Molecular dynamics simulations have become instrumental in replacing our view of proteins as relatively rigid structures with the realization that they were dynamic systems, whose internal motions play a functional role. Over the years, such simulations have become a central part of biophysics. Applications of molecular dynamics in biophysics range over many areas. They are used in the structure determination of macromolecules with x-ray and NMR data, the modelling of unknown structures from their sequence, the study of enzyme mechanisms, the estimation of ligand-binding free energies, the evaluation of the role of conformational change in protein function, and drug design for targets of known structures. The widespread application of molecular dynamics and related methodologies suggests that it would be useful to have available an introductory self-contained course by which students with a relatively limited background in chemistry, biology and computer literacy, can learn the fundamentals of the field. This Guide to Biomolecular Simulations tries to fill this need. The Guide consists of six chapters which provide the fundamentals of the field and six chapters which introduce the reader to more specialized but important applications of the methodology.

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.

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.

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.

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 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.

In this Festschrift dedicated to the 60th birthday of V. Barone, selected researchers in theoretical chemistry present research highlights on major developments in the field. Originally published in the journal Theoretical Chemistry Accounts, these outstanding contributions are now available in a hardcover print format. This volume is of benefit in particular to those research groups and libraries that have chosen to have only electronic access to the journal. It also provides valuable content for all researchers in theoretical chemistry.

In this festschrift dedicated to Professor Eluvathingal D. Jemmis on the occasion of his 60th birthday, selected researchers in theoretical chemistry present research highlights on major developments in the field. Originally published in the journal Theoretical Chemistry Accounts, these outstanding contributions are now available in a hardcover print format. This volume will be of benefit in particular to those research groups and libraries that have chosen to have only electronic access to the journal. It also provides valuable content for all researchers in theoretical chemistry.

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 2011. 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 allows readers to compare the performance levels and usability of various architectures. As HLRS operates not only a large cluster system but also one of the largest NEC vector systems in the world, this book also offers excellent insights into the potential of vector systems. The book covers the main methods used in high-performance computing. Its outstanding results in achieving highest performance for production codes are of particular interest for scientists and engineers alike. The book comes with a wealth of color illustrations and tables of results.

The series Topics in Current Chemistry presents critical reviews of the present and future trends in modern chemical research. The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience. 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 are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field. Review articles for the individual volumes are invited by the volume editors. Readership: research chemists at universities or in industry, graduate students

This multi-author contributed volume includes methodological advances and original applications to actual chemical or biochemical phenomena which were not possible before the increased sophistication of modern computers. The chapters contain detailed reviews of the developments of various computational techniques, used to study complex molecular systems such as molecular liquids and solutions (particularly aqueous solutions), liquid-gas, solid-gas interphase and biomacromolecular systems. Quantum modeling of complex molecular systems is a useful resource for graduate students and fledgling researchers and is also an excellent companion for research professionals engaged in computational chemistry, material science, nanotechnology, physics, drug design, and molecular biochemistry.

This work explores the scope and flexibility afforded by integrated quantum photonics, both in terms of practical problem-solving, and for the pursuit of fundamental science. The author demonstrates and fully characterizes a two-qubit quantum photonic chip, capable of arbitrary two-qubit state preparation. Making use of the unprecedented degree of reconfigurability afforded by this device, a novel variation on Wheeler's delayed choice experiment is implemented, and a new technique to obtain nonlocal statistics without a shared reference frame is tested. Also presented is a new algorithm for quantum chemistry, simulating the helium hydride ion. Finally, multiphoton quantum interference in a large Hilbert space is demonstrated, and its implications for computational complexity are examined.

In this Festschrift dedicated to the late Isaiah Shavitt (1925-2012) , selected researchers in theoretical chemistry present research highlights on major developments in the field. Originally published in the journal Theoretical Chemistry Accounts, these outstanding contributions are now available in a hardcover print format, as well as a special electronic edition. This volume provides valuable content for all researchers in theoretical chemistry, and will especially benefit those research groups and libraries with limited access to the journal.

This overview compiles the on-going research in Europe to enlarge and deepen the understanding of the reaction mechanisms and pathways associated with the combustion of an increased range of fuels. Focus is given to the formation of a large number of hazardous minor pollutants and the inability of current combustion models to predict the formation of minor products such as alkenes, dienes, aromatics, aldehydes and soot nano-particles which have a deleterious impact on both the environment and on human health. Cleaner Combustion describes, at a fundamental level, the reactive chemistry of minor pollutants within extensively validated detailed mechanisms for traditional fuels, but also innovative surrogates, describing the complex chemistry of new environmentally important bio-fuels. Divided into five sections, a broad yet detailed coverage of related research is provided. Beginning with the development of detailed kinetic mechanisms, chapters go on to explore techniques to obtain reliable experimental data, soot and polycyclic aromatic hydrocarbons, mechanism reduction and uncertainty analysis, and elementary reactions. This comprehensive coverage of current research provides a solid foundation for researchers, managers, policy makers and industry operators working in or developing this innovative and globally relevant field.

