This book provides an introduction to two important aspects of modern bioch- istry, molecular biology, and biophysics: computer simulation and data analysis. My aim is to introduce the tools that will enable students to learn and use some f- damental methods to construct quantitative models of biological mechanisms, both deterministicandwithsomeelementsofrandomness;tolearnhowconceptsofpr- ability can help to understand important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data. The availability of very capable but inexpensive personal computers and software makes it possible to do such work at a much higher level, but in a much easier way, than ever before. TheExecutiveSummaryofthein?uential2003reportfromtheNationalAcademy of Sciences, "BIO 2010: Transforming Undergraduate Education for Future - search Biologists" [12], begins The interplay of the recombinant DNA, instrumentation, and digital revolutions has p- foundly transformed biological research. The con?uence of these three innovations has led to important discoveries, such as the mapping of the human genome. How biologists design, perform, and analyze experiments is changing swiftly. Biological concepts and models are becoming more quantitative, and biological research has become critically dependent on concepts and methods drawn from other scienti?c disciplines. The connections between the biological sciences and the physical sciences, mathematics, and computer science are rapidly becoming deeper and more extensive.

Physics, mathematics and chemistry all play a vital role in understanding the true nature and functioning of biological membranes, key elements of living processes. Besides simple spectroscopic observations and electrical measurements of membranes we address in this book the phenomena of coexistence and independent existence of different membrane components using various theoretical approaches. This treatment will be helpful for readers who want to understand biological processes by applying both simple observations and fundamental scientific analysis. It provides a deep understanding of the causes and effects of processes inside membranes, and will thus eventually open new doors for high-level pharmaceutical approaches towards fighting membrane- and cell-related diseases.

Pediatric Injury Biomechanics: Archive and Textbook consolidates and describes the current state of the art in pediatric injury biomechanics research in the automotive crash environment. Written by the most respected scientists in the field, the objective of this ground-breaking project is to provide a comprehensive archive and analysis of pediatric injury biomechanics research; to be the go-to reference for the epidemiology of motor vehicle related childhood injury data, pediatric anthropometry, pediatric biomechanical properties, tissue tolerance, and computational models. This book provides essential information needed by researchers working in the field of pediatric injury including those involved in rulemaking activities, injury criteria development, child dummy development, and child injury interventions development. In addition to the text, a companion archive will include valuable information and tools to assist in the identification of gaps in research and future research directions.This living document will be regularly updated with current research and advancements in pediatric injury biomechanics.

Over the past decade, numerous books have attempted to explain ions in aqueous solutions in relation to biophysical phenomena. Ions in Water and Biophysical Implications, from Chaos to Cosmos offers a physicochemical point of view of the spread of this matter and suggests innovative solutions that will challenge the biophysics research establishment. Starting with a throughout discussion of the properties of liquid water, in particular as a structured liquid with an extensive hydrogen bonded structure, the book examines water as a solvent for gases, non-electrolytes, and electrolytes and reviews the properties, sizes and thermodynamics of isolated and aqueous ions, as well as their interactions, including those of polyelectrolytes. The effects of ions on water structure, including those on solvent dynamics and certain thermodynamic quantities, are presented. This volume investigates water surfaces with its vapour, with another liquid, and with a solid, as well as the effects of solutes, including simple ions and the water-miscible non-electrolytes. Surfaces are relevant to biomolecular and colloidal systems and the book discusses briefly surfactants, micelles and vesicles. Finally, the book concludes with a review of the various biophysical implications involving chaotropic and kosmotropic ions in homogeneous solutions and the Hofmeister series for ions concerning biomolecular and colloidal systems and some aspects of protein hydration and K+/Na+ selectivity in ion channels. Ions in Water and Biophysical Implications, from Chaos to Cosmos will appeal to physical chemists, biophysicists, biochemists, as well as to all students and researchers involved in the study of aqueous solutions.

