This work establishes linear-scaling density-functional theory (DFT) as a powerful tool for understanding enzyme catalysis, one that can complement quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics simulations. The thesis reviews benchmark studies demonstrating techniques capable of simulating entire enzymes at the ab initio quantum-mechanical level of accuracy. DFT has transformed the physical sciences by allowing researchers to perform parameter-free quantum-mechanical calculations to predict a broad range of physical and chemical properties of materials. In principle, similar methods could be applied to biological problems. However, even the simplest biological systems contain many thousands of atoms and are characterized by extremely complex configuration spaces associated with a vast number of degrees of freedom. The development of linear-scaling density-functional codes makes biological molecules accessible to quantum-mechanical calculation, but has yet to resolve the complexity of the phase space. Furthermore, these calculations on systems containing up to 2,000 atoms can capture contributions to the energy that are not accounted for in QM/MM methods (for which the Nobel prize in Chemistry was awarded in 2013) and the results presented here reveal profound shortcomings in said methods.

Howard Pattee is a physicist who for many years has taken his own path in studying the physics of symbols, which is now a foundation for biosemiotics. By extending von Neumann's logical requirements for self-replication, to the physical requirements of symbolic instruction at the molecular level, he concludes that a form of quantum measurement is necessary for life. He explains why all non-dynamic symbolic and informational controls act as special (allosteric) constraints on dynamical systems. Pattee also points out that symbols do not exist in isolation but in coordinated symbol systems we call languages. Such insights turn out to be necessary to situate biosemiotics as an objective scientific endeavor. By proposing a way to relate quiescent symbolic constraints to dynamics, Pattee's work builds a bridge between physical, biological, and psychological models that are based on dynamical systems theory. Pattee's work awakes new interest in cognitive scientists, where his recognition of the necessary separation-the epistemic cut-between the subject and object provides a basis for a complementary third way of relating the purely symbolic, computational models of cognition and the purely dynamic, non-representational models. This selection of Pattee's papers also addresses several other fields, including hierarchy theory, artificial life, self-organization, complexity theory, and the complementary epistemologies of the physical and biological sciences.

Long before the advent of the global economy, foreign goods were transported, traded, and exchanged through myriad means, over short and long distances. Archaeological tools for identifying foreign objects, such as provenance studies, stylistic analyses, and economic documentary sources reveal non-local materials in historic and prehistoric assemblages.

Trade and exchange represent more than mere production and consumption. Exchange of goods also led to an exchange of cultural and social experiences. Discoveries of the sources of alien objects surpass archaeological expectations of exchange and geographic distance, revealing important technological advances.

With thirteen case studies from around the world, this comprehensive work provides a fresh perspective on material culture studies. Evidence of ongoing negotiation between individuals, villages, and nations provides insight into the impact of trade on the micro-, meso-, and macro-level. Covering a wide array of time periods and areas, this work will be of interest to archaeologists, anthropologists, and anyone working in cultural studies.

Agriculture is the main occupation in India and about 75% of its population depends directly or indirectly on agriculture for their livelihood. It is the dominant sector that contributes 18% of the gross domestic product. Thus, agriculture is the foundation of the Indian economy. The maximum share of Indian exports is also from the agriculture sector. As the population of the country is increasing trem- dously, approximately at the rate of 19 million every year over the existing popu- tion of more than 1 billion (approximately 1. 18 billion), the food grain production must necessarily be increased. This can be done by increasing crop production to match the population growth rate of 2. 2% per annum, which is expected to stabilize at 1. 53 billion around 2050. There is no doubt that the Green Revolution in India during the late 1960s brought self-sufficiency in food grain production, mainly through the increase in rice and wheat crop yields - the two main crops of the country which play an important role from food security point of view. However, the excessive use of fertilizers and pesticides, and the neglect of organic manures for these crops, has resulted in the deterioration of physical, chemical and biological health of the ri- and wheat-growing soils. Owing to the deterioration of the health of these soils, the productivity of the rice-wheat cropping system has now either got reduced or in some places has become constant for the last decade.

Agriculture is the lifeblood of the majority of people in Africa. It is not just a provider of food, it is a way of life for rural people. Whilst subsistence farming is the most practiced form of agriculture, there are many parts of Africa where agriculture is highly developed and progressive. In many instances it is the very diversity of agricultural practices that raises complex problems and issues. These issues often manifest themselves in ways that create ethical dilemmas for farmers, policy-makers, academics, politicians and the general lay-person. In particular, the role of biotechnology in African agriculture has become a contentious issue. Some people hold the view that biotechnology will solve the food shortages experienced in many parts of Africa, however, there is an opposing viewpoint that Africa may become a dumping ground for technology that has not been acceptable in other parts of the world. The ethical issues in agriculture in Africa do not focus only on biotechnology. The role of nutrition in the persistence of HIV/AIDS is highly debated and sometimes controversial. Land-related issues also generate heated debates in communities and amongst policy-makers. The single core that runs through all of these and many other related issues is, what are ethically acceptable solutions to these problems? This book attempts, in simple, unambiguous terms, to discuss the most important issues in African agriculture that have an ethical thread.

