Computational biology has developed rapidly during the last two decades following the genomic revolution which culminated in the sequencing of the human genome. More than ever it has developed into a field which embraces computational methods from different branches of the exact sciences: pure and applied mathematics, computer science, theoretical physics. This Second Edition provides a solid introduction to the techniques of statistical mechanics for graduate students and researchers in computational biology and biophysics. Material has been reorganized to clarify equilbrium and nonequilibrium aspects of biomolecular systems Content has been expanded, in particular in the treatment of the electrostatic interactions of biomolecules and the application of non-equilibrium statistical mechanics to biomolecules New network-based approaches for the study of proteins are presented. All treated topics are put firmly in the context of the current research literature, allowing the reader to easily follow an individual path into a specific research field. Exercises and Tasks accompany the presentations of the topics with the intention of enabling the readers to test their comprehension of the developed basic concepts.

Quantum physics provides the concepts and their mathematical formalization that lend themselves to describe important properties of biological networks topology, such as vulnerability to external stress and their dynamic response to changing physiological conditions. A theory of networks enhanced with mathematical concepts and tools of quantum physics opens a new area of biological physics, the one of systems biological physics.

This book encompasses the full breadth of the super-resolution imaging field, representing modern techniques that exceed the traditional diffraction limit, thereby opening up new applications in biomedicine. It shows readers how to use the new tools to increase resolution in sub-nanometer-scale images of living cells and tissue, which leads to new information about molecules, pathways and dynamics. The book highlights the advantages and disadvantages of the techniques, and gives state-of-the-art examples of applications using microscopes currently available on the market. It covers key techniques such as stimulated emission depletion (STED), structured illumination microscopy (SSIM), photoactivated localization microscopy (PALM), and stochastic optical reconstruction microscopy (STORM). It will be a useful reference for biomedical researchers who want to work with super-resolution imaging, learn the proper technique for their application, and simultaneously obtain a solid footing in other techniques.

"Taken together, the body of information contained in this book provides readers with a bird's-eye view of different aspects of exciting work at the convergence of disciplines that will ultimately lead to a future where we understand how immunity is regulated, and how we can harness this knowledge toward practical ends that reduce human suffering. I commend the editors for putting this volume together." -Arup K. Chakraborty, Robert T. Haslam Professor of Chemical Engineering, and Professor of Physics, Chemistry, and Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA New experimental techniques in immunology have produced large and complex data sets that require quantitative modeling for analysis. This book provides a complete overview of computational immunology, from basic concepts to mathematical modeling at the single molecule, cellular, organism, and population levels. It showcases modern mechanistic models and their use in making predictions, designing experiments, and elucidating underlying biochemical processes. It begins with an introduction to data analysis, approximations, and assumptions used in model building. Core chapters address models and methods for studying immune responses, with fundamental concepts clearly defined. Readers from immunology, quantitative biology, and applied physics will benefit from the following: Fundamental principles of computational immunology and modern quantitative methods for studying immune response at the single molecule, cellular, organism, and population levels. An overview of basic concepts in modeling and data analysis. Coverage of topics where mechanistic modeling has contributed substantially to current understanding. Discussion of genetic diversity of the immune system, cell signaling in the immune system, immune response at the cell population scale, and ecology of host-pathogen interactions.

While structure-function relationships of proteins have been studied for a long time, structural studies of RNA face additional challenges. Nevertheless, with the continuous discovery of novel RNA molecules with key cellular functions and of novel pathways and interaction networks, the need for structural information of RNA is still increasing. This volume provides an introduction into techniques to assess structure and folding of RNA. Each chapter explains the theoretical background of one technique, and illustrates possibilities and limitations in selected application examples.