This brief is based on computations performed on unary neutral and charged iron clusters, binary iron clusters, and iron clusters interacting with carbon and oxygen atoms as well as with a number of diatomics and water. The author considers geometrical structure, thermodynamic stability and electronic properties which are compared with experimental data. Special attention is paid to the dependence of total spin magnetic moments of iron clusters on their size, charge and interactions with dopant and absorbed atoms. In the dopant case, species such as 3d-metal, 4d-metal, Al, and Gd atoms are considered. In the adsorption case interactions of carbon atoms with iron clusters as the initial stage of catalyzed carbon nanotube growth are presented. Interactions of iron clusters with oxygen atoms are presented and the superexchange mechanism is discussed. Of special interest is the tracking of changes due to the evolution from a few atoms to a nanocluster.

For design purposes one needs to relate the structure of proposed materials to their NLO (nonlinear optical) and other properties, which is a situation where theoretical approaches can be very helpful in providing suggestions for candidate systems that subsequently can be synthesized and studied experimentally. This brief describes the quantum-mechanical treatment of the response to one or more external oscillating electric fields for molecular and macroscopic, crystalline systems. To calculate NLO properties of large systems, a linear scaling generalized elongation method for the efficient and accurate calculation is introduced. The reader should be aware that this treatment is particularly feasible for complicated three-dimensional and/or delocalized systems that are intractable when applied to conventional or other linear scaling methods.

The aim of this brief is to present, in sufficient detail, a non-perturbative technique for calculating optical hyperpolarizabilities. The ability to efficiently compute hyperpolarizabilities, for a variety of different molecular systems, makes this brief invaluable for those engaged in the computational design of new electro-optical materials. The resulting computation is very predictable and suitable for automation, in contrast to perturbative methods that typically rely on iterative methods. The methodology which is wholly applicable to atoms, molecules, clusters (and with some modifications) to condensed matter, is described and illustrated at a level that is accessible to theoreticians and supplemented with details that should be of interest to practitioners.

This textbook introduces modern techniques based on computer simulation to study materials science. It starts from first principles calculations enabling to calculate the physical and chemical properties by solving a many-body Schroedinger equation with Coulomb forces. For the exchange-correlation term, the local density approximation is usually applied. After the introduction of the first principles treatment, tight-binding and classical potential methods are briefly introduced to indicate how one can increase the number of atoms in the system. In the second half of the book, Monte Carlo simulation is discussed in detail. Problems and solutions are provided to facilitate understanding. Readers will gain sufficient knowledge to begin theoretical studies in modern materials research. This second edition includes a lot of recent theoretical techniques in materials research. With the computers power now available, it is possible to use these numerical techniques to study various physical and chemical properties of complex materials from first principles. The new edition also covers empirical methods, such as tight-binding and molecular dynamics.

Thin-Film Capacitors for Packaged Electronics deals with the capacitors of a wanted kind, still needed and capable of keeping pace with the demands posed by ever greater levels of integration. It spans a wide range of topics, from materials properties to limits of what's the best one can achieve in capacitor properties to process modeling to application examples. Some of the topics covered are the following: -Novel insights into fundamental relationships between dielectric constant and the breakdown field of materials and related capacitance density and breakdown voltage of capacitor structures, -Electrical characterization techniques for a wide range of frequencies (1 kHz to 20 GHz), -Process modeling to determine stable operating points, -Prevention of metal (Cu) diffusion into the dielectric, -Measurements and modeling of the dielectric micro-roughness.

The science and technology relating to nanostructures continues to receive significant attention for its applications to various fields including microelectronics, nanophotonics, and biotechnology. This book describes the basic quantum mechanical principles underlining this fast developing field. From the fundamental principles of quantum mechanics to nanomaterial properties, from device physics to research and development of new systems, this title is aimed at undergraduates, graduates, postgraduates, and researchers.

The quantum and relativity theories of physics are considered to underpin all of science in an absolute sense. This monograph argues against this proposition primarily on the basis of the two theories' incompatibility and of some untenable philosophical implications of the quantum model. Elementary matter is assumed in both theories to occur as zero-dimensional point particles. In relativity theory this requires the space-like region of the underlying Minkowski space-time to be rejected as unphysical, despite its precise mathematical characterization. In quantum theory it leads to an incomprehensible interpretation of the wave nature of matter in terms of a probability function and the equally obscure concept of wave-particle duality. The most worrisome aspect about quantum mechanics as a theory of chemistry is its total inability, despite unsubstantiated claims to the contrary, to account for the fundamental concepts of electron spin, molecular structure, and the periodic table of the elements. A remedy of all these defects by reformulation of both theories as nonlinear wave models in four-dimensional space-time is described.

