Volume 16

Reviews In Computational Chemistry

Kenny B. Lipkowitz and Donald B. Boyd

The focus of this book is on methods useful in molecular design. Tutorials and reviews span (1) methods for designing compound libraries for combinatorial chemistry and high throughput screening, (2) the workings of artificial neural networks and their use in chemistry, (3) force field methods for modeling materials and designing new substances, and (4) free energy perturbation methods of practical usefulness in ligand design.

From Reviews of the Series

"This series spans all the subdisciplines in the field, from techniques to practical applications, and includes reviews from many of the acknowledged leaders in the field. the reviews cross many subdisciplines yet are both general enough to be of wide interest while including detailed information of use to workers in particular subdisciplines." –Journal of the American Chemical Society

Safe Storage of Laboratory Chemicals, Second Edition is a comprehensive guide which allows readers to assess and improve the safety of their laboratory operations when storing chemicals. By applying the information in this book, readers can create a safer place to workthrough a safer storage environment, wiser storage practices and procedures, informed personnel, and the intelligent use of information. There has seen a surge in the demand for chemical safety and information relating to a safe workplace. This book covers chemical storage, the requirements of OSHA and EPA, requirements in codes and standards for storage, and advances and applications for chemical health and safety. This book offers a balanced approach to the safe storage of laboratory chemicals. Applied knowledge for identifying chemical storage hazards, solutions and alternative measures for storing specific hazard classes of chemicals, and innovative case histories provide a wealth of information from which readers may draw to enhance the safety of their storage situations.

This work is based on experiences acquired by the authors regarding often asked questions and problems during manifold education of beginners in analytical transmission electron microscopy. These experiences are summarised illustratively in this textbook. Explanations based on simple models and hints for the practical work are the focal points. This practically- oriented textbook represents a clear and comprehensible introduction for all persons who want to use a transmission electron microscope in practice but who are not specially qualified electron microscopists up to now.

Radionuclides produced by past nuclear weapon test explosions comprise the largest source of anthropogenic radioactivity released into the earth's atmosphere to date. This volume presents data and models about the fate of the released radionuclides and their possible effects on human health. It is divided into the following three parts: - Source Term Studies;- Dose Reconstruction;- Ecological and Health Effects,and comprises both Western and formerly secret Soviet research studies, illuminates past and current research.

The first book to chronicle how innovation in laboratory designs for botanical research energized the emergence of physiological plant ecology as a vibrant subdiscipline   Laboratory innovation since the mid-twentieth century has powered advances in the study of plant adaptation, evolution, and ecosystem function. The phytotron, an integrated complex of controlled-environment greenhouse and laboratory spaces, invented by Frits W. Went in the 1950s, set off a worldwide laboratory movement and transformed the plant sciences. Sharon Kingsland explores this revolution through a comparative study of work in the United States, France, Australia, Israel, the USSR, and Hungary.   These advances in botanical research energized physiological plant ecology. Case studies explore the development of phytotron spinoffs such as mobile laboratories, rhizotrons, and ecotrons. Scientific problems include the significance of plant emissions of volatile organic compounds, symbiosis between plants and soil fungi, and the discovery of new pathways for photosynthesis as an adaptation to hot, dry climates. The advancement of knowledge through synthesis is a running theme: linking disciplines, combining laboratory and field research, and moving across ecological scales from leaf to ecosystem. The book also charts the history of modern scientific responses to the emerging crisis of food insecurity in the era of global warming.

Written for animal researchers, this book provides a comprehensive guide to the design and statistical analysis of animal experiments. It has long been recognised that the proper implementation of these techniques helps reduce the number of animals needed. By using real-life examples to make them more accessible, this book explains the statistical tools employed by practitioners. A wide range of design types are considered, including block, factorial, nested, cross-over, dose-escalation and repeated measures and techniques are introduced to analyse the experimental data generated. Each analysis technique is described in non-mathematical terms, helping readers without a statistical background to understand key techniques such as t-tests, ANOVA, repeated measures, analysis of covariance, multiple comparison tests, non-parametric and survival analysis. This is also the first text to describe technical aspects of InVivoStat, a powerful open-source software package developed by the authors to enable animal researchers to analyse their data and obtain informative results.

