniques used to determine, examine and model structures fall within the purview of Structure and Bonding to the extent that the focus is on the scientific results obtained and not on specialist information concerning the techniques themselves. Issues associated with the development of bonding models and generalizations that illuminate the reactivity pathways and rates of chemical processes are also relevant. The individual volumes in the series are thematic. The goal of each volume is to give the reader, whether at a university or in industry, a comprehensive overview of an area where new insights are emerging that are of interest to a larger scientific audience. Thus each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years should be presented using selected examples to illustrate the principles discussed. A description of the physical basis of the experimental techniques that have been used to provide the primary data may also be appropriate, if it has not been covered in detail elsewhere. The coverage need not be exhaustive in data, but should rather be conceptual, concentrating on the new principles being developed that will allow the reader, who is not a specialist in the area covered, to understand the data presented. Discussion of possible future research directions in the area is welcomed. Review articles for the individual volumes are invited by the volume editors

This book reflects on the significant and highly original scientific contributions of Hans Primas. A professor of chemistry at ETH Zurich from 1962 to 1995, Primas continued his research activities until his death in 2014. Over these 50 years and more, he worked on the foundations of nuclear magnetic resonance spectroscopy, contributed to a number of significant issues in theoretical chemistry, helped to clarify central topics in quantum theory and the philosophy of physics, suggested innovative ways of addressing interlevel relations in the philosophy of science, and introduced cutting-edge approaches in the flourishing young field of scientific studies of consciousness. His work in these areas of research and its continuing impact is described by noted experts, colleagues, and collaborators of Primas. All authors contextualize their contributions to facilitate the mutual dialog between these fields.

This brief explains in detail fundamental concepts in acoustic cavitation and bubble dynamics, and describes derivations of the fundamental equations of bubble dynamics in order to support those readers just beginning research in this field. Further, it provides an in-depth understanding of the physical basis of the phenomena. With regard to sonochemistry, the brief presents the results of numerical simulations of chemical reactions inside a bubble under ultrasound, especially for a single-bubble system and including unsolved problems. Written so as to be accessible both with and without prior knowledge of fundamental fluid dynamics, the brief offers a valuable resource for students and researchers alike, especially those who are unfamiliar with this field. A grasp of fundamental undergraduate mathematics such as partial derivative and fundamental integration is advantageous; however, even without any background in mathematics, readers can skip the equations and still understand the fundamental physics of the phenomena using the book's wealth of illustrations and figures. As such, it is also suitable as an introduction to the field.

This brief provides an overview of theoretical research in organic ferromagnetic material design using quantum chemical approaches based on molecular orbital theory from primary Huckel to ab initio levels of theory. Most of the content describes the authors' approach to identify simple and efficient guidelines for magnetic design, which have not been described in other books. Individual chapters cover quantum chemistry methods that may be used to find hydrocarbon systems with degenerate non-bonding molecular orbitals that interact with each other, to identify high-spin-preferred systems using an analytical index that allows for simple design of high-spin systems as well as to analyze the effect of high-spin stability through orbital interactions. The extension of these methods to large systems is discussed.This book is a valuable resource for students and researchers who are interested in quantum chemistry related to magnetic property.

The articles in this volume summarize the research results obtained in the former SFB 359 "Reactive Flow, Diffusion and Transport" which has been supported by the DFG over the period 1993-2004. The main subjects are physical-chemical processes sharing the difficulty of interacting diffusion, transport and reaction which cannot be considered separately. The modeling and simulation within this book is accompanied by experiments.

This comprehensive presentation of the integral equation method as applied to electro-analytical experiments is suitable for electrochemists, mathematicians and industrial chemists. The discussion focuses on how integral equations can be derived for various kinds of electroanalytical models. The book begins with models independent of spatial coordinates, goes on to address models in one dimensional space geometry and ends with models dependent on two spatial coordinates. Bieniasz considers both semi-infinite and finite spatial domains as well as ways to deal with diffusion, convection, homogeneous reactions, adsorbed reactants and ohmic drops. Bieniasz also discusses mathematical characteristics of the integral equations in the wider context of integral equations known in mathematics. Part of the book is devoted to the solution methodology for the integral equations. As analytical solutions are rarely possible, attention is paid mostly to numerical methods and relevant software. This book includes examples taken from the literature and a thorough literature overview with emphasis on crucial aspects of the integral equation methodology.

Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.

This book has emerged from an undergraduate course as well as a graduate one, which I have taught for a number of years. Recently, many universities have experimented by bringing quantum theory forward in the curriculum and we follow their example. This book is intended to serve as an introduction to theoretical mechanics and quantum mechanics for chemists. I have included those parts of quantum mechanics which are of greatest fundamental interest and utility, and have developed those parts of classical mechanics which relate to and illuminate them. I try to give a comprehensive treatment wherever possible. The book would acquaint chemists with the quantum structure of the basic object of chemistry, the atom. My intention is to bridge the gap between classical physics, general and inorganic chemistry, and quantum mechanics. For these reasons: 1. I present in one course the basics of theoretical mechanics and quantum mechanics, to emphasise the continuity between them; 2. I have chosen the topics of theoretical mechanics based upon two criteria: a) usefulness for chemical problems: two-body problem; rotational motion of a charged particles (free and in an atom); interaction of a magnetic field with a magnetic dipole; details of small oscillations and oscillations of molecules; b) the need for transition from classical to quantum mechanics: basics of Lagrangian mechanics; basics of Hamiltonian mechanics; 3. I give detailed explanation of an application of the quantum method to simple systems: one-dimensional potential, harmonic oscillator, hydrogen atom, and hydrog- like atoms.

This comprehensive collection of lectures by leading experts in the field introduces and reviews all relevant computer simulation methods and their applications in condensed matter systems. Volume 1 is an in-depth introduction to a vast spectrum of computational techniques for statistical mechanical systems of condensed matter. Volume 2 is a collection of state-of-the-art surveys on numerical experiments carried out for a great number of systems.

This book presents the state-of-the-art in simulation on supercomputers. Leading researchers present results achieved on systems of the High Performance Computing Center Stuttgart (HLRS) for the year 2010. The reports cover all fields of computational science and engineering, ranging from CFD to computational physics and chemistry to computer science, with a special emphasis on industrially relevant applications. Presenting results for both vector systems and microprocessor-based systems, the book makes it possible to compare the performance levels and usability of various architectures. As HLRS operates the largest NEC SX-8 vector system in the world, this book gives an excellent insight into the potential of vector systems, covering the main methods in high performance computing. Its outstanding results in achieving the highest performance for production codes are of particular interest for both scientists and engineers. The book includes a wealth of color illustrations and tables.

The book presents the state of the art in high performance computing and simulation on modern supercomputer architectures. It covers trends in hardware and software development in general and specifically the future of vector-based systems and heterogeneous architectures. The application contributions cover computational fluid dynamics, material science, medical applications and climate research. Innovative fields like coupled multi-physics or multi-scale simulations are presented. All papers were chosen from presentations given at the 13th Teraflop Workshop held in October 2010 at Tohoku University, Japan.