Christopher M. Cheatum and Amnon Kohen, Relationship of Femtosecond-Picosecond Dynamics to Enzyme-Catalyzed H-Transfer. Cindy Schulenburg and Donald Hilvert, Protein Conformational Disorder and Enzyme Catalysis. A. Joshua Wand, Veronica R. Moorman and Kyle W. Harpole, A Surprising Role for Conformational Entropy in Protein Function. Travis P. Schrank, James O. Wrabl and Vincent J. Hilser, Conformational Heterogeneity Within the LID Domain Mediates Substrate Binding to Escherichia coli Adenylate Kinase: Function Follows Fluctuations. Buyong Ma and Ruth Nussinov, Structured Crowding and Its Effects on Enzyme Catalysis. Michael D. Daily, Haibo Yu, George N. Phillips Jr and Qiang Cui, Allosteric Activation Transitions in Enzymes and Biomolecular Motors: Insights from Atomistic and Coarse-Grained Simulations. Karunesh Arora and Charles L. Brooks III, Multiple Intermediates, Diverse Conformations, and Cooperative Conformational Changes Underlie the Catalytic Hydride Transfer Reaction of Dihydrofolate Reductase. Steven D. Schwartz, Protein Dynamics and the Enzymatic Reaction Coordinate.

This brief goes back to basics and describes the Quantitative structure-activity/property relationships (QSARs/QSPRs) that represent predictive models derived from the application of statistical tools correlating biological activity (including therapeutic and toxic) and properties of chemicals (drugs/toxicants/environmental pollutants) with descriptors representative of molecular structure and/or properties. It explains how the sub-discipline of Cheminformatics is used for many applications such as risk assessment, toxicity prediction, property prediction and regulatory decisions apart from drug discovery and lead optimization. The authors also present, in basic terms, how QSARs and related chemometric tools are extensively involved in medicinal chemistry, environmental chemistry and agricultural chemistry for ranking of potential compounds and prioritizing experiments. At present, there is no standard or introductory publication available that introduces this important topic to students of chemistry and pharmacy. With this in mind, the authors have carefully compiled this brief in order to provide a thorough and painless introduction to the fundamental concepts of QSAR/QSPR modelling. The brief is aimed at novice readers.

Discovery of Frustrated Lewis Pairs: Intermolecular FLPs for Activation of Small Molecules, by Douglas W. Stephan Intramolecular Frustrated Lewis Pairs: Formation and Chemical Features, by Gerald Kehr, Sina Schwendemann, Gerhard Erker Frustrated Lewis Pair Mediated Hydrogenations, by Douglas W. Stephan, Gerhard Erker Amine-Borane Mediated Metal-Free Hydrogen Activation and Catalytic Hydrogenation, by Victor Sumerin, Konstantin Chernichenko, Felix Schulz, Markku Leskela, Bernhard Rieger, Timo Repo Hydrogen Activation by Frustrated Lewis Pairs: Insights from Computational Studies, by Tibor Andras Rokob, Imre Papai Quantum Chemistry of FLPs and Their Activation of Small Molecules: Methodological Aspects, by Birgitta Schirmer, Stefan Grimme Computational Design of Metal-Free Molecules for Activation of Small Molecules, Hydrogenation, and Hydroamination, by Zhi-Xiang Wang, Lili Zhao, Gang Lu, Haixia Li, Fang Huang Computational Studies of Lewis Acidity and Basicity in Frustrated Lewis Pairs, by Thomas M. Gilbert Solid-State NMR as a Spectroscopic Tool for Characterizing Phosphane - Borane Frustrated Lewis Pairs, by Thomas Wiegand, Hellmut Eckert, Stefan Grimme

In this thesis, the author outlines the discovery of an effect common to representative examples of all Li salt-free Wittig Reactions. The implications of such a universally applicable effect are that all such Wittig reactions occur through the same mechanism. Although the Wittig reaction was first discovered in 1953, its reaction mechanism has never been definitively settled with many different variants proposed and disproved. The work in this thesis shows conclusively that for [2+2] cycloadditions all Wittig reactions occur by the same irreversible mechanism. In addition, the author also describes a new chromatography-free method for the removal of phosphine oxide from the alkene crude product of the Wittig reaction. The work in this thesis has led to several publications in high-profile journals.