A comprehensive presentation of essential topics for biological engineers, focusing on the development and application of dynamic models of biomolecular and cellular phenomena. This book describes the fundamental molecular and cellular events responsible for biological function, develops models to study biomolecular and cellular phenomena, and shows, with examples, how models are applied in the design and interpretation of experiments on biological systems. Integrating molecular cell biology with quantitative engineering analysis and design, it is the first textbook to offer a comprehensive presentation of these essential topics for chemical and biological engineering. The book systematically develops the concepts necessary to understand and study complex biological phenomena, moving from the simplest elements at the smallest scale and progressively adding complexity at the cellular organizational level, focusing on experimental testing of mechanistic hypotheses. After introducing the motivations for formulation of mathematical rate process models in biology, the text goes on to cover such topics as noncovalent binding interactions; quantitative descriptions of the transient, steady state, and equilibrium interactions of proteins and their ligands; enzyme kinetics; gene expression and protein trafficking; network dynamics; quantitative descriptions of growth dynamics; coupled transport and reaction; and discrete stochastic processes. The textbook is intended for advanced undergraduate and graduate courses in chemical engineering and bioengineering, and has been developed by the authors for classes they teach at MIT and the University of Minnesota.
An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules. Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility. The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.
From the big bang, to the origin and evolution of intelligent life in a search for the meaning of human existence, Why are We Here?, by author Bruce Brodie, offers a look at evolution and the future of life on the planet. Through many years of research and study, Brodie addresses a host of questions: • How did chemistry come to life? • How did the release of oxygen by cyanobacteria change the natural history of life? • How did mass extinctions reset the clock and reshape the course of biological evolution? • Why are homo sapiens so dominant? • Why do humans build vast civilizations, while chimps, with whom we share more than 98 percent of our DNA, are confined to forests and experimental laboratories and zoos? • How will cultural and technological evolution, which have transcended the slow pace of biological evolution, shape the future of life on the planet? • Can we escape the many existential threats that hover over us? Why are We Here? offers a new perspective on how we think about the world, and our place and our purpose in the universe and the future of humanity. It presents a lasting sense of the amazing wonder and mystery of life.
This book explains the anatomy and physiology of cartilage tissue in an integrated way. The emphasis is on how cartilage tissue functions and maintains homeostasis in a challenging mechanical environment. Supported by hundreds of references, the book posts new hypotheses explaining how cartilage adapts and achieves homeostasis in vivo, and tests them against available data. This exploratory approach creates a sense of discovery that the reader can join, or perhaps test themselves through their own research. The main benefit will be obtained by research students and professors looking to understand the deeper concepts that will further their own research, or clinicians (including health professionals and surgeons) who want to gain a deeper physiological understanding of cartilage tissue, which can then serve as a basis for more rational clinical decision-making they need to make on a daily basis. To help bridge the gap between basic science and clinically relevant joint disease, applications and interpretations of key physiological concepts are discussed in the context of osteoarthritis at the end of most chapters.
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