Nano-science and nano-technology are rapidly developing scientific and technological areas that deal with physical, chemical and biological processes that occur on nano-meter scale - one millionth of a millimeter. Self-organization and pattern formation play crucial role on nano-scales and promise new, effective routes to control various nano-scales processes. This book contains lecture notes written by the lecturers of the NATO Advanced Study Institute "Self-Assembly, Pattern Formation and Growth Phenomena in Nano-Systems" that took place in St Etienne de Tinee, France, in the fall 2004. They give examples of self-organization phenomena on micro- and nano-scale as well as examples of the interplay between phenomena on nano- and macro-scales leading to complex behavior in various physical, chemical and biological systems. They discuss such fascinating nano-scale self-organization phenomena as self-assembly of quantum dots in thin solid films, pattern formation in liquid crystals caused by light, self-organization of micro-tubules and molecular motors, as well as basic physical and chemical phenomena that lead to self-assembly of the most important molecule on the basis of which most of living organisms are built - DNA. A review of general features of all pattern forming systems is also given. The authors of these lecture notes are the leading experts in the field of self-organization, pattern formation and nonlinear dynamics in non-equilibrium, complex systems.

Image processing algorithms based on the mammalian visual cortex are powerful tools for extraction information and manipulating images. This book reviews the neural theory and translates them into digital models. Applications are given in areas of image recognition, foveation, image fusion and information extraction. The third edition reflects renewed international interest in pulse image processing with updated sections presenting several newly developed applications. This edition also introduces a suite of Python scripts that assist readers in replicating results presented in the text and to further develop their own applications.

Membrane bioenergetics is one of the most rapidly growing areas within physico-chemical biology. Main aspects treated in this book include energy conservation and utilization by membrane-linked molecular mechanisms such as intracellular respiration, photosynthesis, transport phenomena, rotation of bacterial flagella, and the regulation of heat production.

Visual Prosthetics provides an in-depth analysis of the principles of operation, current state, anticipated developments, and functional aspects of visual prosthetics restoring sight to visually impaired individuals. This volume uniquely describes the human visual system in health and disease in a pedagogical and didactic manner, fitting to professionals and researchers with a bioengineering background. Readers will find a balanced overview of electrical, molecular chemical and synthetic chromophore stimulation, in addition to the biophysics and psychological aspects of vision restoration. Unlike competitive texts, this introduction also includes the need and methods for functional evaluation and rehabilitation. Professionals in the field of biomedical engineering and graduate and postgraduate researchers will find Visual Prosthetics a valuable reference.

The key element of any fluorescence sensing or imaging technology is the fluorescence reporter, which transforms the information on molecular interactions and dynamics into measurable signals of fluorescence emission. This book, written by a team of frontline researchers, demonstrates the broad field of applications of fluorescence reporters, starting from nanoscopic properties of materials, such as self-assembled thin films, polymers and ionic liquids, through biological macromolecules and further to living cell, tissue and body imaging. Basic information on obtaining and interpreting experimental data is presented and recent progress in these practically important areas is highlighted. The book is addressed to a broad interdisciplinary audience.

Nature provides many examples of coherent nonlinear structures and waves, and these have been observed and studied in various fields ranging from fluids and plasmas through solid-state physics to chemistry and biology. These proceedings reflect the remarkable process in understanding and modeling nonlinear phenomena in various systems that has recently been made.Experimental, numerical, and theoretical activities interact in various studies that are presented according to the following classification: magnetic and optical systems, biosystems and molecular systems, lattice excitations and localized modes, two-dimensional structures, theoretical physics, and mathematical methods. The book addresses researchers and graduate students from biology, engineering, mathematics, and physics.

The purpose of this monograph is to bring together under one cover results of research on phenomena drawn from the fields of chemistry, biochemistry, bio physics, virology,and cell biology. The processes and reactions considered have one important feature in common: they are endothermic and, therefore, entropy driven. They are, in the main, reversible reactions leading to the formation of large structures, some of which play critical roles in life processes. If one thinks only of the subunits and of the structures they form upon poly merization, it seems to be a contradiction that such reactions can be driven by an increase in entropy; entropy is a measure of disorder. The increase in entropy must come from some other source, usually from the release of something coincidental to polymerization. That something has been shown to be water for the case of the polymerization of tobacco mosaic virus protein. Because of the remarkable similarity of the other processes to this one, it is a permissable inference that the release of water is the source of the entropy increase and therefore the driving force for all of them. The reactions and processes brought together in this book are still the sub jects of active research. ;~ny of the detailed interpretations presented here must be regarded as tentative, subject to modification as new information becomes available. However, the main characteristic of each reaction or pro cess, its endothermic or entropy-driven nature, is well established in all but one or two instances.