Considering the increased need to test and develop ventilation both for normobaric and hyperbaric use in underwater technology industries (diving equipment, submarines and other underwater facilities), mining, and other relevant industries, this book presents a complete study in the field of normobaric and hyperbaric ventilation. It focuses on development and verification of the research-based mathematical modeling approach for deterministic modeling of ventilation processes, both for objects with semi-closed and closed circulation of breathing gas. It also proposes validated analytical models of ventilation processes, and a new type of carbon dioxide emission simulator that was also developed. Features Describes ventilation processes by replacing semi-empirical models with more accurate analytical models. Includes concepts based on deterministic models (cause-and-effect models). Focuses on analytical mathematical model of the ventilation process. Covers both the objects with semi-closed and closed circulation of breathing gas, for hyperbaric and normobaric conditions. Summarizes relevant research results and their validation in real conditions and implemented into operational practice. This book is aimed at researchers, professionals, and graduate students in hyperbaric facility processing, building ventilation processing, life support system design, shipbuilding, marine engineering, and diving submarine safety.

Computational Biomechanics for Medicine: Solid and fluid mechanics for the benefit of patients contributions and papers from the MICCAI Computational Biomechanics for Medicine Workshop help in conjunction with Medical Image Computing and Computer Assisted Intervention conference (MICCAI 2020) in Lima, Peru. The content is dedicated to research in the field of methods and applications of computational biomechanics to medical image analysis, image-guided surgery, surgical simulation, surgical intervention planning, disease prognosis and diagnostics, analysis of injury mechanisms, implant and prostheses design, as well as artificial organ design and medical robotics. This book appeals to researchers, students and professionals in the field.

This volume contains the Proceedings of the NATO Advanced Research Workshop (ARW) and Emil-Warburg-Symposium (EWS) "Nonlinear Coherent Structures in Phy sics and Biology" held at the University of Bayreuth from June 1 -4, 1993. Director of the ARW was K. H. Spatschek, while F.G. Mertens acted as the co-director, host, and organizer of the EWS. The other members of the scientific organizing committee were A.R. Bishop (Los Alamos), J.C. Eilbeck (Edinburgh), and M. Remoissenet (Dijon). This was the eighth meeting in a series of interdisciplinary workshops founded by our French colleagues who had organized all the previous workshops, e.g. 1989 in Montpel lier and 1991 in Dijon. We were asked to organize the meeting this time in Germany. Of course, we wanted to keep the character defined by the previous meetings, which were always characterized by an open and friendly atmosphere, being not too large in quantity, but high in quality. This time altogether 103 participants attended the workshop. During the past years most of the participants met several times and discussed problems connected with the generation of nonlinear coherent structures in physics and biology."

The Geometric Induction of Bone Formation describes new biomimetic biomaterials that offer mechanistic osteogenic surfaces for the autonomous and spontaneous induction of bone formation without the addition of osteogenic soluble molecular signals of the transforming growth factor- supergene family. The chapters frame our understanding of regenerative medicine in primate species, including humans. The goal is to unravel the fundamental biological mechanisms of bone formation unique to non-human and human primates. The broad target audience dovetails with several disciplines both in the academic and private biotech sectors primarily involved in molecular biology, tissue biology, tissue engineering, biomaterial science, and reconstructive, orthopedic, plastic, and dental surgery. Key Features Includes outstanding images of undecalcified whole mounted sections Summarizes non-human primate research - ideal for clinical translation Reviews methods for creating devices capable of making bone autonomously, i.e. an intrinsically osteo-inductive bioreactor and/or biomaterial Describes the spontaneous induction of bone formation including a whole spectrum of tissue biology, from basic molecular biology to clear-cut morphology and pre-clinical application in non-human primate species Intended for audiences in both academic research and the biotech industry

While the effects of pressure change are readily quantified in physics, chemistry, and engineering applications, the physiology, medicine, and biology of pressure changes in living systems are much more complicated. This complex science translated to technical diving is discussed in a five-part series, with each topic self-contained and strategically developed in relationship to diving, spanning many disciplines and focusing on a number of technical areas. A suite of application exercises is provided at strategic points in the text. Additional material focusing on diving data, statistical correlations, underwater tests, and risk is included.