This review emerged from several interdisciplinary meetings and schools gathering a group of astronomers, geologists, biologists, and chemists, attempting to share their specialized knowledge around a common question: how did life emerge on Earth? Their ultimate goal was to provide some kind of answer as a prerequisite to an even more demanding question: is life universal? The resulting state-of-the-art articles were written by twenty-five scientists telling a not-so linear story, but on the contrary, highlighting problems, gaps, and controversies. Needless to say, this approach yielded no definitive answers to both questions. However, by adopting a chronological approach to the question of the emergence of life on Earth, the only place where we know for sure that life exists; it was possible to break down this question into several sub-topics that can be addressed by the different disciplines.

The main chapters of this review present the formation and evolution of the solar system (3); the building of a habitable planet (4); prebiotic chemistry, biochemistry, and the emergence of life (5); the environmental context of the early Earth (6); and the ancient fossil record and early evolution (7). The concluding chapter (9) provides the highlights of the review and presents the different points of view about the universality of life. Two pedagogical chapters are included; one on chronometers (2), another in the form of a "frieze" (8) which summarizes in graphical form the present state of knowledge about the chronology of the emergence of life on Earth, before the Cambrian explosion.

Reviews of Environmental Contamination and Toxicology attempts to provide concise, critical reviews of timely advances, philosophy and significant areas of accomplished or needed endeavor in the total field of xenobiotics, in any segment of the environment, as well as toxicological implications.

The central theme of this book "Microbial BioEnergy: Hydrogen Production" is focused on the biological machinery that microorganisms use to produce hydrogen gas.The book summarizes the achievements over the past decade in the biochemistry, structural and molecular biology, genomics and applied aspects of microbial H2-production, including microbial fuel cells (MFC), by phototrophs such as purple sulfur and non-sulfur bacteria ("Thiocapsa" spp., "Rhodobacter "and "Rhodopseudomonas" spp.) microalgae ("Chlamydomonas")and cyanobacteria ("Anabaena spp.") along with anaerobes and thermophiles such as "Caldicellulosiruptor "and "Thermotoga." This is the first bookof this series entirely devoted to microbial bio-hydrogen production and is intended to be a precious source of information for PhD students, researchers and undergraduates from disciplines such as microbiology, biochemistry, biotechnology, photochemistry and chemical engineering, interested in basic and applied sciences."

This book is a biography of a scientist who pioneered the development of plant pathology in Australia in the 19th and early 20th century, and was internationally acclaimed. After 20 years as a plant pathologist, he was asked to find the cause and cure of a serious physiological disorder of apples. While the cause eluded him, and everyone else for another 60 years, he again won international gratitude for the improvements he brought to the apple industry. However because he did not find the cause, he was deemed to have failed by his political masters who were malignantly influenced by a jealous rival. The discovery in 2012-2013 of government files covering the period of the bitter pit investigation, from 1911 to 1916; reveal the extent of the unjust criticism of McAlpine while history has vindicated the management recommendations made to reduce bitter-pit losses. The focus on bitter-pit management late in McAlpine's Career also meant that those who value his memory have been less aware of the remarkable achievements of McAlpine in the time before he left Great Britain - the brilliance of his teaching and drawing skills -featured in the early teaching texts for botany and zoology (the latter with his brother) which are now accessible on-line. The objective of this book is to demonstrate that (i) the view that McAlpine had failed in his quest was wrong and seriously unjust (ii) McAlpine achievements extend beyond plant pathology and include significant contributions to the 19th century teaching of botany and zoology, contributions which reinforce the adage - a picture is worth a 1,000 words.

The integrin family is composed of 24 members and approximately ten years ago (2003) we published a book devoted to the nine I domain integrin subunits. In this second edition, I am pleased that most of the original authors have been able to contribute to the updated version.

I domain containing integrins include collagen receptors and leukocyte receptors. In 2003 the knockout mouse phenotypes for all of the I domain integrins had not yet been published; they are now, and are summarized and discussed in this edition.

Interestingly, a recent 10 integrin mutation in dogs has indicated that collagen-binding integrins in the musculoskeletal system might have much more severe phenotypes in larger animals/humans compared to the mild integrin phenotypes observed in collagen-binding integrin deficient mice. This finding is further discussed in the book.

In the cancer field, the microenvironment is taking center stage, and here collagen receptors on fibroblasts are predicted to play important roles in paracrine signaling, in regulating tissue stiffness and matrix remodeling.

