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Stephen Hawking said that he could not have written this A Brief History of Time book without my communication system. The software, called Equalizer, was donated by Walt Waltosz of Words Plus Inc., in Lancaster, California. Stephen Hawking says that his speech synthesizer was donated by Speech Plus, of Sunnyvale, California. The synthesizer and laptop computer was mounted on my wheelchair by David Mason, of Cambridge Adaptive Communication Ltd.

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The Indian Council of Agricultural Research (ICAR) in view of the suggestions of the Fourth Deans Committee has recently modified the course curriculum for both undergraduate and postgraduate students of Agricultural Sciences. The Council has prescribed three courses each of three credits, namely, Diseases of Field Crops, Diseases of Fruit and Flowering Crops, and Diseases of Plantation, Spice and Medicinal Plants; and Diseases of Vegetable Crops for postgraduate students as optional courses.

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In this Plant Nematodes of Agricultural Importance, the book defines Soil and plant nematodes are one of the most numerous groups of organisms occurring in the soil. They are microscopic organisms and, with a few exceptions, are not visible to the naked eye. The majority of the soilborne nematodes are not pests of crops and feed on other organisms, particularly bacteria and fungi. Those that parasitize of crop plants can be very damaging and, because of their microscopic size, associating them with crop damage is therefore mainly dependent on determining the symptoms of their effects on plant growth.

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If you demand maximal freshness, nutrient retention, and great flavor, purchase your products locally or domestically. A great way to make this happen is by joining a community-supported agriculture program, or CSA. CSAs allow consumers to buy local, seasonal food directly from a farm.

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Microbiology Principles and Explorations development of microbiology—from Leeuwenhoek’s astonished observations of ‘‘animalcules,’’ to Pasteur’s first use of rabies vaccine on a human, to Fleming’s discovery of penicillin, to today’s race to develop an AIDS vaccine is one of the most dramatic stories in the history of science. To understand the roles microbes play in our lives, including the interplay between microorganisms and humans, we must examine, learn about, and study their world—the world of microbiology.

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The heart is the most important organs of the human body. It is a muscular organ responsible for pumping blood through the blood vessels by repeated, rhythmic contractions. The term cardiac means related to the heart and comes from the Greek word Kardia, for “heart.” The heart pumps the blood, which carries all the vital materials that help in various body functions.

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Author:

S. A. Snyder

Published in: Georg Thieme Verlag Release Year: 2016 ISBN: 978-3-13-202851-7 Pages: 736 Edition: Applications of Domino Transformations in Organic Synthesis 1 File Size: 5 MB File Type: pdf Language: English

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Description of Applications of Domino Transformations in Organic Synthesis

As the pace and breadth of research intensify, organic synthesis is playing an increasingly central role in the discovery process within all imaginable areas of science: from pharmaceuticals, agrochemicals, and materials science to areas of biology and physics, the most impactful investigations are becoming more and more molecular. As an enabling science, synthetic organic chemistry is uniquely poised to provide access to compounds with exciting and valuable new properties. Organic molecules of extreme complexity can, given expert knowledge, be prepared with exquisite efficiency and selectivity, allowing virtually any phenomenon to be probed at levels never before imagined. With ready access to materials of remarkable structural diversity, critical studies can be conducted that reveal the intimate workings of chemical, biological, or physical processes with stunning detail. The sheer variety of chemical structural space required for these investigations and the design elements necessary to assemble molecular targets of increasing intricacy place extraordinary demands on the individual synthetic methods used. They must be robust and provide reliably high yields on both small and large scales, have broad applicability, and exhibit high selectivity. Increasingly, synthetic approaches to organic molecules must take into account environmental sustainability. Thus, the atom economy and the overall environmental impact of the transformations are taking on increased importance. The need to provide a dependable source of information on evaluated synthetic methods in organic chemistry embracing these characteristics was first acknowledged over 100 years ago when the highly regarded reference source Houben–Weyl Methoden der Organischen Chemie was first introduced. Recognizing the necessity to provide a modernized, comprehensive, and critical assessment of synthetic organic chemistry, in 2000 Thieme launched Science of Synthesis, Houben–Weyl Methods of Molecular Transformations. This effort, assembled by almost 1000 leading experts from both industry and academia, provides a balanced and critical analysis of the entire literature from the early 1800s until the year of publication. The accompanying online version of Science of Synthesis provides text, structure, substructure, and reaction searching capabilities by a powerful, yet easy-to-use, intuitive interface. From 2010 onward, Science of Synthesis is being updated quarterly with high-quality content via Science of Synthesis Knowledge Updates. The goal of the Science of Synthesis Knowledge Updates is to provide a continuous review of the field of synthetic organic chemistry, with an eye toward evaluating and analyzing significant new developments in synthetic methods. A list of stringent criteria for the inclusion of each synthetic transformation ensures that only the best and most reliable synthetic methods are incorporated. These efforts guarantee that the Science of Synthesis will continue to be the most up-to-date electronic database available for the documentation of validated synthetic methods. Also from 2010, Science of Synthesis includes the Science of Synthesis Reference Library, comprising volumes covering special topics of organic chemistry in a modular fashion, with six main classifications: (1) Classical, (2) Advances, (3) Transformations, (4) Applications, (5) Structures, and (6) Techniques. Titles will include Stereoselective Synthesis, Water in Organic Synthesis, and Asymmetric Organocatalysis, among others. With expert evaluated content focusing on subjects of particular current interest, the Science of Synthesis Reference Library complements the Science of Synthesis Knowledge Updates, to make Science of Synthesis the complete information source for the modern synthetic chemist. The overarching goal of the Science of Synthesis Editorial Board is to make the suite of Science of Synthesis resources the first and foremost focal point for critically evaluated information on chemical transformations for those individuals involved in the design and construction of organic molecules. Throughout the years, the chemical community has benefited tremendously from the outstanding contribution of hundreds of highly dedicated expert authors who have devoted their energies and intellectual capital to these projects. We thank all of these individuals for the heroic efforts they have made throughout the entire publication process to make Science of Synthesis a reference work of the highest integrity and quality.

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Author:

Eberhard Passarge

Published in: Georg Thieme Verlag Release Year: 2007 ISBN: 978-1-58890-336-5 Pages: 497 Edition: Third Edition File Size: 64 MB File Type: pdf Language: English

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Description of Color Atlas of Genetics pdf

The aim of Color Atlas of Genetics pdf book is to give an account of the scientific field of genetics-based on visual displays of selected concepts and related facts. Additional information is presented in the introduction, with a chronological list of important discoveries and advances in the history of genetics, in an appendix with supplementary data in tables, in an extensive glossary explaining genetic terms, and in references, including websites for further in-depth studies. Color Atlas of Genetics pdf book is written for two kinds of readers: for students of biology and medicine, as an introductory overview, and for their mentors, as a teaching aid. Other interested individuals will also be able to gain information about current developments and achievements in this rapidly growing field. Gerhardus Kremer (1512–1594), the mathematician and cartographer knew as Mercator first used the term atlas in 1594 for a book containing a collection of 107 maps. The frontispiece shows a figure of the Titan Atlas holding the globe on his shoulders. When the book was published a year after Kremer’s death, many regions were still unmapped. Genetic maps are a leitmotif in genetics and a recurrent theme in Color Atlas of Genetics pdf book. Establishing genetic maps is an activity not unlike mapping new, unknown territories 500 years ago. Color Atlas of Genetics pdf third edition has been extensively rewritten, updated, and expanded. Every sentence and illustration were visited and many changed to improve clarity. The general structure of the previous editions, which have appeared in 11 languages, has been maintained: Part I, Fundamentals; Part II, Genomics; Part III, Genetics and Medicine. Each color plate is accompanied by an explanatory text on the opposite page. Each double-page constitutes a small, self-contained chapter. The limited space necessitates a concentration on the most important threads of information at the expense of related details not included. Therefore, Color Atlas of Genetics pdf book is a supplement to, rather than a substitute for, classic textbooks. New topics in Color Atlas of Genetics pdf third edition, represented by new plates, include overviews of the taxonomy of living organisms (“tree of life”), cell communication, signaling and metabolic pathways, epigenetic modifications, apoptosis (programmed cell death), RNA interference, studies in genomics, origins of cancer, principles of gene therapy, and other topics. A single-author book of Color Atlas of Genetics pdf size cannot provide all the details on which specialized scientific knowledge is based. However, it can present an individual perspective suitable as an introduction. This hopefully will stimulate further interest. I have selected many topics to emphasize the intersection of theoretical fundamentals and the medical applications of genetics. Diseases are included as examples representing genetic principles but without the many details required in practice. Throughout the book, I have emphasized the importance of evolution in understanding genetics. As noted by the great geneticist Theodosius Dobzhansky, “Nothing in biology makes sense except in the light of evolution.” Indeed, genetics and the science of evolution are intimately connected. For the many young readers naturally interested in the future, I have included a historical perspective. Whenever possible and appropriate, I have referred to the first description of a discovery. This is a reminder that the platform of knowledge today rests on previous advances. All color plates were prepared for publication by Jürgen Wirth, Professor of Visual Communication at the Faculty of Design, University of Applied Sciences, Darmstadt, Germany 1986-2005. He created all the illustrations from computer drawings, hand sketches, or photographs assembled for each plate by the author. I am deeply indebted to Professor Jürgen Wirth for the most pleasant cooperation. His most skillful work is a fundament of Color Atlas of Genetics pdf book. I thank my wife, Mary Fetter Passarge, MD, for her careful editing of the manuscript and for her numerous helpful suggestions. At Thieme International, Stuttgart, I was guided and supported by Stephan Konnry. I also wish to thank Stefanie Langner and Elisabeth Kurz of the Production Department for pleasant cooperation.