The modern electron microscope, as a result of recent revolutionary developments and many evolutionary ones, now yields a wealth of quantitative knowledge pertaining to structure, dynamics, and function barely matched by any other single scientific instrument. It is also poised to contribute much new spatially-resolved and time-resolved insights of central importance in the exploration of most aspects of condensed matter, ranging from the physical to the biological sciences.Whereas in all conventional EM methods, imaging, diffraction, and chemical analyses have been conducted in a static - time-integrated - manner, now it has become possible to unite the time domain with the spatial one, thereby creating four-dimensional (4D) electron microscopy. This advance is based on the fundamental concept of timed, coherent single-electron packets, or electron pulses, which are liberated with femtosecond durations. Structural phase transitions, mechanical deformations, and the embryonic stages of melting and crystallization are examples of phenomena that can now be imaged in unprecedented structural detail with high spatial resolution, and ten orders of magnitude as fast as hitherto.No monograph in existence attempts to cover the revolutionary dimensions that EM in its various modes of operation nowadays makes possible. The authors of this book chart these developments, and also compare the merits of coherent electron waves with those of synchrotron radiation. They judge it prudent to recall some important basic procedural and theoretical aspects of imaging and diffraction so that the reader may better comprehend the significance of the new vistas and applications now afoot.This book is not a vade mecum - numerous other texts are available for the practitioner for that purpose. It is instead an in-depth expose of the paradigm concepts and the developed techniques that can now be executed to gain new knowledge in the entire domain of biological and physical science, and in the four dimensions of space and time.

The best source of practical, easily accessible information on this exciting new technique

CAPILLARY ELECTROPHORESIS

Analytical chemists and biochemists have been turning to the technique of capillary electrophoresis with increasing frequency: it is fast, sensitive, easy to automate, requires only small sample volumes and reagent amounts, and has been successfully applied to an ever-expanding list of sample types. In Capillary Electrophoresis, analytical practitioners will find a complete, practical guide to the principles, forms, and instrumentation of this technique. The book presents clear and straightforward explanations of the method, its operating principles, and its different modes, including capillary zone electrophoresis, micellar electrokinetic capillary chromatography, capillary gel electrophoresis, capillary isoelectric focusing, and capillary isotachophoresis. Especially helpful is the material on developing a method: it offers practical guidance on CE modes, capillaries, run buffers, voltage requirements, sample pretreatments, injection modes and amounts, temperature settings, detector selections, buffer replenishment, and data reporting.

Capillary Electrophoresis will serve both as an excellent introduction to those who are new to the technique and as a comprehensive reference book to experienced practitioners. A complete and detailed index will assist the reader in quickly finding any topic of interest.

Solid state NMR is rapidly emerging as a universally applicable method for the characterization of ordered structures that cannot be studied with solution methods or diffraction techniques. This proceedings -; from a recent international workshop - captures an image of the latest developments and future directions for solid state NMR in biological research, particularly on membrane proteins. Detailed information on how hormones or drugs bind to their membrane receptor targets is needed, e.g. for rational drug design. Higher fields are bringing clear improvements, and the power of solid state NMR techniques for studying amorphous and membrane associated peptides, proteins and complexes is shown by examples of applications at ultra-high fields. Progress in protein expression, experimental design and data analysis are also presented by leaders in these research areas.

This comprehensive reference work details the latest developments in fluorescence imaging and related biological quantification. It explores the most recent techniques in this imaging technology through the utilization and incorporation of quantification analysis which makes this book unique. It also covers super resolution microscopy with the introduction of 3D imaging and high resolution fluorescence. Many of the chapter authors are world class experts in this medical imaging technology.