New technologies, new mouse models in combination with analyses of I integrins in larger animals/humans are thus predicted to increase our knowledge about this group of receptors. With this in mind we look forward to another 10 years of research with I domain integrins.

Data Mining and Applications in Genomics contains the data mining algorithms and their applications in genomics, with frontier case studies based on the recent and current works at the University of Hong Kong and the Oxford University Computing Laboratory, University of Oxford. It provides a systematic introduction to the use of data mining algorithms as an investigative tool for applications in genomics. Data Mining and Applications in Genomics offers state of the art of tremendous advances in data mining algorithms and applications in genomics and also serves as an excellent reference work for researchers and graduate students working on data mining algorithms and applications in genomics.

This volume is the second part of the thematic on Ion Channels as Therapeutic Targets. The popular Advances in Protein Chemistry and Structural Biology series, an essential resource for protein chemists, brings forth new information about protocols and analysis of proteins, with each thematically organized volume guest edited by leading experts in a broad range of protein-related topics.

Insights into Enzyme Mechanisms and Functions from Experimental and Computational Methods is the latest volume in the popular Advances in Protein Chemistry and Structural Biology series, an essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins, with each thematically organized volume guest edited by leading experts in a broad range of protein-related topics.

-Morphology of Filamentous Fungi: Linking Cellular Biology to Process Engineering Using Aspergillus niger, By Rainer Krull, Christiana Cordes, Harald Horn, Ingo Kampen, Arno Kwade, Thomas R. Neu, and Bernd Noertemann; -Multi-Scale Spatio-Temporal Modeling: Lifelines of Microorganisms in Bioreactors and Tracking Molecules in Cells, By Alexei Lapin, Michael Klann, and Matthias Reuss; -Impact of Profiling Technologies in the Understanding of Recombinant Protein Production, By Chandran Vijayendran and Erwin Flaschel -Engineering the Escherichia coli Fermentative Metabolism, By M. Orencio-Trejo, J. Utrilla, M.T. Fernandez-Sandoval, G. Huerta-Beristain, G. Gosset, and A. Martinez; -Modeling Languages for Biochemical Network Simulation: Reaction vs Equation Based Approaches, By Wolfgang Wiechert, Stephan Noack, and Atya Elsheikh; -Impact of Thermodynamic Principles in Systems Biology, By J.J. Heijnen;

Propelled by the success of the sequencing of the human and many related genomes, molecular and cellular biology has delivered significant scientific breakthroughs. Mathematics (broadly defined) continues to play a major role in this effort, helping to discover the secrets of life by working collaboratively with bench biologists, chemists and physicists.

Because of its outstanding record of interdisciplinary research and training, the IMA was an ideal venue for the 2007-2008 IMA thematic year on Mathematics of Molecular and Cellular Biology. The kickoff event for this thematic year was a tutorial on Mathematics of Nucleic Acids, followed by the workshop Mathematics of Molecular and Cellular Biology, held September 15--21 at the IMA. This volume is dedicated to the memory of Nicholas R. Cozzarelli, a dynamic leader who fostered research and training at the interface between mathematics and molecular biology. It contains a personal remembrance of Nick Cozzarelli, plus 15 papers contributed by workshop speakers. The papers give an overview of state-of-the-art mathematical approaches to the understanding of DNA structure and function, and the interaction of DNA with proteins that mediate vital life processes.

Design of Artificial Human Joints & Organs is intended to present the basics of the normal systems and how, due to aging, diseases or trauma, body parts may need to be replaced with manmade materials. The movement of the body generates forces in various work situations and also internally at various joints, muscles and ligaments. It is essential to figure out the forces, moments, pressure etc to design replacements that manage these stresses without breaking down. The mechanical characterization of the hard and the soft tissues are presented systematically using the principles of solid mechanics. The viscoelastic properties of the tissue will also discussed. This text covers the design science and methodology from concept to blueprint to the final component being replaced. Each chapter will be a brief overview of various joint/organ replacement systems. Engineers working on artificial joints and organs, as well as students of Mechanical Engineering and Biomedical Engineering are the main intended audience, however, the pedagogy is simple enough for those who are learning the subject for the first time.

Gregor Johann Mendel continues to fascinate the general public as well as scholars, the former for his life and the latter for his achievements. "Solitude of a Humble Genius" is a two-volume biography presenting Mendel in the context of the history of biology and philosophy, and in the context of the setting in which he lived and worked. In this first volume the authors set the stage for a new interpretation of Mendel s achievements and personality. The period of Mendel s life covered by this volume is critical to understanding why he saw what other biologists, including Charles Darwin, for example, didn t. In searching for clues to Mendel s thinking, the authors discuss at length the origin of his genes; the history of the region of his birth; they also spend a day and then the four seasons of the year with his family; and finally they examine the schooling he received, as well as the cultural and political influences he was exposed to.