Content of Color Atlas of Genetics pdf

Introduction 1 Part I. Fundamentals 23 Prologue 24 Molecular Basis of Genetics 30 Prokaryotic Cells and Viruses 94 Eukaryotic Cells 110 Mitochondrial Genetics 130 Formal Genetics 138 Chromosomes 176 Regulation of Gene Function 208 Epigenetic Modifications 228 Part II. Genomics 237 Part III. Genetics and Medicine 269 Cell-to-Cell Interactions 270 Sensory Perception 286 Genes in Embryonic Development 298 Immune System 308 Origins of Cancer 324 Hemoglobin 342 Lysosomes and Peroxisomes 356 Cholesterol Metabolism 364 Homeostasis 372 Maintaining Cell and Tissue Shape 386 Sex Determination and Differentiation 398 Atypical Patterns of Genetic Transmission 406 Karyotype–Phenotype Relationship 412 A Brief Guide to Genetic Diagnosis 418 Morbid Anatomy of the Human Genome 422 Chromosomal Location—Alphabetical List 428 Appendix—Supplementary Data 433 Glossary 447 Index 469

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Author:

Anthony J.F. Griffiths, William M. Gelbart,  Richard C. Lewontin, Jeffrey H. Miller

Published in: W. H. Freeman Release Year: 2002 ISBN: 978-0716-7-4382-8 Pages: 736 Edition: 2nd Edition File Size: 22 MB File Type: rar Language: English

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Description of Modern Genetic Analysis

As teachers of genetics and the authors of An Introduction to Genetic Analysis, we are aware of the quiet revolution in the way that genetics is taught to beginning students. Many instructors are finding that a strictly chronological, or historical, approach no longer fits their method of teaching genetics, nor does it meet their students' needs. More and more, molecular genetics is being introduced earlier in the course and integrated with phenotypic and genotypic analysis.

This Book 'Modern Genetic Analysis' was written for instructors and students who need a textbook that supports the "DNA first" approach. Regardless of whether the presentation is traditional or modern, it is essential that students learn to think like geneticists. Thus, as in An Introduction to Genetic Analysis, the focus is on teaching students to analyze data and draw conclusions.

Content of Modern Genetic Analysis

Preface

Supplements

Acknowledgments

1. Genetics and the Organism

2. The Structure of Genes and Genomes

3. Gene Function

4. The Inheritance of Genes

5. Recombination of Genes

6. Gene Interaction

7. Gene Mutations

8. Chromosome Mutations

9. The Genetics of Bacteria and Phages

10. Recombinant DNA Technology

11. Applications of Recombinant DNA Technology

12. Genomics

13. Transposable Genetic Elements

14. Regulation of Gene Transcription

15. Regulation of Cell Number: Normal and Cancer Cells

16. The Genetic Basis of Development

17. Population and Evolutionary Genetics

18. Quantitative Genetics

Answers to Selected Problems

Glossary

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Author:

DENNIS LENDREM

Published in: TIMBER PRESS Release Year: 1986 ISBN: 978-94-011-6568-6 Pages: 225 Edition: First Edition File Size: 6 MB File Type: pdf Language: English

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Description of Modelling in Behavioural Ecology

This book began as a series of lectures delivered to final year zoologists at the The University of Nottingham and the University of Newcastle upon Tyne. I am indebted to Chris Barnard, and Pete Garson for letting me try out chunks of the book on their final year behavioural ecologists; my thanks to those students who helped make the book better than the lectures. In order to gain insight into the development of mathematical models and counter the feeling that they are plucked from thin air, I have been careful to augment the published models with much unpublished (and some unpublishable!) material. I am especially grateful to John Krebs, Alex Kacelnik, Tom Caraco, Richard Sibly, David McFarland, Ron Ydenberg, Alasdair Houston, and Professor John Maynard Smith for a free and frank discussion of their models (, warts and all' as one of them put it). A great number of people helped get this book off the ground. I would especially like to thank Alex Kacelnik, Tom Caraco, Chris Barnard, Des Thompson, Andy Hart, Richard Sibly, Robin McCleery, David McFarland, Ron Ydenberg, Alasdair Houston, Professor William Hamilton and John Lazarus for reading various chunks of die manuscript. I am especially grateful to John Lazarus for working his way through the entire book, discussing modelling in general and games theory in particular. David Stretch fed me with ideas, and Philip Jones gave me a crash revision course on solving differential equations. My thanks also to Rebecca Torrance for preparing the chapter vignettes. My greatest debt is to my wife Wendy and son Tom without whom I would probably have completed this book long before the contract deadline.

Content of Modelling in Behavioural Ecology

Chapter 1. Introduction 1 Chapter 2. Mathematical Methods 7 Chapter 3. Optimizing a Single Behaviour 1: Optimal Foraging Theory 35 Chapter 4. Optimizing a Single Behaviour 2: Stochastic Models of Foraging Behaviour 58 Chapter 5. Temporal Patterns: Vigilance in Birds 83 Chapter 6. Behaviour Sequences: Feeding and Vigilance 103 Chapter 7. Short-term and Long-term Optimality Models: Territoriality 123 Chapter 8. Games Theory Models: Social Behaviour 162 Chapter 9. Conclusions 196 Appendix 1: Greek Symbols Appendix 2: Indices References

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Author:

Eli Grushka & Nelu Grinberg

Published in: CRC Press Release Year: 2017 ISBN: 978-1-4987-2678-8 Pages: 370 Edition: Volume 53 File Size: 15 MB File Type: pdf Language: English

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Description of Advances In Chromatography

Since the beginning of chiral chromatography in the 1930s, researchers have taken an interest in mechanisms responsible for the resolution of racemic mixtures on optically active adsorbents. It was understood that behind this phenomenon lies “the asymmetric character of the adsorbing surface, which causes it to react differently towards the enantiomorphous components of the racemic compound” [1]. From this, it immediately followed that the stereochemical configuration of enantiomers was the major factor affecting their interaction with the chiral surface. Hence, a study of the dependence of the adsorption affinity on the spatial configuration of solutes seemed to be a key step in the elucidation of the nature of Enantioseparation. This fundamental program of research took impulse after the famous publication by Dalgliesh, who attempted to explain the separation of enantiomers of amino acids on cellulose-based on spatial considerations. At that time, there were no tools to investigate interactions between a solute and an adsorbent on the molecular level, so researchers used indirect integral characteristics, such as retention factor (k′) and enantioselectivity (α), to elucidate mechanisms resulting in different migration velocities of optical antipodes in a chiral media. This approach is called macroscopic because it disregards the molecular structure of the system under investigation and operates with quantities averaged (in a thermodynamic sense) over large ensembles of molecules and over a certain period of time. Tremendous improvements in molecular techniques made in the past three decades, in particular, in molecular modeling as well as in spectrometric methods (NMR, FT-IR, VCD, etc.) and x-ray crystallography allowed researchers to study solute– selector binding at the microscopic level. Both these approaches are important in chromatographic research. The application of the molecular techniques makes it possible to understand how a chiral selector discriminates between optical antipodes. These methods cannot, however, explain in full the phenomenon of retention on the chiral stationary phase (CSP). This is because the CSP is not a uniform array of identical chiral sites, each interacting in the same manner with a solute. A real CSP is a heterogeneous solid, including both enantioselective (chiral) sites and nonselective sites; each group of the sites may be, in its turn, heterogeneous as each individual site may slightly differ from other ones of the same type due to differences in the surrounding, minor conformational changes, location in the porous structure of a stationary phase, and so on. A mechanistic understanding of the interaction of a solute with a real stationary phase is a task of an utmost complexity, not yet resolved.