Adrenergic receptors are important modulators in the sympathetic c- trol of various metabolic processes in the central and peripheral nervous s- tems. These receptors are localized at multiple sites throughout the central nervous system (CNS) and serve as important regulators of CNS-mediated behavior and neural functions, including mood, memory, neuroendocrine c- trol, and stimulation of autonomic function. Adrenergic Receptor Protocols consists of 35 chapters dealing with va- ous aspects of adrenergic receptor analyses, including the use of genetic, RNA, protein expression, transactivator, second messenger, immunocytochemical, electrophysiological, transgenic, and in situ hybridization approaches. This volume details the use of various methods to examine the adrenergic receptor system, using aspects of the genetic flow of information as a guide (DNA? RNA ? transactivator ? protein expression ? second messenger analyses ? cellular analyses ? transgenic whole animal approaches). Adrenergic Receptor Protocols displays step-by-step methods for s- cessful replication of experimental procedures, and would be useful for both experienced investigators and newcomers in the field, including those beg- ning graduate study or undergoing postdoctoral training. The Notes section contained in each chapter provides valuable troubleshooting guides to help develop working protocols for your laboratory. With Adrenergic Receptor Protocols, it has been my intent to develop a comprehensive collection of modern molecular methods for analyzing adrenergic receptors. I would like to thank the many chapter authors for their contributions.

As the selection of material for particular engineering properties becomes increasingly important in keeping costs down, methods for evaluating material properties also become more relevant. One such method examines the geometry of grain boundaries, which reveals much about the properties of the material. Studying material properties from their geometrical measurements, The Measurement of Grain Boundary Geometry provides a framework for a specialized application of electron microscopy for metals and alloys and, by extension, for ceramics, minerals, and semiconductors. The book presents an overview of the developments in the theory of grain boundary geometry and its practical applications in material engineering. It also covers the tunneling electron microscope (TEM), experimental aspects of data collection, data processing, and examples from actual investigations. Each step of the analysis process is clearly described, from data collection through processing, analysis, representation, and display to applications. The book also includes a glossary of terms. Exploring both the experimental and analytical aspects of the subject, this practical reference guide is essential for researchers and students involved in material properties, whether in physics, materials science, metallurgy, or physical chemistry.

This book derives from a 3 day intensive course on Pressure Vessel Design given regularly in the UK and around the world since 1986. It is written by experts in their field and although the main thrust of the Course has been directed to BS5500, the treatment of the material is of a general nature thus providing insight into other national standards.

Successful Management of the Analytical Laboratory provides a comprehensive discussion of the problems that face analytical laboratory managers and presents proven techniques for improving the operation and performance of analytical labs. A wide range of topics are covered, including functions of various laboratory types (including a discussion of legal proceedings that involve defending laboratory data), staffing and organization, motivation, management and development of personnel, personal relations and communication, sample handling, workload optimization, equipment selection and justification, budgeting and cost control (including methods for calculating the dollar return on investments in capital equipment), and information management systems. The book emphasizes measures that managers can take to ensure quality performance in both the laboratory and its personnel while maintaining the overall cost effectiveness of the operation. The author uses case histories from his experience to illustrate the application of the management principles presented in this excellent book for new and experienced lab managers alike.

Scanning and stationary-beam electron microscopes have become an indispensable tool for both research and routine evaluation in materials science, the semi- conductor industry, nanotechnology and the biological, forensic, and medical sciences. This book provides an introduction to the theory and current practice of electron microscopy, aimed primarily at undergraduates who need to learn how the basic principles of physics are applied in an important area of science and technology that has contributed greatly to our knowledge of life processes and inner space. However, it will be equally valuable for technologists who make use of electron microscopes and for graduate students, university teachers and researchers who need a concise text that deals with the basic principles of microscopy. Less technical but broader in scope than other microscopy textbooks, Physical Principles of Electron Microscopy is appropriate for undergraduates and technologists with limited math...

Image Analysis of Food Microstructure offers a condensed guide to the most common procedures and techniques by which quantitative microstructural information about food can be obtained from images. The images are selected from a broad range of food items, including macroscopic images of meat and finished products such as pizza, and the microstructures of cheeses, dough and baked goods, ice cream, fruits and vegetables, emulsions, foams, and gels. The book informs food scientists about the image processing and measurement tools used to characterize a variety of microstructures in foods, using high-quality image techniques to illustrate chemical composition, thermo-mechanical processing, and genetic and structural properties. These different types of images used to measure various aspects of structure include: macroscopic light photography, confocal light microscopy, electron microscopy, atomic force microscope images, magnetic resonance, and computed tomography. Then the text explains how to interpret images to produce data, plot the results in different graphs, and identify trends. Examples using these image analysis techniques show typical results that researchers can expect and recreate. Image Analysis of Food Microstructure summarizes the basic procedures that can be useful in various aspects of food research, from nutraceuticals to cooking and food processing. It presents the processing of images and mathematical principles needed for image analyses in a step-by-step approach to extract key information from the images obtained.

