This book presents a variety of techniques for tackling phenomena that are not amenable to the conventional approach based on the concept of probabilities. The methods described rely on the use of path integration, thermal Green functions, time-temperature propagators, Liouville operators, second quantization, and field correlators at finite density and temperature. Also exploring the statistical mechanics of unstable quantum systems, the book is intended as a supplementary or reference text for use in one-semester graduate courses on Quantum Mechanics, Thermodynamics, Electromagnetism, and Mathematical Methods in Physics.

This book highlights the genomic findings, observations, and analysis of DNA/RNA sequences and protein structure of the dreadful virus of this decade- COVID-19. The Corona group of viruses though known species, the strain that caused the Pandemic of 2019 is a completely new strain, belonging to the same corona family with a novel genetic make-up. This makes it a new pathogen which is causing the current outbreak leaving the global scientific community clueless of any therapeutic breakthrough. NCOV enjoys life threatening pathogenicity with mysterious genetic annotations. This book details and offers insights into its viral genetic arrangement, Virulence factors, probable mutations leading to the evolution of this new strain and more. It contains chapters on Virus evolutionary status and Genetic makeup leading to its pathogenicity which can be a new insight in understanding the nature of this clever microorganism and can pave way to the development of new drugs and Vaccines or a novel diagnostic approach for the early prognosis of the disease. A dedicated chapter on annotation of NCOV-19 virulence genes, translation of the genes to protein product, annotation of the antigenic sites on these proteins is also included. In all, this brief is a complete genomic annotation insight of NCOV-19 using AI, Data analytics and Bioinformatics analysis. In the current situation, this book is an extensive preliminary resource for Medical practitioners, Researchers, Academicians, Scientists, Biochemists, Bioinformaticians and other professionals interested in understanding the genetics of Novel Coronavirus 19, the best possible drug targets, ideal vaccine candidates and novel prognostic and diagnostic biomarkers.

This book provides a comprehensive review of both traditional and cutting-edge methodologies that are currently used in computational toxicology and specifically features its application in regulatory decision making. The authors from various government agencies such as FDA, NCATS and NIEHS industry, and academic institutes share their real-world experience and discuss most current practices in computational toxicology and potential applications in regulatory science. Among the topics covered are molecular modeling and molecular dynamics simulations, machine learning methods for toxicity analysis, network-based approaches for the assessment of drug toxicity and toxicogenomic analyses. Offering a valuable reference guide to computational toxicology and potential applications in regulatory science, this book will appeal to chemists, toxicologists, drug discovery and development researchers as well as to regulatory scientists, government reviewers and graduate students interested in this field.

Maximilian Scheurer presents a method for modeling excited states in atomistic, heterogeneous environments. The method utilizes the polarizable embedding (PE) model to mimic electrostatic and polarization interactions of a molecule with its environment. For high-level modeling of the molecule's excited states, the algebraic-diagrammatic construction scheme for the polarization propagator (ADC) is employed. The presented work outlines the theoretical foundations of PE and ADC and the combination of both methods, termed PE-ADC. The accuracy of PE-ADC is tested, and the charge-transfer (CT) excitation in the dodecin protein is studied. This book presents a comprehensive elaboration on the new PE-ADC method and a state-of-the-art application of PE-ADC to a photo-biochemical process.

The types of forces that are involved in the interactions between molecules vary across a wide spectrum from very strong, as in ion-ion interactions, to the much weaker forces that are involved in van der Waals complexes. This book provides an introduction to the theoretical methods that are used to analyze each sort of force and provide the reader with a guide to the most appropriate method for a given problem. Examples are used to illustrate the points, and the pitfalls that a novice might encounter are outlined. These examples range from very small complexes to much larger systems with biological relevance.

This brief introduces readers to an alternative thermochemical reference system that makes it possible to use the heats of formation of organic compounds to deduce the energies that depend entirely on their structures, and which provides calculated values for most of the characteristic structures appearing in organic molecules. These structure-dependent energies are provided e.g. for selected compounds of normal and cyclic alkanes, open chain and cyclic olefins (including conjugated polyenes), alkynes, aromatic hydrocarbons and their substituted derivatives. The oxygen, sulfur and nitrogen derivatives of the above-mentioned compounds are also represented with calculated structure-dependent energies including alcohols, ethers, aldehydes and ketones, carboxylic acids, thiols, sulfides, amines, amides, heterocyclic compounds and others. Most organic reactions can be interpreted as the disappearance of certain structures and formation of others. If the structure-dependent energies are known, it can be shown how the disappearing and the newly formed structures contribute to the heat of reactions and to the driving forces. As experienced by the author, who pioneered the concept, structure dependent energies can help teachers to make organic chemistry more accessible for their students. Accordingly, the brief offers a valuable resource for all those who teach organic chemistry at universities, and for those who are learning it.