It is now well established that all living systems emit a weak but permanent photon flux in the visible and ultraviolet range. This biophoton emission is correlated with many, if not all, biological and physiological functions. There are indications of a hitherto-overlooked information channel within the living system. Biophotons may trigger chemical reactivity in cells, growth control, differentiation and intercellular communication, i.e. biological rhythms. Biophotonics is becoming one of the most fashionable fields in modern science and biotechnology. Biophotonics and Coherent Systems in Biology is an account of the original papers presented by the participants of the 3rd Alexander Gurwitsch Conference on the Biophotonics and Coherent Systems in Biology, Biophysics and Biotechnology which took place in Tauric University (Crimea, Ukraine) September 27-October 1, 2004.

The role of metal ions in protein folding and structure is a critical topic to a range of scientists in numerous fields, particularly those working in structural biology and bioinorganic chemistry, those studying protein folding and disease, and those involved in the molecular and cellular aspects of metals in biological systems. Protein Folding and Metal Ions: Mechanisms, Biology and Disease presents the contributions of a cadre of international experts who offer a comprehensive exploration of this timely subject at the forefront of current research. Divided into four sections, this volume: Provides case study examples of protein folding and stability studies in particular systems or proteins that comprise different metal ions of co-factors Reviews the proteins that shuttle metal ions in the cell to a particular target metalloprotein Illustrates how metal binding can be connected to pathological protein conformations in unrelated diseases, from cancer to protein deposition disorders such as Parkinson's disease Addresses protein redesign of metal-containing proteins by computational methods, folding simulation studies, and work on model peptides - dissecting the relative energetic contribution of metals sites to protein folding and stability Together, the 13 chapters in this text cogently describe the state of the science today, illuminate current challenges, propose future possibilities, and encourage further study in this area that offers much promise especially with regard to novel approaches to the treatment of some of the most challenging and tragic diseases.

Experimental microdosimetry deals with the measurement of charged particle energy deposition in tissue equivalent volumes, ranging in size from nanometres to micrometres. Microdosimetry is employed to improve our understanding of the relationship between radiation energy deposition, the resulting biological effects, and the appropriate quantities to be used in characterizing and quantifying radiation quality. Although many reviews and contributions to the field have been published over the past fifty years, this new book is the first to provide a single, up to date, and easily accessible account of experimental microdosimetry. This book is designed to be used in medical, radiation, and health physics courses and by Master’s and PhD students. In addition to serving as an introductory text to the field for graduate students, this book will also be of interest as a teaching and reference resource for graduate supervisors and established researchers. Drs. Lennart Lindborg and Anthony Waker have spent a life-time career in experimental microdosimetry research in academic, industrial and regulatory environments and have observed the development of the field from its early days as a recognized discipline; they bring to this book particular knowledge and experience in the design, construction, operation and use of tissue equivalent gas ionization counters and chambers.

Stem Cell Labeling for Delivery and Tracking Using Noninvasive Imaging provides a comprehensive overview of cell therapy imaging, ranging from the basic biology of cell therapeutic choices to the preclinical and clinical applications of cell therapy. It emphasizes the use of medical imaging for therapeutic delivery/targeting, cell tracking, and determining therapeutic efficacy. The book first presents background information and insight on the major classes of stem and progenitor cells. It then describes the main imaging modalities and state-of-the-art techniques that are currently employed for stem cell tracking. In the final chapters, leading scholars offer clinical perspectives on existing and potential uses of stem cells as well as the impact of image-guided delivery and tracking in major organ systems. Through clear descriptions and color images, this volume illustrates how noninvasive imaging is used to track stem cells as they repair damaged tissue in the body. With contributions from some of the most prominent preclinical and clinical researchers in the field, the book helps readers to understand the evolving concepts of stem cell labeling and tracking as the field continues to move forward.