Electron microscopy is now a mainstay characterization tool for solid state physicists and chemists as well as materials scientists. Containing the proceedings from the Electron Microscopy and Analysis Group (EMAG) conference in September 2003, this volume covers current developments in the field, primarily in the UK. These conferences are biennial events organized by the EMAG of the Institute of Physics to provide a forum for discussion of the latest developments in instrumentation, techniques, and applications of electron and scanning probe microscopies.

Efficiency and life time of solar cells, energy and power density of the batteries, and costs of the fuel cells alike cannot be improved unless the complex electronic, optoelectronic, and ionic mechanisms underpinning operation of these materials and devices are understood on the nanometer level of individual defects. Only by probing these phenomena locally can we hope to link materials structure and functionality, thus opening pathway for predictive modeling and synthesis. While structures of these materials are now accessible on length scales from macroscopic to atomic, their functionality has remained Terra Incognitae. In this volume, we provide a summary of recent advances in scanning probe microscopy studies of local functionality of energy materials and devices ranging from photovoltaics to batteries, fuel cells, and energy harvesting systems. Recently emergent SPM modes and combined SPM-electron microscopy approaches are also discussed. Contributions by internationally renowned leaders in the field describe the frontiers in this important field.

Scanning Probe Microscopy (SPM) is the enabling tool for nano(bio)technology, which has opened new vistas in many interdisciplinary research areas. Concomitant with the developments in SPM instrumentation and techniques are new and previously unthought-of opportunities in materials nanofabrication and characterisation. In particular, the developments in addressing and manipulating matter at the level of single atoms or molecules, and studies of biological materials (e.g. live cells, or cell membranes) result in new and exciting discoveries.The rising importance of SPM demands a concise treatment in the form of a book which is accessible to interdisciplinary practitioners. This book highlights recent advances in the field of SPM with sufficient depth and breadth to provide an intellectually stimulating overview of the current state of the art. The book is based on a set of carefully selected original works from renowned contributors on topics that range from atom technology, scanning tunneling spectroscopy of self-assembled nanostructures, SPM probe fabrication, scanning force microscopy applications in biology and materials science down to the single molecule level, novel scanning probe techniques, and nanolithography.The variety of topics underlines the strong interdisciplinary character of SPM related research and the combined expertise of the contributors gives us a unique opportunity to discuss possible future trends in SPM related research. This makes the book not merely a collection of already published material but an enlightening insight into cutting edge research and global SPM research trends.

The 1989 International Conference on Nuclear Analytical Methods in theUfe Scienceswas a continuationofa seriesofconfer encesheldbytheInternationalAtomicEnergyAgency. Thefirsttook placeinAmsterdamin 1967, thesecondin Bledin 1972, andthethird inViennain 1978. Theaimoftheseconferenceshasbeentostimulate discussions between scientists who are working as biologists, envi ronmentalists, and physicians, and those who are working on the advancementofnuclear analytical techniques. The 1989 Conference was held at the National Institute of Standards and Technology (NIST, formerly the National Bureau of Standards)inGaithersburg, Maryland. ThefocalpointoftheConfer ence was the presentation of results from multidisciplinary research involvingnuclear analytical techniques and their applications to the life sciences. Wehave obtained contributions from life sciencefields thatrelatethenuclear analyticalmethods to abroad scopeofbiologi cal, medical, and environmental applications. Deliberately, our defi nition of nuclear analytical techniques was made flexible. Methods and applications were treated in a more comprehensive way than thoseatestablished meetings. Particularconsideration was given to contributions from developing countries. We are indebted to many people and organizations for their assistancein making this symposium possible. TheConference was organizedbytheUSDepartmentofCommerce'sNISTincooperation with the International Atomic Energy Agency, by supplying both financial support and scientific expertise. The meeting was cospon soredbytheAmericanNuclearSociety, theUSDepartmentofEnergy, andtheFoodandDrugAdministration, whoprovidedbothorganiza tional and financial support. We hope that the results of this Conference, presented here, will stimulatethe developmentofnew collaborativeresearch efforts betweenthe life sciencesand analytical fields. Acontinuationofthis series ofconferences willbe a measureofthe successofthis interdis ciplinary collaboration."