Hydrogen bonding is crucial in many chemical and biochemical reactions, as well as in determining material properties. A good insight into the theoretical methods of treating hydrogen bonding is essential for those wishing to model its effects computationally in a wide range of fields involving hydrogen bonding, as well as those wishing to extract the maximal amount of information from experimental data. Theoretical Treatments of Hydrogen Bonding presents the reader with the state of the art of the key theoretical approaches to hydrogen bonding and considers the hydrogen bond from the various aspects. The first five chapters are devoted to the methods used for treating the electronic basis of hydrogen bonding, including a consideration of the electrostatic model, density functional theory and molecular orbital methods. Later chapters consider the dynamics of hydrogen bonds with particular attention to the treatment of proton transfer; manifestations of dynamics as reflected in infrared spectra and nuclear magnetic relaxation are also considered. Hydrogen bonding in liquids and solids such as ferroelectrics are included. The book concludes with an epilogue which discusses the likely development of hydrogen bond computations in very large chemical systems. Theoretical Treatments of Hydrogen Bonding offers the reader a comprehensive view of the current theoretical approaches to hydrogen bonding. It is a valuable presentation of theoretical tools useful to those looking for the most appropriate approach for treating a particular problem involving hydrogen bonding.

Designing molecules and materials with desired properties is an important prerequisite for advancing technology in our modern societies. This requires both the ability to calculate accurate microscopic properties, such as energies, forces and electrostatic multipoles of specific configurations, as well as efficient sampling of potential energy surfaces to obtain corresponding macroscopic properties. Tools that can provide this are accurate first-principles calculations rooted in quantum mechanics, and statistical mechanics, respectively. Unfortunately, they come at a high computational cost that prohibits calculations for large systems and long time-scales, thus presenting a severe bottleneck both for searching the vast chemical compound space and the stupendously many dynamical configurations that a molecule can assume. To overcome this challenge, recently there have been increased efforts to accelerate quantum simulations with machine learning (ML). This emerging interdisciplinary community encompasses chemists, material scientists, physicists, mathematicians and computer scientists, joining forces to contribute to the exciting hot topic of progressing machine learning and AI for molecules and materials. The book that has emerged from a series of workshops provides a snapshot of this rapidly developing field. It contains tutorial material explaining the relevant foundations needed in chemistry, physics as well as machine learning to give an easy starting point for interested readers. In addition, a number of research papers defining the current state-of-the-art are included. The book has five parts (Fundamentals, Incorporating Prior Knowledge, Deep Learning of Atomistic Representations, Atomistic Simulations and Discovery and Design), each prefaced by editorial commentary that puts the respective parts into a broader scientific context.

This concise book introduces and discusses the basic theory of conical intersections with applications in atomic, molecular and condensed matter physics. Conical intersections are linked to the energy of quantum systems. They can occur in any physical system characterized by both slow and fast degrees of freedom - such as e.g. the fast electrons and slow nuclei of a vibrating and rotating molecule - and are important when studying the evolution of quantum systems controlled by classical parameters. Furthermore, they play a relevant role for understanding the topological properties of condensed matter systems. Conical intersections are associated with many interesting features, such as a breakdown of the Born-Oppenheimer approximation and the appearance of nontrivial artificial gauge structures, similar to the Aharonov-Bohm effect. Some applications presented in this book include - Molecular Systems: some molecules in nonlinear nuclear configurations undergo Jahn-Teller distortions under which the molecule lower their symmetry if the electronic states belong to a degenerate irreducible representation of the molecular point group. - Solid State Physics: different types of Berry phases associated with conical intersections can be used to detect topologically nontrivial states of matter, such as topological insulators, Weyl semi-metals, as well as Majorana fermions in superconductors. - Cold Atoms: the motion of cold atoms in slowly varying inhomogeneous laser fields is governed by artificial gauge fields that arise when averaging over the fast internal degrees of freedom of the atoms. These gauge fields can be Abelian or non-Abelian, which opens up the possibility to create analogs to various relativistic effects at low speed.