Content of Advances In Chromatography

Chapter 1 Solute–Stationary Phase Interaction in Chiral Chromatography ........1 Leonid D. Asnin, Alberto Cavazzini, and Nicola Marchetti Chapter 2 The Role of Chromatography in Alzheimer’s Disease Drug Discovery ............................................................................................ 75 Jessica Fiori, Angela De Simone, Marina Naldi, and Vincenza Andrisano Chapter 3 Characterization of the Kinetic Performance of Silica Monolithic Columns for Reversed-Phase Chromatography Separations ....................................................................................... 109 Gert Desmet, Sander Deridder, and Deirdre Cabooter Chapter 4 Recent Advances in the Characterization and Analysis of Therapeutic Oligonucleotides by Analytical Separation Methods Coupling with Mass Spectrometry .................................... 143 Su Pan and Yueer Shi Chapter 5 Uncertainty Evaluation in Chromatography .................................... 179 Veronika R. Meyer Chapter 6 Comprehensive Two-Dimensional Hydrophilic Interaction Chromatography × Reversed-Phase Liquid Chromatography (HILIC × RP–LC): Theory, Practice, and Applications .................. 217 André de Villiers and Kathithileni Martha Kalili Chapter 7 Sample Preparation for Thin Layer Chromatography ...................... 301 Mieczysław Sajewicz, Teresa Kowalska, and Joseph Sherma Chapter 8 Modeling of HPLC Methods Using QbD Principles in HPLC ........ 331 Imre Molnár, Hans-Jürgen Rieger, and Robert Kormány Index ...................................................................................................................... 351

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Author:

Stacey L. McDonald

Published in: Springer International Publishing Release Year: 2016 ISBN: 978-3-319-38878-6 Pages: 162 Edition: First Edition File Size: 7 MB File Type: pdf Language: English

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Description of Catalyzed Electrophilic Amidation

Catalyzed Electrophilic Amidation books a number of individuals deserve my gratitude for personal and scientific support during my time at Duke and prior to this time. I would like to mention a few. First and foremost, I must thank my husband, Michael. You have been very patient through this entire process, and without your love and support, I can’t imagine how I would have survived these past 6 years. I am also grateful to my mom and dad, Carolyn and Michael Turner. Thank you for your encouragement and support in all my academic pursuits and for always pushing me to be my best, both personally and academically. I would also like to extend my gratitude to my research advisor, Qiu Wang. Thank you for taking me in and pushing me to be the best scientist I could be each and every day. Your guidance and encouragement over the past 3 years have been greatly appreciated. It has been a distinct privilege working with you, and I am extremely grateful for this experience. Lastly, I need to thank my fellow graduate students who have worked with me in the Wang laboratory. To Chuck Hendrick, Jerry Ortiz, and Lily Du: You guys have been there since the beginning, and it has been wonderful to work with you. I couldn’t imagine better people to have by my side going through this experience. Thank you so much for being there through the research lows and highs and for putting up with me. Thanks also to the rest of the Wang laboratory, and you have all helped me in various ways and made my time spent in the laboratory even more worthwhile. Again, thank you to all of those who have supported me through my time in graduate school.

Content of Catalyzed Electrophilic Amidation

1 Electrophilic Amination for the Synthesis of Alkyl and Aryl Amines .................................................. 1 1.1 Synthesis of Amines via C–N Bond Formation ............... 1 1.1.1 Electrophilic Amination Reagents and Reactions ........ 3 1.1.2 Direct Electrophilic Amination of C–H Bonds .......... 11 1.1.3 Conclusions..................................... 16 References................................................ 18 2 Selective a-Amination and a-Acylation of Esters and Amides via Dual Reactivity of O-Acylhydroxylamines Toward Zinc Enolates ................................................. 25 2.1 a-Functionalization of Esters and Amides ................... 25 2.1.1 a-Amination of Carbonyl Compounds ................ 25 2.1.2 a-Acylation of Carbonyl Compounds ................. 31 2.1.3 Zinc Enolates for a-Functionalization of Carbonyl Compounds........................... 32 2.2 Results and Discussion .................................. 32 2.2.1 Electrophilic Amination and Acylation of Esters and Amides via Zinc Enolates....................... 32 2.2.2 Initial Amination Studies Using the Reformatsky Reagent........................................ 33 2.2.3 Amination Studies Using Zn(tmp)2 for Zinc Enolate Formation................................ 35 2.2.4 a-Acylation of Ester and Amide Zinc Enolates.......... 38 2.2.5 Proposed Mechanism for the a-Amination and a-Acylation Reactions ......................... 41 2.3 Conclusion ........................................... 43 2.3.1 Supplemental Information .......................... 43 2.3.2 Characterization of Compounds ..................... 46 References................................................ 56

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Author:

Errol G. Lewars

Published in: Springer International Publishing Release Year: 2012 ISBN: 978-3-319-30916-3 Pages: 739 Edition: Third Edition File Size: 14 MB File Type: pdf Language: English

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Description of Computational Chemistry

Every attempt to employ mathematical methods in the study of chemical questions must be considered profoundly irrational and contrary to the spirit of chemistry. If mathematical analysis should ever hold a prominent place in chemistry-an aberration which is happily almost impossible-it would occasion a rapid and widespread degeneration of that science. Augustus Compte, French philosopher, 1798–1857; in Philosophie Positive, 1830. A dissenting view: The more progress the physical sciences make, the more they tend to enter the domain of mathematics, which is a kind of center to which they all converge. We may even judge the degree of perfection to which a science has arrived by the facility to which it may be submitted to calculation. Adolphe Quetelet, French astronomer, mathematician, statistician, and sociologist, 1796–1874, writing in 1828. Computational Chemistry third edition differs from the second in these ways: 1. The typographical errors that were found in the first edition have been (I hope) corrected. 2. Sentences and paragraphs have on occasion been altered to clarify an explanation. 3. The biographical footnotes have been updated as necessary. 4. Significant developments since 2010 (the year of the latest references in the second edition), up to the end of 2015, have been added and referenced in the relevant places. As might be inferred from the word Introduction, the purpose of Computational Chemistry book, like that of previous editions, is to teach the basics of the core concepts and methods of computational chemistry. Computational Chemistry is a textbook, and no attempt has been made to please every reviewer by dealing with esoteric “advanced” topics. Some fundamental concepts are the idea of a potential energy surface, the mechanical picture of a molecule as used in molecular mechanics, and the Schr€odinger equation and it's elegant taming with matrix methods to give energy levels and molecular orbitals. All the needed matrix algebra is explained before it is used.  The fundamental techniques of computational chemistry are molecular mechanics, ab initio, semiempirical, and density functional methods. Molecular dynamics and Monte Carlo methods are only mentioned; while these are important, they utilize several fundamental concepts and methods explained here, and if presented at the level of the topics treated here would require a book of their own. I wrote the first edition (2003) because there seemed to be no text quite right for an introductory course in computational chemistry for a fairly general chemical audience, and the second (2011) the edition was issued in the same belief; although there are several good books on quantum chemistry and on its disciplinary associate (“handmaiden” might seem somewhat disparaging) computational chemistry, Computational Chemistryedition is submitted in the same spirit as the first two.  I hope it will be useful to anyone who wants to learn enough about the subject to start reading the literature and to start doing computational chemistry. As implied above, there are excellent books on the field, but evidently, none that seeks to familiarize the general student of chemistry with computational chemistry in quite the same sense that standard textbooks of those subjects make organic or physical chemistry accessible. To that end the mathematics has been held on a leash; no attempt is made to prove that molecular orbitals are vectors in Hilbert space, or that a finite-dimensional inner-product space must have an orthonormal basis, and the only sections that the nonspecialist may justifiably view with some trepidation are the (outlined) derivation of the Hartree-Fock and Kohn-Sham equations. These sections should be read, if only to get the flavor of the procedures, but should not stop anyone from getting on with the rest of the book. Computational chemistry has become a tool used in much the same spirit as infrared or NMR spectroscopy, and to use it sensibly it is no more necessary to be able to write your own programs than the fruitful use of infrared or NMR spectroscopy requires you to be able to build your own spectrometer. I have tried to give enough theory to provide a reasonably good idea of how standard procedures in the programs work. In this regard, the concept of constructing and diagonalizing a Fock matrix is introduced early, and there is little talk of computationally less relevant secular determinants (except for historical reasons in connection with the simple Hückel method). Many results of actual computations, some done specifically for Computational Chemistry book, are given. Almost all the assertions in these pages are accompanied by literature references, which should make the text useful to researchers who need to track down methods or results, and to anyone who may wish to delve deeper.  It would be clearly inappropriate, if not impossible, to exhaustively reference each topic discussed. The choice of references has been oriented toward (besides justifying a particular assertion) reviews, and publications illustrating a topic in a general way, rather than some specialized aspect of it. In this age of the Internet, once one is aware of the existence of some subject, it is usually not hard to obtain more information about it. The material should be suitable for senior undergraduates, graduate students, and novice researchers in computational chemistry. Knowledge of the shapes of molecules, covalent and ionic bonds, spectroscopy, and some familiarity with thermodynamics at about the second- or third-year undergraduate level is assumed. Some readers may wish to review basic concepts from physical and organic chemistry. The reader, then, should be able to acquire the basic theory of, and a fair idea of the kinds of results to be obtained from, common computational chemistry techniques. You will learn how one can calculate the geometry of (some may quibble and say “a geometry for”) a molecule, its IR and UV spectra and its thermodynamic and kinetic stability, and other information needed to make a plausible guess at its chemistry. Computational chemistry is more accessible than ever. Hardware has become cheaper than it was even a few years ago, and powerful programs once available only for expensive workstations have been adapted to run on inexpensive personal computers. The actual use of a program is best explained by its manuals and by books written for a specific program, and the directions for setting up the various computations are not given here. Information on various programs is provided in Chap. 9. Read the book, get some programs, and go out and do computational chemistry. You may make mistakes, but they are unlikely to put you in the same kind of danger that a mistake in a wet lab might.