Structure-Based Drug Design brings together scientists working on different aspects of the subject, demonstrating the necessary collaboration and interdisciplinary approach to this complex area. The focus is on X-ray crystallographic and computational approaches. The general aspects of these approaches are introduced in the first six articles. The remaining articles provide examples of the application of X-ray crystallography, molecular modelling, molecular dynamics, QSAR, database analysis, and homology modelling. The papers cover a wealth of interesting problems in the design of new and enhanced pharmaceuticals.

Data Processing Handbook for Complex Biological Data provides relevant and to the point content for those who need to understand the different types of biological data and the techniques to process and interpret them. The book includes feedback the editor received from students studying at both undergraduate and graduate levels, and from her peers. In order to succeed in data processing for biological data sources, it is necessary to master the type of data and general methods and tools for modern data processing. For instance, many labs follow the path of interdisciplinary studies and get their data validated by several methods. Researchers at those labs may not perform all the techniques themselves, but either in collaboration or through outsourcing, they make use of a range of them, because, in the absence of cross validation using different techniques, the chances for acceptance of an article for publication in high profile journals is weakened.

This book presents a detailed analysis of up-to-date literature on in vitro morphogenesis at cell, tissue, organ, and whole plant levels. Its driving force is the substantial advances made in the field of morphogenesis in tissue cultures during the last 25 years.

Molecular recognition, also known as biorecognition, is the heart of all biological interactions. Originating from protein stretching experiments, dynamic force spectroscopy (DFS) allows for the extraction of detailed information on the unbinding process of biomolecular complexes. It is becoming progressively more important in biochemical studies and is finding wider applications in areas such as biophysics and polymer science. In six chapters, Dynamic Force Spectroscopy and Biomolecular Recognition covers the most recent ideas and advances in the field of DFS applied to biorecognition: Chapter 1: Reviews the basic and novel aspects of biorecognition and discusses the emerging capabilities of single-molecule techniques to disclose kinetic properties and molecular mechanisms usually hidden in bulk measurements Chapter 2: Describes the basic principle of atomic force microsocopy (AFM) and DFS, with particular attention to instrumental and theoretical aspects more strictly related to the study of biomolecules Chapter 3: Overviews the theoretical background in which experimental data taken in nonequilibrum measurements of biomolecular unbinding forces are extrapolated to equilibrium conditions Chapter 4: Reviews the most common and efficient strategies adopted in DFS experiments to immobilize the interacting biomolecules to the AFM tip and to the substrate Chapter 5: Presents and discusses the most representative aspects related to the analysis of DFS data and the challenges of integrating well-defined criteria to calibrate data in automatic routinary procedures Chapter 6: Overviews the most relevant DFS applications to study biorecognition processes, including the biotin/avidin pair, and selected results on various biological complexes, including antigen/antibody, proteins/DNA, and complexes involved in adhesion processes Chapter 7: Summarizes the main results obtained by DFS applied to study biorecognition processes with forthcoming theoretical and experimental advances Although DFS is a widespread, worldwide technique, no books focused on this subject have been available until now. Dynamic Force Spectroscopy and Biomolecular Recognition provides the state of the art of experimental data analysis and theoretical procedures, making it a useful tool for researchers applying DFS to study biorecognition processes.

A revision of the leading text on experimental physics. The feature of this book that has made it one of the most loved texts on the subject is that it goes far beyond a mere description of key experiments in physics. The author successfully provides the reader with an understanding and appreciation of the 'physics' behind the experiments. The second edition will be an extensive revision introducing many new devices, including the use of computers and software programs, that have come into use since the publication of the first edition. In addition the important areas of condensed matter physics and optical physics will be added, including two entirely new chapters on lasers and optics.
.Modern analysis and acquisition techniques
.Integration with matlab for data analysis and display
.New experiments include fundamentals of lasers