This book sheds new light on the dynamical behaviour of electron spins in molecules containing two unpaired electrons (i.e. a radical pair). The quantum dynamics of these spins are made complicated by the interaction between the electrons and the many nuclear spins of the molecule; they are intractable using analytical techniques, and a naive numerical diagonalization is not remotely possible using current computational resources. Hence, this book presents a new method for obtaining the exact quantum-mechanical dynamics of radical pairs with a modest number of nuclear spins. Readers will learn how a calculation that would take 13 years using conventional wavepacket propagation can now be done in 1 day, and will also discover a new semiclassical method for approximating the dynamics in the presence of many nuclear spins. The new methods covered in this book are shown to provide significant insights into three topical and diverse areas: charge recombination in molecular wires (which can be used in artificially mimicking photosynthesis), magnetoelectroluminescence in organic light-emitting diodes, and avian magnetoreception (how birds sense the Earth's magnetic field in order to navigate).

This book reviews various aspects of molecular spectroscopy and its application in materials science, chemistry, physics, medicine, the arts and the earth sciences. Written by an international group of recognized experts, it examines how complementary applications of diverse spectroscopic methods can be used to study the structure and properties of different materials. The chapters cover the whole spectrum of topics related to theoretical and computational methods, as well as the practical application of spectroscopic techniques to study the structure and dynamics of molecular systems, solid-state crystalline and amorphous materials, surfaces and interfaces, and biological systems. As such, the book offers an invaluable resource for all researchers and postgraduate students interested in the latest developments in the theory, experimentation, measurement and application of various advanced spectroscopic methods for the study of materials.

This book introduces basic concepts of mathematical physics to chemists. Many textbooks and monographs of mathematical physics may appear daunting to them. Unlike other, related books, however, this one contains a practical selection of material, particularly for graduate and undergraduate students majoring in chemistry. The book first describes quantum mechanics and electromagnetism, with the relation between the two being emphasized. Although quantum mechanics covers a broad field in modern physics, the author focuses on a hydrogen(like) atom and a harmonic oscillator with regard to the operator method. This approach helps chemists understand the basic concepts of quantum mechanics aided by their intuitive understanding without abstract argument, as chemists tend to think of natural phenomena and other factors intuitively rather than only logically. The study of light propagation, reflection, and transmission in dielectric media is of fundamental importance. This book explains these processes on the basis of Maxwell equations. The latter half of the volume deals with mathematical physics in terms of vectors and their transformation in a vector space. Finally, as an example of chemical applications, quantum chemical treatment of methane is introduced, including a basic but essential explanation of Green functions and group theory. Methodology developed by the author will also prove to be useful to physicists.

On-surface synthesis is appearing as an extremely promising strategy to create organic nanoarchitectures with atomic precision. Molecular building blocks holding adequate functional groups are dosed onto surfaces that support or even drive their covalent linkage. The surface confinement and the frequent lack of solvents (most commonly being performed under vacuum conditions) create a completely new scenario fully complementary to conventional chemistry. In a pedagogical way and based on the most recent developments, this volume presents our current understanding in the field, addressing fundamental reaction mechanisms, synthetic strategies to influence the reactions according to our needs, as well as the ultimate growth and characterization of functional materials. Verging on chemistry, physics and materials science, the book is aimed at students and researchers interested in nanochemistry, surface science, supramolecular materials and molecular devices. Chapters "Mechanistic insights into surface-supported chemical reactions", "Reactivity on and of Graphene Layers: Scanning Probe Microscopy Reviels" and "Bottom-up fabrication of atomically precise graphene nanoribbons" of this book are available open access under a CC BY 4.0 license at link.springer.com

This book describes the latest developments in the new research discipline of X-ray nanochemistry, which uses nanomaterials to enhance the effectiveness of X-ray irradiation. Nanomaterials now can be synthesized in such a way as to meet the demand for complex functions that enhance the X-ray effect. Innovative methods of delivering the X-rays, which can interact with those nanomaterials much more strongly than energetic electrons and gamma rays, also create new opportunities to enhance the X-ray effect. As a result, new concepts are conceived and new developments are made in the last decade, which are discussed and summarized in this book. This book will help define the discipline and encourage more students and scientists to work in this discipline. These efforts will eventually lead to formation of a full set of physical, chemical and materials principles for this new research field.