Content of Computational Chemistry

1 An Outline of What Computational Chemistry Is All About ...... 1 1.1 What You Can Do with Computational Chemistry . . . ......... 1 1.2 The Tools of Computational Chemistry . . . . . . . . . . . . . . . . . . . . 2 1.3 Putting it All Together . ............................... 4 1.4 The Philosophy of Computational Chemistry . . .............. 5 1.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Easier Questions ......................................... 6 Harder Questions . . . . .................................... 6 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 2 The Concept of the Potential Energy Surface .................. 9 2.1 Perspective ........................................ 9 2.2 Stationary Points . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 2.3 The Born-Oppenheimer Approximation . . . . . . . . . . . . . . . . . . . . 22 2.4 Geometry Optimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 2.5 Stationary Points and Normal-Mode Vibrations. Zero Point Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 2.6 Symmetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 2.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 Easier Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 Harder Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 3 Molecular Mechanics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 3.1 Perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 3.2 The Basic Principles of Molecular Mechanics . . . . . . . . . . . . . . . 54 3.2.1 Developing a Forcefield . . . . . . . . . . . . . . . . . . . . . . . . . . 54 3.2.2 Parameterizing a Forcefield . . . . . . . . . . . . . . . . . . . . . . . 59 3.2.3 A Calculation Using our Forcefield . . . . . . . . . . . . . . . . . 64 3.3 Examples of the Use of Molecular Mechanics . . . . . . . . . . . . . . . 68 3.3.1 To Obtain Reasonable Input Geometries for Lengthier (ab Initio, Semiempirical or Density Functional) Kinds of Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 3.3.2 To Obtain (Often Excellent) Geometries . . . . . . . . . . . . . . 72 3.3.3 To Obtain (Sometimes Excellent) Relative Energies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78 3.3.4 To Generate the Potential Energy Function Under Which Molecules Move, for Molecular Dynamics or Monte Carlo Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 3.3.5 As a (Usually Quick) Guide to the Feasibility of, or Likely Outcome of, Reactions in Organic Synthesis . . . 86 3.4 Frequencies and Vibrational Spectra Calculated by MM . . . . . . . . 88 3.5 Strengths and Weaknesses of Molecular Mechanics . . . . . . . . . . . 91 3.5.1 Strengths . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 3.5.2 Weaknesses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 3.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95 Easier Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95 Harder Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 4 Introduction to Quantum Mechanics in Computational Chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 4.1 Perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 4.2 The Development of Quantum Mechanics. The Schr€odinger Equation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103 4.2.1 The Origins of Quantum Theory: Blackbody Radiation and the Photoelectric Effect . . . . . . . . . . . . . . . . . . . . . . . 103 4.2.2 Radioactivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 4.2.3 Relativity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108 4.2.4 The Nuclear Atom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108 4.2.5 The Bohr Atom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 4.2.6 The Wave Mechanical Atom and the Schr€odinger Equation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113 4.3 The Application of the Schr€odinger Equation to Chemistry by Hückel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119 4.3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119 4.3.2 Hybridization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120 4.3.3 Matrices and Determinants . . . . . . . . . . . . . . . . . . . . . . . . 125 4.3.4 The Simple Hückel Method–Theory . . . . . . . . . . . . . . . . . 135 4.3.5 The Simple Hückel Method–Applications . . . . . . . . . . . . . 150 4.3.6 Strengths and Weaknesses of the Simple Hückel Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 4.3.7 The Determinant Method of Calculating the Hückel c’s and Energy Levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 4.4 The Extended Hückel Method . . . . . . . . . . . . . . . . . . . . . . . . . . . 171 4.4.1 Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171 4.4.2 An Illustration of the EHM: The Protonated Helium Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179 4.4.3 The Extended Hückel Method–Applications . . . . . . . . . . . 182 4.4.4 Strengths and Weaknesses of the Extended Hückel Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182 4.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184 Easier Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186 Harder Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187 5 Ab initio Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193 5.1 Perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193 5.2 The Basic Principles of the Ab initio Method . . . . . . . . . . . . . . . . 194 5.2.1 Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194 5.2.2 The Hartree SCF Method . . . . . . . . . . . . . . . . . . . . . . . . . 195 5.2.3 The Hartree-Fock Equations . . . . . . . . . . . . . . . . . . . . . . . 199 5.3 Basis Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253 5.3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253 5.3.2 Gaussian Functions; Basis Set Preliminaries; Direct SCF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253 5.3.3 Types of Basis Sets and Their Uses . . . . . . . . . . . . . . . . . 258 5.4 Post-Hartree-Fock Calculations: Electron Correlation . . . . . . . . . . 276 5.4.1 Electron Correlation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276 5.4.2 The Møller-Plesset Approach to Electron Correlation . . . . 282 5.4.3 The Configuration Interaction Approach to Electron Correlation. The Coupled Cluster Method . . . . . . . . . . . . . 291 5.5 Applications of The Ab initio Method . . . . . . . . . . . . . . . . . . . . . 303 5.5.1 Geometries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303 5.5.2 Energies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 314 5.5.3 Frequencies and Vibrational (IR) Spectra . . . . . . . . . . . . . 356 5.5.4 Properties Arising from Electron Distribution: Dipole Moments, Charges, Bond Orders, Electrostatic Potentials, Atoms-in-Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . 363 5.5.5 Miscellaneous Properties–UV and NMR Spectra, Ionization Energies, and Electron Affinities . . . . . . . . . . . 386 5.5.6 Visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 393 5.6 Strengths and Weaknesses of Ab initio Calculations . . . . . . . . . . . 400 5.6.1 Strengths . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 400 5.6.2 Weaknesses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 400 5.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401 Easier Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 402 Harder Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403 6 Semiempirical Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421 6.1 Perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421 6.2 The Basic Principles of SCF Semiempirical Methods . . . . . . . . . . 423 6.2.1 Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 423 6.2.2 The Pariser-Parr-Pople (PPP) method . . . . . . . . . . . . . . . . 426 6.2.3 The Complete Neglect of Differential Overlap (CNDO) Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 428 6.2.4 The Intermediate Neglect of Differential Overlap (INDO) Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429 6.2.5 The Neglect of Diatomic Differential Overlap (NDDO) Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 430 6.3 Applications of Semiempirical Methods . . . . . . . . . . . . . . . . . . . 445 6.3.1 Geometries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 445 6.3.2 Energies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 452 6.3.3 Frequencies and Vibrational Spectra . . . . . . . . . . . . . . . . . 460 6.3.4 Properties Arising from Electron Distribution: Dipole Moments, Charges, Bond Orders . . . . . . . . . . . . . . . . . . . 464 6.3.5 Miscellaneous Properties–UV Spectra, Ionization Energies, and Electron Affinities . . . . . . . . . . . . . . . . . . . 468 6.3.6 Visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471 6.3.7 Some General Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . 472 6.4 Strengths and Weaknesses of Semiempirical Methods . . . . . . . . . 473 6.4.1 Strengths . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473 6.4.2 Weaknesses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473 6.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 474 Easier Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 475 Harder Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 476 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 477 7 Density Functional Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 483 7.1 Perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 483 7.2 The Basic Principles of Density Functional Theory . . . . . . . . . . . 485 7.2.1 Preliminaries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 485 7.2.2 Forerunners to Current DFT Methods . . . . . . . . . . . . . . . . 487 7.2.3 Current DFT Methods: The Kohn-Sham Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 487 7.3 Applications of Density Functional Theory . . . . . . . . . . . . . . . . . 508 7.3.1 Geometries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 509 7.3.2 Energies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 519 7.3.3 Frequencies and Vibrational Spectra . . . . . . . . . . . . . . . . . 527 7.3.4 Properties Arising from Electron Distribution–Dipole Moments, Charges, Bond Orders, Atoms-in-Molecules . . . 530 7.3.5 Miscellaneous Properties–UV and NMR Spectra, Ionization Energies and Electron Affinities, Electronegativity, Hardness, Softness and the Fukui Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 534 7.3.6 Visualization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 552 7.4 Strengths and Weaknesses of DFT . . . . . . . . . . . . . . . . . . . . . . . 553 7.4.1 Strengths . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 553 7.4.2 Weaknesses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 553 7.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554 Easier Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 556 Harder Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 556 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 557 8 Some “Special” Topics: (Section 8.1) Solvation, (Section 8.2) Singlet Diradicals, (Section 8.3) A Note on Heavy Atoms and Transition Metals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 565 8.1 Solvation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 565 8.1.1 Perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 566 8.1.2 Ways of Treating Solvation . . . . . . . . . . . . . . . . . . . . . . . 566 8.2 Singlet Diradicals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 583 8.2.1 Perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 584 8.2.2 Problems with Singlet Diradicals and Model Chemistries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 585 8.2.3 Singlet Diradicals, Beyond Model Chemistries . . . . . . . . . 587 8.3 A Note on Heavy Atoms and Transition Metals . . . . . . . . . . . . . . 598 8.3.1 Perspective . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 599 8.3.2 Heavy Atoms and Relativistic Corrections . . . . . . . . . . . . 599 8.3.3 Some Heavy Atom Calculations . . . . . . . . . . . . . . . . . . . . 600 8.3.4 Transition Metals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601 8.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 604 Solvation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 605 Easier Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 605 Harder Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 605 Singlet Diradicals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 606 Easier Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 606 Harder Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 606 Heavy Atoms and Transition Metals . . . . . . . . . . . . . . . . . . . . . . . . . . 606 Easier Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 606 Harder Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 607 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 607 9 Selected Literature Highlights, Books, Websites, Software and Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 613 9.1 From the Literature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 613 9.1.1 Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 613 9.1.2 Mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 622 9.1.3 Concepts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 626 9.2 To the Literature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 630 9.2.1 Books . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 630 9.2.2 Websites for Computational Chemistry in General . . . . . . 633 9.3 Software and Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 635 9.3.1 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 635 9.3.2 Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 639 9.3.3 Postscript . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 640 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 641 Answers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 645 Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 715