The international symposium CAR '89 (the third in a row), held in Berlin in June 1989, was again focused on the fundamental principles of applying Computer Assisted Radiology (CAR) in health care. The book contains all the presentations of the symposium and this provides an up-to-date, complete state-of-the-art-report of this interdisciplinary subject, in which physicians, engineers, physicists and computer scientists cooperate.

This book is based on presentations to the International Conference of X-Ray Micro scopy and Spectromicroscopy, XRM 96, which took place in Wiirzburg, August 19- 23, 1996. The conference also celebrated the lOOth anniversary of the discovery of X rays by Wilhelm Conrad Rontgen on November 8, 1895, in Wiirzburg. This book contains state-of-the-art reviews and up-to-date progress reports in the field of X-ray microscopy and spectromicroscopy, including related new X-ray optics and X-ray sources. It reflects the lively activities within a relatively new field of science which combines the development of new instruments and methods with their applications to numerous topical scientific questions. The applications range from biological and medical topics, colloid physics, and soil sciences to solid-state physics, material sciences, and surface sciences. Their variety demonstrates the interdisci plinary and cooperative character of this field and the growing demand for micro scopic and spectromicroscopic information on the nanometer scale and under specific sample conditions, for example in wet (natural) surroundings or on a solid surface.

This book is devoted to the applications of the mathematical theory of solitons to physics, statistical mechanics, and molecular biology. It contains contributions on the signature and spectrum of solitons, nonlinear excitations in prebiological systems, experimental and theoretical studies on chains of hydrogen-bonded molecules, nonlinear phenomena in solid-state physics, including charge density waves, nonlinear wave propagation, defects, gap solitons, and Josephson junctions. The content is interdisciplinary in nature and displays the new trends in nonlinear physics.

Recent advances in single molecule science have presented a new branch of science: single molecule cellular biophysics, combining classical cell biology with cutting-edge single molecule biophysics. This textbook explains the essential elements of this new discipline, from the state-of-the-art single molecule techniques to real-world applications in unravelling the inner workings of the cell. Every effort has been made to ensure the text can be easily understood by students from both the physical and life sciences. Mathematical derivations are kept to a minimum whilst unnecessary biological terminology is avoided and text boxes provide readers from either background with additional information. 100 end-of-chapter exercises are divided into those aimed at physical sciences students, those aimed at life science students and those that can be tackled by students from both disciplines. The use of case studies and real research examples make this textbook indispensable for undergraduate students entering this exciting field.

This book presents an overview of the general field of biomimetics - lessons from nature. It presents various examples of biomimetics, including roughness-induced superomniphobic surfaces which provide functionality of commercial interest. The major focus in the book is on lotus effect, rose petal effect, shark skin effect, and gecko adhesion. For each example, the book first presents characterization of an object to understand how a natural object provides functionality, followed by modeling and then fabrication of structures in the lab using nature's route to verify one's understanding of nature and provide guidance for development of optimum structures. Once it is understood how nature does it, examples of fabrication of optimum structures using smart materials and fabrication techniques, are presented. Examples of nature inspired objects are also presented throughout.