This book presents a collection of invited research and review contributions on recent advances in (mainly) theoretical condensed matter physics, theoretical chemistry, and theoretical physics. The volume celebrates the 90th birthday of N.H. March (Emeritus Professor, Oxford University, UK), a prominent figure in all of these fields. Given the broad range of interests in the research activity of Professor March, who collaborated with a number of eminent scientists in physics and chemistry, the volume embraces quite diverse topics in physics and chemistry, at various dimensions and energy scales. One thread connecting all these topics is correlation in aggregated states of matter, ranging from nuclear physics to molecules, clusters, disordered condensed phases such as the liquid state, and solid state physics, and the various phase transitions, both structural and electronic, occurring therein. A final chapter leaps to an even larger scale of matter aggregation, namely the universe and gravitation. A further no less important common thread is methodological, with the application of theoretical physics and chemistry, particularly density functional theory and statistical field theory, to both nuclear and condensed matter.

This book describes fundamental theory and recent advances of sum frequency generation (SFG) spectroscopy. SFG spectroscopy is widely used as a powerful tool of surface characterization, although theoretical interpretation of the obtained spectra has been a major bottleneck for most users. Recent advances in SFG theory have brought about a breakthrough in the analysis methods beyond conventional empirical ones, and molecular dynamics (MD) simulation of SFG spectroscopy allows for simultaneous understanding of observed spectra and interface structure in unprecedented detail. This book explains these recently understood theoretical aspects of SFG spectroscopy by the major developer of the theory. The theoretical topics are treated at basic levels for undergraduate students and are described in relation to computational chemistry, such as molecular modeling and MD simulation, toward close collaboration of SFG spectroscopy and computational chemistry in the near future.

This thesis focuses on the nanomanufacturing of graphene-a newly discovered, two-dimensional material with extraordinary properties-in order to realize its numerous potential applications. Combining experimental implementation with theoretical modelling, it investigates three classes of graphene nanostructure fabrication using particle beam irradiation: (i) doping of graphene using low energy nitrogen irradiation; (ii) joining of graphene sheets with laser and C, N, and Ar ion beam irradiation; and (iii) fabrication of graphene nanopores by means of focused ion beam and electron beam irradiation. The feasibility of the nanomanufacture of graphene using particle beam irradiation is demonstrated by various experimental methods, and the mechanisms involved under different types of beam irradiation are revealed using theoretical calculations. Further, the book analyzes the mechanical and electrical properties of the fabricated graphene nanostructures by means of atomic simulations to predict the application potentials of the proposed methods. The findings help promote the implementation of graphene-structure applications in industry.

This book is intended as an introductory lecture in material physics, in which the modern computational group theory and the electronic structure calculation are in collaboration. The first part explains how to use computer algebra for applications in solid-state simulation, based on the GAP computer algebra package. Computer algebra enables us to easily obtain various group theoretical properties, such as the representations, character tables, and subgroups. Furthermore it offers a new perspective on material design, which could be executed in a mathematically rigorous and systematic way. The second part then analyzes the relation between the structural symmetry and the electronic structure in C60 (as an example of a system without periodicity). The principal object of the study was to illustrate the hierarchical change in the quantum-physical properties of the molecule, which correlates to the reduction in the symmetry (as it descends down in the ladder of subgroups). The book also presents the computation of the vibrational modes of the C60 by means of the computer algebra. In order to serve the common interests of researchers, the details of the computations (the required initial data and the small programs developed for the purpose) are explained in as much detail as possible.