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  GET THIS BOOK

Author:

Marco Bandini

Published in: Springer International Publishing Release Year: 2016 ISBN: 978-3-319-35144-5 Pages: 294 Edition: 46 Topics in Heterocyclic Chemistry File Size: 24 MB File Type: pdf Language: English

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Description of Au-Catalyzed Synthesis and Functionalization of Heterocycles

“Noble,” “coinage,” “precious”...so many “labels” have been utilized over the years to describe gold. All of them are certainly correct with the exception of the one that probably affected mostly the role of the late-transition metal in chemical reactivity: “inert”. As a matter of fact, besides the intrinsic inertness of gold in the elemental form, [Au(I)] and [Au(III)] species have displayed unique physical-chemical properties that led to unexpected applications in homogeneous catalysis with particular regard to electrophilic activations of unactivated unsaturated hydrocarbons. Doubtless, the chemistry of π-systems has faced a revolution in terms of chemical scope, the mildness of reaction conditions, and selectivity over the past fifteen years, due to the establishment of this metal in catalysis. A rough search on the database dealing with the item “gold catalysis” can better highlight the state-of-the-art impact of organometallic gold species in organic synthesis. Impressively, gold (141 articles in 2014) has already reached longtime used metals such as palladium (125 articles in 2014) and copper (60 articles in 2014) and already overcame other “neighbors” in the periodic table such as silver (30 articles in 2014) and rhodium (38 articles in 2014). The innate tolerance of gold catalysis toward “hard” hetero moieties contributed to its diffusion on the synthesis of densely functionalized molecular scaffolds including heterocyclic cores. Au-Catalyzed Synthesis and Functionalization of Heterocycles volume provides an overview of the most efficient and synthetically useful approaches to the construction of heterocyclic motifs by means of homogeneous gold catalysis. The chapters have been written by leading experts; emphasis has been addressed to both scope and limitation of the methodologies. Additionally, mechanistic insights are provided in order to ensure a proper ratio of the chemical outcomes. Main activation modes and reaction machinery (i.e., electrophilic additions), triggered by gold coordination to π-systems, have been highlighted with particular regard to alkynes, alkenes, and allenes. Besides these intriguing C–X bond-forming events, gold catalysis found substantial applications also in the manipulation of C–C triple bonds via rearrangement reactions as well as site-selective oxidative protocols. Recent and leading examples in these realms have been also accounted for and described in dedicated chapters. Additionally, the well-established attitude of gold-based catalytic systems in assisting the activation/functionalization of inert C–H bonds have been documented with the aim of shedding light on the applicability of readily available and unfunctionalized heteroarenes for the synthesis of added-value compounds. The latter two chapters have been dedicated to the impact of gold on asymmetric transformations and the total synthesis of natural products. I personally consider these frameworks two hot topics of the nowadays-homogeneous gold catalysis. Obviously, I feel indebted to the colleagues who agreed to contribute in the realization of this account, and I apologize to the authors left out this time. I do really hope that the book could contribute to stimulating new perspectives and developments in the blooming research area and could encourage even more practitioners in engaging in this fascinating research topic.

Content of Au-Catalyzed Synthesis and Functionalization of Heterocycles

Synthesis of Oxygenated Heterocyclic Compounds via Gold-Catalyzed Functionalization of π-Systems ............................... 1 Jose L. Mascare~nas and Fernando Lo ́pez Gold-Catalyzed Synthesis of Nitrogen Heterocyclic Compounds via Hydroamination Reactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 Antonio Arcadi Synthesis of Oxygenated and Nitrogen-Containing Heterocycles by Gold-Catalyzed Alkyne Oxidation . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 Longwu Ye and Liming Zhang Synthesis of Heterocyclic Compounds via Gold-Catalysed Enyne Rearrangements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 Marı ́a Teresa Quiro ́s and Marı ́a Paz Mu~noz C–H Functionalisation of Heteroaromatic Compounds via Gold Catalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175 Nanna Ahlsten, Xacobe C. Cambeiro, Gregory J.P. Perry, and Igor Larrosa Enantioselective Gold-Catalyzed Synthesis of Heterocyclic Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227 Dillon H. Miles and F. Dean Toste Gold Catalysis in the Synthesis of Natural Products: Heterocycle Construction via Direct C–X-Bond-Forming Reactions . . . . . . . . . . . . . 249 Yu-Hui Wang, Zhong-Yan Cao, and Jian Zhou Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285

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Description of Applied Photochemistry

The conversion of light energy into chemical fuels by artificial means is a challenging goal of modern science, of great potential impact on long-term energy and environmental problems. As such, Artificial Photosynthesis is one of the most active research areas in applied photochemistry. In this tutorial review, the basic ingredients of a biomimetic, supramolecular approach to Artificial Photosynthesis are outlined. First, a brief summary of the relevant structural-functional aspects of natural photosynthesis is provided, as a guide to plausible artificial architectures. Then, candidate energy converting reactions are examined, focusing attention on water splitting. The main functional units of an artificial photosynthetic system are dealt with in some detail, namely, charge separation systems, light-harvesting antenna systems, water oxidation catalysts, and hydrogen evolving catalysts. For each type of system, design principles and mechanistic aspects are highlighted with specifically selected examples. Some attempts at integrating the various units into light-to-fuels converting devices are finally discussed. Throughout the review, the emphasis is on systems of molecular and supramolecular nature.

Content of Applied Photochemistry

1 Supramolecular Artificial Photosynthesis .................... 1 Mirco Natali and Franco Scandola 2 Solar Energy Conversion in Photoelectrochemical Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 Stefano Caramori, Federico Ronconi, Roberto Argazzi, Stefano Carli, Rita Boaretto, Eva Busatto, and Carlo Alberto Bignozzi 3 Organic Light-Emitting Diodes (OLEDs): Working Principles and Device Technology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145 Umberto Giovanella, Mariacecilia Pasini, and Chiara Botta 4 Light-Emitting Electrochemical Cells . . . . . . . . . . . . . . . . . . . . . . . 197 Chia-Yu Cheng and Hai-Ching Su 5 Industrial Photochromism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227 Andrew D. Towns 6 Application of Visible and Solar Light in Organic Synthesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281 Davide Ravelli, Stefano Protti, and Maurizio Fagnoni 7 Photochemical Reactions in Sunlit Surface Waters . . . . . . . . . . . . . 343 Davide Vione 8 Photodynamic Therapy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 377 Barbara Krammer and Thomas Verwanger 9 Polymer Nanoparticles for Cancer Photodynamic Therapy Combined with Nitric Oxide Photorelease and Chemotherapy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397 Fabiana Quaglia and Salvatore Sortino 10 Chemiluminescence in Biomedicine . . . . . . . . . . . . . . . . . . . . . . . . 427 Mara Mirasoli, Massimo Guardigli, and Aldo Roda 11 Solar Filters: A Strategy of Photoprotection . . . . . . . . . . . . . . . . . . 459 Susana Encinas Perea 12 Luminescent Chemosensors: From Molecules to Nanostructures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 479 Nelsi Zaccheroni, Francesco Palomba, and Enrico Rampazzo 13 Photochemistry for Cultural Heritage . . . . . . . . . . . . . . . . . . . . . . 499 Maria Jo~ao Melo, Joana Lia Ferreira, Anto ́nio Jorge Parola, and Jo~ao Se ́rgio Seixas de Melo Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 531

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J. D. Murray

Published in: Springer Release Year: 2003 ISBN: 0-387-95228-4 Pages: 839 Edition: Third Edition File Size: 12 MB File Type: pdf Language: English

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Description of Mathematical Biology II Spatial Models and Biomedical Applications,