This book offers an overview of state-of-the-art in non amplified DNA detection methods and provides chemists, biochemists, biotechnologists and material scientists with an introduction to these methods. In fact all these fields have dedicated resources to the problem of nucleic acid detection, each contributing with their own specific methods and concepts. This book will explain the basic principles of the different non amplified DNA detection methods available, highlighting their respective advantages and limitations. Non-amplified DNA detection can be achieved by adopting different techniques. Such techniques have allowed the commercialization of innovative platforms for DNA detection that are expected to break into the DNA diagnostics market. The enhanced sensitivity required for the detection of non amplified genomic DNA has prompted new strategies that can achieve ultrasensitivity by combining specific materials with specific detection tools. Advanced materials play multiple roles in ultrasensitive detection. Optical and electrochemical detection tools are among the most widely investigated to analyze non amplified nucleic acids. Biosensors based on piezoelectric crystal have been also used to detect unamplified genomic DNA. The main scientific topics related to DNA diagnostics are discussed by an outstanding set of authors with proven experience in this field.

This thesis presents a novel coarse-grained model of DNA, in which bases are represented as rigid nucleotides. The model is shown to quantitatively reproduce many phenomena, including elastic properties of the double-stranded state, hairpin formation in single strands and hybridization of pairs of strands to form duplexes, the first time such a wide range of properties has been captured by a coarse-grained model. The scope and potential of the model is demonstrated by simulating DNA tweezers, an iconic nanodevice, and a two-footed DNA walker - the first time that coarse-grained modelling has been applied to dynamic DNA nanotechnology.

Many naturally occurring biopolymers have unique structures and unique physical or mechanical properties. The understan- ding of the moleclar basisof these biomolecules, their syn- thesis, assembly and processing is a prerequisit for any ap- plication to the design of novel biomolecular materials. Se- veral classes of biopolymers are sampled in depth in this volume, such as nanolaminated ceramics, adhesive proteins, eggshellproteins, protein fibres and silk which are synthe- sized by a variety of organisms (mulluscs, parasitic trema- todes, fish and insects). The reader will be introduced to the biological systems to understand Nature's use of each biopolymer and the highly differentiated cells responsible for their synthesis. Corresponding to the variety of organ- isms and possible applications of biopolymers, the combined expertise of interdisciplinary teams of scientists - such as the authors of this volume - have the greatestopportunity to decipher and exploit Nature's skill in biopolymer engi- neering.

The aim of this book is to provide a uniquely comprehensive source of information on the entire field of radiation therapy physics. The very significant advances in imaging, computational, and accelerator technologies receive full consideration, as do such topics as the dosimetry of radiolabeled antibodies and dose calculation models. The scope of the book and the expertise of the authors make it essential reading for interested physicians and physicists and for radiation dosimetrists.

Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.

Local and global spatial coupling mechanisms form the basis of transport processes that are of fundamental importance for the occurrence and the dynamic evolution of patterns on a mesoscopic and macroscopic scale. The present volume deals with these concepts and investigates applications in the fields of biophysics and chemistry.

Respiratory motion causes an important uncertainty in radiotherapy planning of the thorax and upper abdomen. The main objective of radiation therapy is to eradicate or shrink tumor cells without damaging the surrounding tissue by delivering a high radiation dose to the tumor region and a dose as low as possible to healthy organ tissues. Meeting this demand remains a challenge especially in case of lung tumors due to breathing-induced tumor and organ motion where motion amplitudes can measure up to several centimeters. Therefore, modeling of respiratory motion has become increasingly important in radiation therapy. With 4D imaging techniques spatiotemporal image sequences can be acquired to investigate dynamic processes in the patient's body. Furthermore, image registration enables the estimation of the breathing-induced motion and the description of the temporal change in position and shape of the structures of interest by establishing the correspondence between images acquired at different phases of the breathing cycle. In radiation therapy these motion estimations are used to define accurate treatment margins, e.g. to calculate dose distributions and to develop prediction models for gated or robotic radiotherapy. In this book, the increasing role of image registration and motion estimation algorithms for the interpretation of complex 4D medical image sequences is illustrated. Different 4D CT image acquisition techniques and conceptually different motion estimation algorithms are presented. The clinical relevance is demonstrated by means of example applications which are related to the radiation therapy of thoracic and abdominal tumors. The state of the art and perspectives are shown by an insight into the current field of research. The book is addressed to biomedical engineers, medical physicists, researchers and physicians working in the fields of medical image analysis, radiology and radiation therapy.