This textbook extends from the basics of femtosecond physics all the way to some of the latest developments in the field. In this updated edition, the chapter on laser-driven atoms is augmented by the discussion of two-electron atoms interacting with strong and short laser pulses, as well as by a review of ATI rings and low energy structures in photo-electron spectra. In the chapter on laser-driven molecules a discussion of 2D infrared spectroscopy is incorporated. Theoretical investigations of atoms and molecules interacting with pulsed lasers up to atomic field strengths on the order of 10^16 W/cm(2) are leading to an understanding of many challenging experimental discoveries. The presentation starts with a brief introduction to pulsed laser physics. The basis for the non-perturbative treatment of laser-matter interaction in the book is the time-dependent Schroedinger equation. Its analytical as well as numerical solution are laid out in some detail. The light field is treated classically and different possible gauges for the field-matter interaction are discussed. Physical phenomena, ranging from paradigmatic Rabi-oscillations in two-level systems to the ionization of atoms, the generation of high-order harmonics, the ionization and dissociation of molecules, as well as the control of chemical reactions are presented and discussed on a fundamental level. In this way, the theoretical background for state of the art experiments with strong and short laser pulses is given. The new text is augmented by several additional exercises and now contains a total of forty-eight problems, whose worked-out solutions are given in the last chapter. In addition, some detailed calculations are performed in the appendices. Furthermore, each chapter ends with references to more specialized literature.

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.

This thesis presents detailed mechanistic studies on a series of important C-H activation reactions using combined computational methods and mass spectrometry experiments. It also provides guidance on the design and improvement of catalysts and ligands. The reactions investigated include: (i) a nitrile-containing template-assisted meta-selective C-H activation, (ii) Pd/mono-N-protected amino acid (MPAA) catalyzed meta-selective C-H activation, (iii) Pd/MPAA catalyzed asymmetric C-H activation reactions, and (iv) Cu-catalyzed sp3 C-H cross-dehydrogenative-coupling reaction. The book reports on a novel dimeric Pd-M (M = Pd or Ag) model for reaction (i), which successfully explains the meta-selectivity observed experimentally. For reaction (ii), with a combined DFT/MS method, the author successfully reveals the roles of MPAA ligands and a new C-H activation mechanism, which accounts for the improved reactivity and high meta-selectivity and opens new avenues for ligand design. She subsequently applies ion-mobility mass spectrometry to capture and separate the [Pd(MPAA)(substrate)] complex at different stages for the first time, providing support for the internal-base model for reaction (iii). Employing DFT studies, she then establishes a chirality relay model that can be widely applied to MPAA-assisted asymmetric C-H activation reactions. Lastly, for reaction (iv) the author conducts detailed computational studies on several plausible pathways for Cu/O2 and Cu/TBHP systems and finds a reliable method for calculating the single electron transfer (SET) process on the basis of benchmark studies.

This open access book brings out the state of the art on how informatics-based tools are used and expected to be used in nanomaterials research. There has been great progress in the area in which "big-data" generated by experiments or computations are fully utilized to accelerate discovery of new materials, key factors, and design rules. Data-intensive approaches play indispensable roles in advanced materials characterization. "Materials informatics" is the central paradigm in the new trend. "Nanoinformatics" is its essential subset, which focuses on nanostructures of materials such as surfaces, interfaces, dopants, and point defects, playing a critical role in determining materials properties. There have been significant advances in experimental and computational techniques to characterize individual atoms in nanostructures and to gain quantitative information. The collaboration of researchers in materials science and information science is growing actively and is creating a new trend in materials science and engineering.

This book is intended to help advanced undergraduate, graduate, and postdoctoral students in their daily work by offering them a compendium of numerical methods. The choice of methods pays significant attention to error estimates, stability and convergence issues, as well as optimization of program execution speeds. Numerous examples are given throughout the chapters, followed by comprehensive end-of-chapter problems with a more pronounced physics background, while less stress is given to the explanation of individual algorithms. The readers are encouraged to develop a certain amount of skepticism and scrutiny instead of blindly following readily available commercial tools. The second edition has been enriched by a chapter on inverse problems dealing with the solution of integral equations, inverse Sturm-Liouville problems, as well as retrospective and recovery problems for partial differential equations. The revised text now includes an introduction to sparse matrix methods, the solution of matrix equations, and pseudospectra of matrices; it discusses the sparse Fourier, non-uniform Fourier and discrete wavelet transformations, the basics of non-linear regression and the Kolmogorov-Smirnov test; it demonstrates the key concepts in solving stiff differential equations and the asymptotics of Sturm-Liouville eigenvalues and eigenfunctions. Among other updates, it also presents the techniques of state-space reconstruction, methods to calculate the matrix exponential, generate random permutations and compute stable derivatives.

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).