In the thirteen years since the first edition of this book appeared the growth of mathematical biology and the diversity of applications has been astonishing. Its establishment as a distinct discipline is no longer in question. One pragmatic indication is the increasing number of advertised positions in academia, medicine and industry around the world; another is the burgeoning membership of societies. People working in the field now number in the thousands. Mathematical modelling is being applied in every ma- jor discipline in the biomedical sciences. A very different application, and surprisingly successful, is in psychology such as modelling various human interactions, escalation to date rape and predicting divorce. The field has become so large that, inevitably, specialised areas have developed which are, in effect, separate disciplines such as biofluid mechanics, theoretical ecology and so on. It is relevant therefore to ask why I felt there was a case for a new edition of a book called simply Mathematical Biology. It is unrealistic to think that a single book could cover even a significant part of each subdiscipline and this new edition certainly does not even try to do this. I feel, however, that there is still justification for a book which can demonstrate to the uninitiated some of the exciting problems that arise in biology and give some indication of the wide spectrum of topics that modelling can address. In many areas the basics are more or less unchanged but the developments during the past thirteen years have made it impossible to give as comprehensive a picture of the current approaches in and the state of the field as was possible in the late 1980s. Even then important areas were not included such as stochastic modelling, biofluid mechanics and others. Accordingly, in this new edition, only some of the basic modelling concepts are discussed—such as in ecology and to a lesser extent epidemiology—but references are provided for further reading. In other areas, recent advances are discussed together with some new applications of modelling such as in marital interaction (Volume I), growth of cancer tumours (Volume II), temperature-dependent sex determination (Volume I) and wolf territoriality (Volume II). There have been many new and fascinating developments that I would have liked to include but practical space limitations made it impossible and necessitated difficult choices. I have tried to give some idea of the diversity of new developments but the choice is inevitably prejudiced. As to the general approach, if anything it is even more practical in that more emphasis is given to the close connection many of the models have with experiment, clinical data and in estimating real parameter values. In several of the chapters, it is not yet possible to relate the mathematical models to specific experiments or even biological entities. Nevertheless, such an approach has spawned numerous experiments based as much on the modelling approach as on the actual mechanism studied. Some of the more mathematical parts in which the biological connection was less immediate have been excised while others that have been kept have a mathematical and technical pedagogical aim but all within the context of their application to biomedical problems. I feel even more strongly about the philosophy of mathematical modelling espoused in the original preface as regards what constitutes good mathematical biology. One of the most exciting aspects regarding the new chapters has been their genuine interdisciplinary collaborative character. Mathematical or theoretical biology is unquestionably an interdisciplinary science par excellence. The unifying aim of theoretical modelling and experimental investigation in the biomedical sciences is the elucidation of the underlying biological processes that result in a particular observed phenomenon, whether it is pattern formation in development, the dynamics of interacting populations in epidemiology, neuronal connectivity and information processing, the growth of tumours, marital interaction and so on. I must stress, however, that mathematical descriptions of biological phenomena are not biological explanations. The principal use of any theory is in its predictions and, even though different models might be able to create similar spatiotemporal behaviours, they are mainly distinguished by the different experiments they suggest and, of course, how closely they relate to the real biology. There are numerous examples in the book. Why use mathematics to study something as intrinsically complicated and ill-understood as development, angiogenesis, wound healing, interacting population dynamics, regulatory networks, marital interaction and so on? We suggest that mathematics, rather theoretical modelling, must be used if we ever hope to genuinely and realistically convert an understanding of the underlying mechanisms into a predictive science. Mathematics is required to bridge the gap between the level on which most of our knowledge is accumulating (in developmental biology it is cellular and below) and the macroscopic level of the patterns we see. In wound healing and scar formation, for example, a mathematical approach lets us explore the logic of the repair process. Even if the mechanisms were well understood (and they certainly are far from it at this stage) mathematics would be required to explore the consequences of manipulating the various parameters associated with any particular scenario. In the case of such things as wound healing and cancer growth—and now in angiogenesis with its relation to possible cancer therapy, the number of options that are fast becoming available to wound and cancer managers will become overwhelming unless we can find a way to simulate particular treatment protocols before applying them in practice. The latter has been already of use in understanding the efficacy of various treatment scenarios with brain tumours (glioblastomas) and new two-step regimes for skin cancer. The aim in all these applications is not to derive a mathematical model that takes into account every single process because, even if this were possible, the resulting model would yield little or no insight on the crucial interactions within the system. Rather the goal is to develop models which capture the essence of various interactions allowing their outcome to be more fully understood. As more data emerge from the biological system, the models become more sophisticated and the mathematics increasingly challenging. In development (by way of example) it is true that we are a long way from being able to reliably simulate actual biological development, in spite of the plethora of models and theory that abound. Key processes are generally still poorly understood.  Despite these limitations, I feel that exploring the logic of pattern formation is worth-while, or rather essential, even in our present state of knowledge. It allows us to take a hypothetical mechanism and examine its consequences in the form of a mathematical model, make predictions and suggest experiments that would verify or invalidate the model; even the latter casts light on the biology. The very process of constructing a mathematical model can be useful in its own right. Not only must we commit to a particular mechanism, but we are also forced to consider what is truly essential to the process, the central players (variables) and mechanisms by which they evolve. We are thus involved in constructing frameworks on which we can hang our understanding. The model equations, the mathematical analysis and the numerical simulations that follow serve to reveal quantitatively as well as qualitatively the consequences of that logical structure. This new edition is published in two volumes. Volume I is an introduction to the field; the mathematics mainly involves ordinary differential equations but with some basic partial differential equation models and is suitable for undergraduate and graduate courses at different levels. Volume II requires more knowledge of partial differential equations and is more suitable for graduate courses and reference. I would like to acknowledge the encouragement and generosity of the many people who have written to me (including a prison inmate in New England) since the appearance of the first edition of this book, many of whom took the trouble to send me details of errors, misprints, suggestions for extending some of the models, suggesting collaborations and so on. Their input has resulted in many successful interdisciplinary research projects several of which are discussed in this new edition. I would like to thank my colleagues Mark Kot and Hong Qian, many of my former students, in particular, Patricia Burgess, Julian Cook, Trace Jackson, Mark Lewis, Philip Maini, Patrick Nelson, Jonathan Sherratt, Kristin Swanson and Rebecca Tyson for their advice or careful reading of parts of the manuscript. I would also like to thank my former secretary Erik Hinkle for the care, thoughtfulness and dedication with which he put much of the manuscript into LATEX and his general help in tracking down numerous obscure references and material. I am very grateful to Professor John Gottman of the Psychology Department at the University of Washington, a world leader in the clinical study of marital and family interactions, with whom I have had the good fortune to collaborate for nearly ten years. Without his infectious enthusiasm, strong belief in the use of mathematical modelling, perseverance in the face of my initial scepticism and his practical insight into human interactions I would never have become involved in developing with him a general theory of marital interaction. I would also like to acknowledge my debt to Professor Ellworth C. Alvord, Jr., Head of Neuropathology in the University of Washington with whom I have collaborated for the past seven years on the modelling of the growth and control of brain tumours. As to my general, and I hope practical, approach to modelling I am most indebted to Professor George F. Carrier who had the major influence on me when I went to Harvard on first coming to the U.S.A. in 1956. His astonishing insight and ability to extract the key elements from a complex problem and incorporate them into a realistic and informative model is a talent I have tried to acquire throughout my career. Finally, although it is not possible to thank by name all of my past students, postdoctoral, numerous collaborators and colleagues around the world who have encouraged me in this field, I am certainly very much in their debt. Looking back on my involvement with mathematics and the biomedical sciences over the past nearly thirty years my major regret is that I did not start working in the field years earlier.

