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Encyclopedia of Biophysics Encyclopedia of Biophysics Gordon C. K. Roberts Editor Encyclopedia of Biophysics With 1597 Figures and 131 Tables Editor Gordon C. K. Roberts Honorary Professor of Biochemistry Department of Biochemistry University of Leicester Leicester, UK ISBN 978-3-642-16711-9 ISBN 978-3-642-16712-6 (eBook) ISBN 978-3-642-16713-3 (print and electronic bundle) DOI 10.1007/978-3-642-16712-6 Springer Heidelberg New York Dordrecht London Library of Congress Control Number: 2012949366 First Edition: Copyright European Biophysical Societies’ Association (EBSA). English edition published by Springer-Verlag Berlin Heidelberg 2013. All rights reserved. # European Biophysical Societies’ Association (EBSA) 2013 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher nor EBSA can accept any legal responsibility for any errors or omissions that may be made. The publisher and EBSA make no warranty, express or implied, with respect to the material contained herein. Printed on acid-free paper Springer is part of Springer ScienceþBusiness Media (www.springer.com) To Hilary Preface Perhaps the first issue in introducing an Encyclopaedia of Biophysics is the question “What is Biophysics?”. The answer to this has varied considerably over time and between different ‘biophysicists’, particularly depending on whether they have come to biophysics from physics or physiology. For the present purposes, we have adopted the definition given by the Nobel Prize-winning physiologist A. V. Hill (Science 124, 1233, 1956): Biophysics is “the study of biological function, organization, and structure by physical and physicochemical ideas and methods.” – to which one would now add methods of mathematical analysis and computer modelling. An important feature of Hill’s definition is that it includes both physical methods and physical ideas. The astonishing developments in physical methods over the last hundred years have made them ubiquitous in biological laboratories – and indeed in hospitals. However, to quote Hill again “the employment of physical instruments in a biological laboratory does not make one a biophysicist - otherwise any user of a microscope, a balance ..... or a pH meter would drop automatically into that class.” Beyond simply the use of physical methods, it is the combination of both physical and biological ideas, intuitions and experience that makes a Biophysicist. The application of physical methods in biology has a very long history. For example, Antonie van Leeuwenhoek (1632 –1723) developed improved microscope lenses which allowed him to be the first to observe and describe single-celled organisms – the beginning of microbiology. The 18th century saw much speculation about ‘animal electricity’, culminating in the 1780s in Luigi Galvani’s famous experiments on the relation of electricity to muscle contraction. The middle of the 19th century saw what was probably the first explicitly biophysical programme of research, in which a group of physiologists (du Bois-Reymond, Ludwig, von Brucke,€ von Helmholtz) proclaimed their intention to ‘reduce physiology to physics and chemistry’. Of course the state of physics at the time was such as to make Biophysics a very premature venture, but this group did make important discoveries, notably in physiological optics and electrophysiology, using physical methods. An associate of this group, Adolf Fick – well-known for his law of diffusion – published what is probably the first biophysics text, Die Medizinische Physik (1856). In the 20th and 21st centuries there has been a dramatic flowering of Biophysics. The early part of 20th century saw the development of physical tools which are now familiar in biology – from X-ray diffraction (von Laue, Bragg) to the ultracentrifuge (Svedberg) and the electron microscope (Knoll & Ruska) – and this methodological development continues apace, notably with single-molecule techniques. The 1920s and 1930s saw the beginnings of physicochemical (Cohn, Edsall, Linderstrøm-Lang) and structural (Astbury, Bernal, Hodgkin, Perutz) studies of proteins. At the same vii viii Preface time, the first Departments or Institutes of Biophysics began to be established. In Germany these were commonly focussed on the study of radiation effects on organisms, while in the USA they concentrated largely on physiology. Many of these later expanded into other areas of Biophysics, and many more Departments of Biophysics – and Biophysical Societies – were established in the USA, Europe and Israel in the 1940s and 1950s. The power of the Biophysical approach was demonstrated unequivocally in the 1950s with the determination of the first three- dimensional structure of a protein, the structure of DNA and the Hodgkin-Huxley model of the action potential in nerves. Over the last 50 years, Biophysics has continued to develop at an astonishing pace. Biophysicists study life at every level, from atoms and molecules to cells, organisms, and environments. Molecular and Cellular Biophysics: This is perhaps the predom- inant strand of modern biophysics. It includes, for example, structural, functional and simulation studies of macromolecules and macromolecular assemblies of ever- increasing complexity and imaging of cells at ever-increasing resolution. Applied Biophysics: The applications of biophysical methods are perhaps most notable in the area of medical imaging - including X-ray CAT scans, magnetic resonance imaging, positron emission tomography and ultrasound scans. Therapeutic applications include radiation therapy of increasing sophistication and cardiac defibrillators. In addition to medical applications, there are now increasing and exciting applications in nanotechnology. Environmental Biophysics: For many years an important area of biophysics has been the study of the effects of ionising - and indeed non-ionising - radiation on organisms. Another key area of considerable current importance is the development of mathematical models of, e.g., heat and mass transfer at the level of organisms and ecosystems. This Encyclopedia is intended to provide a resource both for biophysicists inter- ested in approaches outside their immediate sub-discipline and for people coming to biophysics from either the physical or biological direction. The emphasis is very much on molecular and cellular biophysics, but some discussion of imaging and of nanotechnology is included. Just as there is overlap between chemistry and physics, so there is overlap between biophysics and biochemistry; our focus is of course on the techniques and uses of biophysics, but biochemical context is included where appropriate. The Encyclopedia consists of two kinds of entries, Systems and Techniques. • In the Systems sections, biophysical approaches to particular biological systems or problems – from protein structure to membranes, ion channels and receptors – are described. These sections, which have an emphasis on the integration of the different techniques, therefore provide an entry into Biophysics from the biolog- ical more than from the technique-oriented physics direction. • In the Techniques sections, each of the wide range of methods which fall under the heading of Biophysics are explained in detail, together with their strengths and the limitations of the information each provides. Experimental techniques covered range from diffraction, through a wide range of spectroscopic methods (X-ray, optical, EPR, NMR), kinetics, thermodynamics and hydrodynamics, to imaging (from electron microscopy to live cell imaging and MRI). The important and increasingly powerful computational, modelling and simulation approaches are also included. Each of the Sections includes concise introductions to the major concepts and methods, and outlines of more specific topics, in each case with links to a limited Preface ix number of carefully selected key reviews and/or papers in the scientific literature. Extensive cross-referencing (hyperlinks in the online version) between different articles allows access to related topics in a user-friendly manner. The online version of the Encyclopedia is intended to develop
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