An indispensible part of the work is Norman Klein s artwork. In this first volume alone, it comprises nearly 80 original drawings and includes cartoons that enliven the narration, scenes from Mendel s life, portraits, and plans and drawings of the cities and buildings in which he lived, studied, and worked."

Synthetic biology is a dynamic, young, ambitious, attractive, and heterogeneous scientific discipline. It is constantly developing and changing, which makes societal evaluation of this emerging new science a challenging task, prone to misunderstandings. Synthetic biology is difficult to capture, and confusion arises not only regarding which part of synthetic biology the discussion is about, but also with respect to the underlying concepts in use. This book offers a useful toolbox to approach this complex and fragmented field. It provides a biological access to the discussion using a 'layer' model that describes the connectivity of synthetic or semisynthetic organisms and cells to the realm of natural organisms derived by evolution.Instead of directly reviewing the field as a whole, firstly our book addresses the characteristic features of synthetic biology that are relevant to the societal discussion. Some of these features apply only to parts of synthetic biology, whereas others are relevant to synthetic biology as a whole. In the next step, these new features are evaluated with respect to the different areas of synthetic biology. Do we have the right words and categories to talk about these new features? In the third step, traditional concepts like "life" and "artificiality" are scrutinized with regard to their discriminatory power. This approach may help to differentiate the discussion on synthetic biology. Lastly our refined view is utilized for societal evaluation. We have investigated the public views and attitudes to synthetic biology. It also includes the analysis of ethical, risk and legal questions, posed by present and future practices of synthetic biology.This book contains the results of an interdisciplinary research project and presents the authors' main findings and recommendations. They are addressed to science, industry, politics and the general public interested in this upcoming field of biotechnology.

A fundamental understanding of algorithmic bioprocesses is key to learning how information processing occurs in nature at the cell level. The field is concerned with the interactions between computer science on the one hand and biology, chemistry, and DNA-oriented nanoscience on the other. In particular, this book offers a comprehensive overview of research into algorithmic self-assembly, RNA folding, the algorithmic foundations for biochemical reactions, and the algorithmic nature of developmental processes.

The editors of the book invited 36 chapters, written by the leading researchers in this area, and their contributions include detailed tutorials on the main topics, surveys of the state of the art in research, experimental results, and discussions of specific research goals. The main subjects addressed are sequence discovery, generation, and analysis; nanoconstructions and self-assembly; membrane computing; formal models and analysis; process calculi and automata; biochemical reactions; and other topics from natural computing, including molecular evolution, regulation of gene expression, light-based computing, cellular automata, realistic modelling of biological systems, and evolutionary computing.

This subject is inherently interdisciplinary, and this book will be of value to researchers in computer science and biology who study the impact of the exciting mutual interaction between our understanding of bioprocesses and our understanding of computation.

The book presents contributions on statistical models and methods applied, for both data science and SDGs, in one place. Measuring and controlling data of SDGs, data driven measurement of progress needs to be distributed to stakeholders. In this situation, the techniques used in data science, specially, in the big data analytics, play an important role rather than the traditional data gathering and manipulation techniques. This book fills this space through its twenty contributions. The contributions have been selected from those presented during the 7th International Conference on Data Science and Sustainable Development Goals organized by the Department of Statistics, University of Rajshahi, Bangladesh; and cover topics mainly on SDGs, bioinformatics, public health, medical informatics, environmental statistics, data science and machine learning. The contents of the volume would be useful to policymakers, researchers, government entities, civil society, and nonprofit organizations for monitoring and accelerating the progress of SDGs.

An ideal text for the natural product scientist looking for new techniques in research, this volume comprises the latest information on natural/plant resources.The comprehensive chapters cover the chemistry and pharmacology of a range of natural products - from Chinese herbal medicine to tea extracts, microbes to marine sponges, and the latest technologies to enhance the synthesis, isolation and purification of bioactive herbal compounds from these products. Adding additional value to the book are chapters on new tools in information technology that can greatly facilitate the research of natural product scientists, and the technologies available for evaluating medicinal herbal products for purity.

Unique blend of asymptotic theory and small sample practice through simulation experiments and data analysis.

Novel reproducing kernel Hilbert space methods for the analysis of smoothing splines and local polynomials. Leading to uniform error bounds and honest confidence bands for the mean function using smoothing splines

Exhaustive exposition of algorithms, including the Kalman filter, for the computation of smoothing splines of arbitrary order.

Financing Life Science Innovation reviews the literature on venture capital, corporate governance, and life science venturing and presents a study of the Swedish life science industry and the venture capital investors being active in financially and managerially supporting life science start-up firms.