Content of Mathematical Biology II Spatial Models and Biomedical Applications,

1. Multi-Species Waves and Practical Applications 1 1.1 Intuitive Expectations . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Waves of Pursuit and Evasion in Predator–Prey Systems . . . . . . . 5 1.3 Competition Model for the Spatial Spread of the Grey Squirrel in Britain . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 1.4 Spread of Genetically Engineered Organisms . . . . . . . . . . . . . 18 1.5 Travelling Fronts in the Belousov–Zhabotinskii Reaction . . . . . . . 35 1.6 Waves in Excitable Media . . . . . . . . . . . . . . . . . . . . . . . 41 1.7 Travelling Wave Trains in Reaction Diffusion Systems with Oscillatory Kinetics . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 1.8 Spiral Waves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 1.9 Spiral Wave Solutions of λ–ω Reaction Diffusion Systems . . . . . . 61 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 2. Spatial Pattern Formation with Reaction Diffusion Systems 71 2.1 Role of Pattern in Biology . . . . . . . . . . . . . . . . . . . . . . . 71 2.2 Reaction Diffusion (Turing) Mechanisms . . . . . . . . . . . . . . . 75 2.3 General Conditions for Diffusion-Driven Instability: Linear Stability Analysis and Evolution of Spatial Pattern . . . . . . . 82 2.4 Detailed Analysis of Pattern Initiation in a Reaction Diffusion Mechanism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 2.5 Dispersion Relation, Turing Space, Scale and Geometry Effects in Pattern Formation Models . . . . . . . . . . . . . . . . . . . . . . 103 2.6 Mode Selection and the Dispersion Relation . . . . . . . . . . . . . . 113 2.7 Pattern Generation with Single-Species Models: Spatial Heterogeneity with the Spruce Budworm Model . . . . . . . . . . . . 120 2.8 Spatial Patterns in Scalar Population Interaction Diffusion Equations with Convection: Ecological Control Strategies . . . . . . . 125 2.9 Nonexistence of Spatial Patterns in Reaction Diffusion Systems: General and Particular Results . . . . . . . . . . . . . . . . . . . . . 130 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 3. Animal Coat Patterns and Other Practical Applications of Reaction Diffusion Mechanisms 141 3.1 Mammalian Coat Patterns—‘How the Leopard Got Its Spots’ . . . . . 142 3.2 Teratologies: Examples of Animal Coat Pattern Abnormalities . . . . 156 3.3 A Pattern Formation Mechanism for Butterfly Wing Patterns . . . . . 161 3.4 Modelling Hair Patterns in a Whorl in Acetabularia . . . . . . . . . . 180 4. Pattern Formation on Growing Domains: Alligators and Snakes 192 4.1 Stripe Pattern Formation in the Alligator: Experiments . . . . . . . . 193 4.2 Modelling Concepts: Determining the Time of Stripe Formation . . . 196 4.3 Stripes and Shadow Stripes on the Alligator . . . . . . . . . . . . . . 200 4.4 Spatial Patterning of Teeth Primordia in the Alligator: Background and Relevance . . . . . . . . . . . . . . . . . . . . . . . 205 4.5 Biology of Tooth Initiation . . . . . . . . . . . . . . . . . . . . . . . 207 4.6 Modelling Tooth Primordium Initiation: Background . . . . . . . . . 213 4.7 Model Mechanism for Alligator Teeth Patterning . . . . . . . . . . . 215 4.8 Results and Comparison with Experimental Data . . . . . . . . . . . 224 4.9 Prediction Experiments . . . . . . . . . . . . . . . . . . . . . . . . . 228 4.10 Concluding Remarks on Alligator Tooth Spatial Patterning . . . . . . 232 4.11 Pigmentation Pattern Formation on Snakes . . . . . . . . . . . . . . . 234 4.12 Cell-Chemotaxis Model Mechanism . . . . . . . . . . . . . . . . . . 238 4.13 Simple and Complex Snake Pattern Elements . . . . . . . . . . . . . 241 4.14 Propagating Pattern Generation with the Cell-Chemotaxis System . . 248 5. Bacterial Patterns and Chemotaxis 253 5.1 Background and Experimental Results . . . . . . . . . . . . . . . . . 253 5.2 Model Mechanism for E. coli in the Semi-Solid Experiments . . . . . 260 5.3 Liquid Phase Model: Intuitive Analysis of Pattern Formation . . . . . 267 5.4 Interpretation of the Analytical Results and Numerical Solutions . . . 274 5.5 Semi-Solid Phase Model Mechanism for S. typhimurium . . . . . . . 279 5.6 Linear Analysis of the Basic Semi-Solid Model . . . . . . . . . . . . 281 5.7 Brief Outline and Results of the Nonlinear Analysis . . . . . . . . . . 287 5.8 Simulation Results, Parameter Spaces and Basic Patterns . . . . . . . 292 5.9 Numerical Results with Initial Conditions from the Experiments . . . 297 5.10 Swarm Ring Patterns with the Semi-Solid Phase Model Mechanism . 299 5.11 Branching Patterns in Bacillus subtilis . . . . . . . . . . . . . . . . . 306 6. Mechanical Theory for Generating Pattern and Form in Development 311 6.1 Introduction, Motivation and Background Biology . . . . . . . . . . . 311 6.2 Mechanical Model for Mesenchymal Morphogenesis . . . . . . . . . 319 6.3 Linear Analysis, Dispersion Relation and Pattern Formation Potential . . . . . . . . . . . . . . . . . . . . . . . . . . . 330 6.4 Simple Mechanical Models Which Generate Spatial Patterns with Complex Dispersion Relations . . . . . . . . . . . . . . . . . . . . . 334 6.5 Periodic Patterns of Feather Germs . . . . . . . . . . . . . . . . . . . 345 6.6 Cartilage Condensations in Limb Morphogenesis and Morphogenetic Rules . . . . . . . . . . . . . . . . . . . . . . . . 350 6.7 Embryonic Fingerprint Formation . . . . . . . . . . . . . . . . . . . 358 6.8 Mechanochemical Model for the Epidermis . . . . . . . . . . . . . . 367 6.9 Formation of Microvilli . . . . . . . . . . . . . . . . . . . . . . . . . 374 6.10 Complex Pattern Formation and Tissue Interaction Models . . . . . . 381 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 394 7. Evolution, Morphogenetic Laws, Developmental Constraints and Teratologies 396 7.1 Evolution and Morphogenesis . . . . . . . . . . . . . . . . . . . . . 396 7.2 Evolution and Morphogenetic Rules in Cartilage Formation in the Vertebrate Limb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 402 7.3 Teratologies (Monsters) . . . . . . . . . . . . . . . . . . . . . . . . . 407 7.4 Developmental Constraints, Morphogenetic Rules and the Consequences for Evolution . . . . . . . . . . . . . . . . . . . . 411 8. A Mechanical Theory of Vascular Network Formation 416 8.1 Biological Background and Motivation . . . . . . . . . . . . . . . . . 416 8.2 Cell–Extracellular Matrix Interactions for Vasculogenesis . . . . . . . 417 8.3 Parameter Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . 425 8.4 Analysis of the Model Equations . . . . . . . . . . . . . . . . . . . . 427 8.5 Network Patterns: Numerical Simulations and Conclusions . . . . . . 433 9. Epidermal Wound Healing 441 9.1 Brief History of Wound Healing . . . . . . . . . . . . . . . . . . . . 441 9.2 Biological Background: Epidermal Wounds . . . . . . . . . . . . . . 444 9.3 Model for Epidermal Wound Healing . . . . . . . . . . . . . . . . . 447 9.4 Nondimensional Form, Linear Stability and Parameter Values . . . . . 450 9.5 Numerical Solution for the Epidermal Wound Repair Model . . . . . 451 9.6 Travelling Wave Solutions for the Epidermal Model . . . . . . . . . . 454 9.7 Clinical Implications of the Epidermal Wound Model . . . . . . . . . 461 9.8 Mechanisms of Epidermal Repair in Embryos . . . . . . . . . . . . . 468 9.9 Actin Alignment in Embryonic Wounds: A Mechanical Model . . . . 471 9.10 Mechanical Model with Stress Alignment of the Actin Filaments in Two Dimensions . . . . . . . . . . . . . . . . . . . . . 482 10. Dermal Wound Healing 491 10.1 Background and Motivation—General and Biological . . . . . . . . . 491 10.2 Logic of Wound Healing and Initial Models . . . . . . . . . . . . . . 495 10.3 Brief Review of Subsequent Developments . . . . . . . . . . . . . . 500 10.4 Model for Fibroblast-Driven Wound Healing: Residual Strain and Tissue Remodelling . . . . . . . . . . . . . . . . . . . . . . . . . . . 503 10.5 Solutions of the Model Equations and Comparison with Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 507 10.6 Wound Healing Model of Cook (1995) . . . . . . . . . . . . . . . . . 511 10.7 Matrix Secretion and Degradation . . . . . . . . . . . . . . . . . . . 515 10.8 Cell Movement in an Oriented Environment . . . . . . . . . . . . . . 518 10.9 Model System for Dermal Wound Healing with Tissue Structure . . . 521 10.10 One-Dimensional Model for the Structure of Pathological Scars . . . 526 10.11 Open Problems in Wound Healing . . . . . . . . . . . . . . . . . . . 530 10.12 Concluding Remarks on Wound Healing . . . . . . . . . . . . . . . . 533 11. Growth and Control of Brain Tumours 536 11.1 Medical Background . . . . . . . . . . . . . . . . . . . . . . . . . . 538 11.2 Basic Mathematical Model of Glioma Growth and Invasion . . . . . . 542 11.3 Tumour Spread In Vitro: Parameter Estimation . . . . . . . . . . . . . 550 11.4 Tumour Invasion in the Rat Brain . . . . . . . . . . . . . . . . . . . . 559 11.5 Tumour Invasion in the Human Brain . . . . . . . . . . . . . . . . . 563 11.6 Modelling Treatment Scenarios: General Comments . . . . . . . . . . 579 11.7 Modelling Tumour Resection in Homogeneous Tissue . . . . . . . . . 580 11.8 Analytical Solution for Tumour Recurrence After Resection . . . . . 584 11.9 Modelling Surgical Resection with Brain Tissue Heterogeneity . . . . 588 11.10 Modelling the Effect of Chemotherapy on Tumour Growth . . . . . . 594 11.11 Modelling Tumour Polyclonality and Cell Mutation . . . . . . . . . . 605 12. Neural Models of Pattern Formation 614 12.1 Spatial Patterning in Neural Firing with a Simple Activation–Inhibition Model . . . . . . . . . . . . . . . . . . 614 12.2 A Mechanism for Stripe Formation in the Visual Cortex . . . . . . . . 622 12.3 A Model for the Brain Mechanism Underlying Visual Hallucination Patterns . . . . . . . . . . . . . . . . . . . . . . . . . . 627 12.4 Neural Activity Model for Shell Patterns . . . . . . . . . . . . . . . . 638 12.5 Shamanism and Rock Art . . . . . . . . . . . . . . . . . . . . . . . . 655 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659 13. Geographic Spread and Control of Epidemics 661 13.1 Simple Model for the Spatial Spread of an Epidemic . . . . . . . . . 661 13.2 Spread of the Black Death in Europe 1347–1350 . . . . . . . . . . . 664 13.3 Brief History of Rabies: Facts and Myths . . . . . . . . . . . . . . . 669 13.4 The Spatial Spread of Rabies Among Foxes I: Background and Simple Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 673 13.5 The Spatial Spread of Rabies Among Foxes II: Three-Species (SIR) Model . . . . . . . . . . . . . . . . . . . . . . . 681 13.6 Control Strategy Based on Wave Propagation into a Nonepidemic Region: Estimate of Width of a Rabies Barrier . . . . . 696 13.7 Analytic Approximation for the Width of the Rabies Control Break . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 700 13.8 Two-Dimensional Epizootic Fronts and Effects of Variable Fox Densities: Quantitative Predictions for a Rabies Outbreak in England . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 704 13.9 Effect of Fox Immunity on the Spatial Spread of Rabies . . . . . . . . 710 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 720 14. Wolf Territoriality, Wolf–Deer Interaction and Survival 722 14.1 Introduction and Wolf Ecology . . . . . . . . . . . . . . . . . . . . . 722 14.2 Models for Wolf Pack Territory Formation: Single Pack—Home Range Model . . . . . . . . . . . . . . . . . . . 729 14.3 Multi-Wolf Pack Territorial Model . . . . . . . . . . . . . . . . . . . 734 14.4 Wolf–Deer Predator–Prey Model . . . . . . . . . . . . . . . . . . . . 745 14.5 Concluding Remarks on Wolf Territoriality and Deer Survival . . . . 751 14.6 Coyote Home Range Patterns . . . . . . . . . . . . . . . . . . . . . . 753 14.7 Chippewa and Sioux Intertribal Conflict c1750–1850 . . . . . . . . . 754 Appendix A. General Results for the Laplacian Operator in Bounded Domains 757 Bibliography 761 Index 791

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Published in: Elsevier Release Year: 2011 ISBN: 978-0-444-53567-2 Pages: 414 Edition: Fourth Edition File Size: 13 MB File Type: pdf Language: English

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Description of Fundamentals of Ecological Modelling

This is the fourth edition of Fundamentals of Ecological Modelling, and we have given it a longer title: Fundamentals of Ecological Modelling: Application in Environmental Management and Research. This was done to emphasize that models, applied in environmental management and ecological research, are particularly considered in the model illustrations included in this book. Giuseppe Bendoricchio, the co-author of the third edition published in 2001, passed away in 2005. We would, therefore, like to dedicate this book to his memory and his considerable contributions in the 1980s and 1990s to the development of ecological modelling. The first two editions of this book (published in 1986 and 1994) focused on the roots of the discipline — the four main model types that dominated the field 30-40 years ago: (1) dynamic biogeochemical models, (2) population dynamic models, (3) ecotoxicological models, and (4) steady-state biogeochemical and energy models. Those editions offered the first comprehensive textbook on the topic of ecological modelling. The third edition, with substantial input from Bendoricchio, focused on the mathematical formulations of ecological processes that are included in ecological models. In the third edition, the chapter called Ecological Processes encompasses 118 pages. The same coverage of this topic today would probably require 200 pages and is better covered in the Encyclopedia of Ecology, which was published in the fall of 2008. This fourth edition uses the four model types previously listed as the foundation and expands the latest model developments in spatial models, structurally dynamic models, and individual-based models. As these seven types of models are very different and require different considerations in the model development phase, we found it important for an up-to-date textbook to devote a chapter to the development of each of the seven model types. Throughout the text, the examples given from the literature emphasize the application of models for environmental management and research. Therefore the book is laid out as follows: Chapter 1: Introduction to Ecological Modelling provides an overview of the topic and sets the stage for the rest of the book. Chapter 2: Concepts of Modelling covers the main modelling elements of compartments (state variables), connections (flows and the mathematical equations used to represent biological, chemical, and physical processes), controls (parameters, constants), and forcing functions that drive the systems. It also describes the modelling procedure from conceptual diagram to verification, calibration, validation, and sensitivity analysis. Chapter 3: An Overview of Different Model Types critiques when each type should or could be applied. Chapter 4: Mediated or Institutionalized Modelling presents a short introduction to using the modelling process to guide research questions and facilitate stakeholder participation in integrated and interdisciplinary projects. Chapter 5: Modelling Population Dynamics covers the growth of a population and the interaction of two or more populations using the Lotka-Volterra model, as well as other more realistic predator–prey and parasitism models. Examples include fishery and harvest models, metapopulation dynamics, and infection models. Chapter 6: Steady-State Models discusses chemostat models, Ecopath software, and ecological network analysis. Chapter 7: Dynamic Biogeochemical Models are used for many applications starting with the original Streeter-Phelps model up to the current complex eutrophication models. Chapter 8: Ecotoxicological Models provides a thorough investigation of the various ecotoxicological models and their use in risk assessment and environmental management. Chapter 9: Individual-based Models discusses the history and rise of individualbased models as a tool to capture the self-motivated and individualistic characteristics individuals have on their environment. Chapter 10: Structurally Dynamic Models presents 21 examples of where model parameters are variable and adjustable to a higher order goal function (typically thermodynamic). Chapter 11: Spatial Modelling covers the models that include spatial characteristics that are important to understanding and managing the system.  This fourth edition is maintained as a textbook with many concrete model illustrations and exercises included in each chapter. The previous editions have been widely used as textbooks for past courses in ecological modelling, and it is the hope of the authors that this edition will be an excellent basis for today’s ecological modelling courses.

Content of Fundamentals of Ecological Modelling

1. Introduction 1 1.1 Physical and Mathematical Models 1 1.2 Models as a Management Tool 3 1.3 Models as a Research Tool 4 1.4 Models and Holism 7 1.5 The Ecosystem as an Object for Research 11 1.6 The Development of Ecological and Environmental Models 13 1.7 State of the Art in the Application of Models 16 2. Concepts of Modelling 19 2.1 Introduction 19 2.2 Modelling Elements 20 2.3 The Modelling Procedure 24 2.4 Verification 31 2.5 Sensitivity Analysis 34 2.6 Calibration 37 2.7 Validation and Assessment of the Model Uncertainty 41 2.8 Model Classes 44 2.9 Selection of Model Complexity and Structure 51 2.10 Parameter Estimation 60 2.11 Ecological Modelling and Quantum Theory 78 2.12 Modelling Constraints 82 Problems 92 3. An Overview of Different Model Types 95 3.1 Introduction 95 3.2 Model types — An Overview 96 3.3 Conceptual Models 100 3.4 Advantages and Disadvantages of the Most Applied Model Types 108 3.5 Applicability of the Different Model Types 116 Problems 118 4. Mediated or Institutionalized Modelling 121 4.1 Introduction: Why Do We Need Mediated Modelling? 121 4.2 The Institutionalized Modelling Process 123 4.3 When Do You Apply Institutionalized or Mediated Modelling (IMM)? 125 Problems 127 5. Modelling Population Dynamics 129 5.1 Introduction 129 5.2 Basic Concepts 129 5.3 Growth Models in Population Dynamics 131 Illustration 5.1 134 5.4 Interaction Between Populations 135 Illustration 5.2 141 Illustration 5.3 142 5.5 Matrix Models 147 Illustration 5.4 149 5.6 Fishery Models 150 5.7 Metapopulation Models 153 5.8 Infection Models 155 Problems 157 6. Steady-State Models 159 6.1 Introduction 159 6.2 A Chemo state Model to Illustrate a Steady-State Biogeochemical Model 160 Illustration 6.1 162 6.3 Ecopath Models 162 6.4 Ecological Network Analysis 163 Problems 174 7. Dynamic Biogeochemical Models 175 7.1 Introduction 175 7.2 Application of Biogeochemical Dynamic Models 177 7.3 The Streeter-Phelps River BOD/DO Model, Using STELLA 179 7.4 Eutrophication Models I: Simple Eutrophication Models with 2–4 State Variables 184 7.5 Eutrophication Models II: A Complex Eutrophication Model 192 7.6 Model of Subsurface Wetland 208 7.7 Global Warming Model 218 Problems 225 8. Ecotoxicological Models 229 8.1 Classification and Application of Ecotoxicological Models 229 8.2 Environmental Risk Assessment 233 8.3 Characteristics and Structure of Ecotoxicological Models 244 8.4 An Overview: The Application of Models in Ecotoxicology 258 8.5 Estimation of Ecotoxicological Parameters 261 8.6 Ecotoxicological Case Study I: Modelling the Distribution of Chromium in a Danish Fjord 271 8.7 Ecotoxicological Case Study II: Contamination of Agricultural Products by Cadmium and Lead 278 8.8 Fugacity Fate Models 284 Illustration 8.1 287 Illustration 8.2 288 9. Individual-Based Models 291 9.1 History of Individual-Based Models 291 9.2 Designing Individual-Based Models 293 9.3 Emergent versus Imposed Behaviors 294 9.4 Orientors 295 9.5 Implementing Individual-Based Models 297 9.6 Pattern-Oriented Modelling 299 9.7 Individual-Based Models for Parameterizing Models 301 9.8 Individual-Based Models and Spatial Models 302 9.9 Example of 304 9.10 Conclusions 308 Problems 308 10. Structurally Dynamic Models 309 10.1 Introduction 309 10.2 Ecosystem Characteristics 310 10.3 How to Construct Structurally Dynamic Models and Definitions of Exergy and Eco-exergy 321 10.4 Development of Structurally Dynamic Models for Darwin’s Finches 333 10.5 Biomanipulation 335 10.6 An Ecotoxicological Structurally Dynamic Models Example 343 Problems 346 11. Spatial Modelling 347 11.1 Introduction 347 11.2 Spatial Ecological Models: The Early Days 353 11.3 Spatial Ecological Models: State-of-the-Art 356 Problems 368 References 369 Index 385