Single-molecule techniques eliminate ensemble averaging, thus revealing transient or rare species in heterogeneous systems [1-3]. These approaches have been employed to probe myriad biological phenomena, including protein and RNA folding [4-6], enzyme kinetics [7, 8], and even protein biosynthesis [1, 9, 10]. In particular, immobilization-based fluorescence te- niques such as total internal reflection fluorescence microscopy (TIRF-M) have recently allowed for the observation of multiple events on the millis- onds to seconds timescale [11-13]. Single-molecule fluorescence methods are challenged by the instability of single fluorophores. The organic fluorophores commonly employed in single-molecule studies of biological systems display fast photobleaching, intensity fluctuations on the millisecond timescale (blinking), or both. These phenomena limit observation time and complicate the interpretation of fl- rescence fluctuations [14, 15]. Molecular oxygen (O) modulates dye stability. Triplet O efficiently 2 2 quenches dye triplet states responsible for blinking. This results in the for- tion of singlet oxygen [16-18]. Singlet O reacts efficiently with organic dyes, 2 amino acids, and nucleobases [19, 20]. Oxidized dyes are no longer fluor- cent; oxidative damage impairs the folding and function of biomolecules. In the presence of saturating dissolved O , blinking of fluorescent dyes is sup- 2 pressed, but oxidative damage to dyes and biomolecules is rapid. Enzymatic O -scavenging systems are commonly employed to ameliorate dye instability. 2 Small molecules are often employed to suppress blinking at low O levels.

The Textbook of Ion Channels is a set of three volumes providing a wide-ranging reference source on ion channels for students, instructors, and researchers. Ion channels are membrane proteins that control the electrical properties of neurons and cardiac cells, mediate the detection and response to sensory stimuli like light, sound, odor, and taste, and regulate the response to physical stimuli like temperature and pressure. In non-excitable tissues, ion channels are instrumental for the regulation of basic salt balance that is critical for homeostasis. Ion channels are located at the surface membrane of cells, giving them the unique ability to communicate with the environment, as well as the membrane of intracellular organelles, allowing them to regulate internal homeostasis. Ion channels are fundamentally important for human health and diseases, and are important targets for pharmaceuticals in mental illness, heart disease, anesthesia, pain and other clinical applications. The modern methods used in their study are powerful and diverse, ranging from single ion-channel measurement techniques to models of ion channel diseases in animals, and human clinical trials for ion channel drugs. Volume I, Part 1 covers fundamental topics such as the basic principles of ion permeation and selectivity, voltage-dependent, ligand-dependent and mechano-dependent ion channel activation mechanisms, the mechanisms for ion channel desensitization and inactivation and basic ion channel pharmacology and inhibition. Volume I, Part 2 aims to offer a practical guide of cardinal methods for researching ion channels, including heterologous expression and voltage-clamp and patch-clamp electrophysiology, isolation of native currents using patch-clamp, modelling ion channel gating, structures and its dynamics, crystallography and cryo- electron microscopy, fluorescence and paramagnetic resonance spectroscopy methods and genetics approaches in model organisms. All three volumes give the reader an introduction to fundamental concepts needed to understand the mechanism of ion channels, a guide to the technical aspects of ion channel research, offer a modern guide to the properties of major ion channel families, and include coverage of key examples of regulatory, physiological, and disease roles for ion channels.

Advanced Chromatic Monitoring provides a major source of information about the novel approach of chromaticity with examples of how chromaticity may be deployed for various monitoring applications. It shows with examples what can be achieved with chromatic methods in producing relevant information with a variety of test techniques and in facilitating the interpretation of complex data about complicated situations. It will be of interest to postgraduates and researchers in a wide breadth of physical disciplines (engineering, medicine, environmental sciences) and those involved with data acquisition and analysis. Key Features: Applicable to a wide range of disciplines (engineering, medical, environmental, etc) and those interested in science, technology, data acquisition and analysis Provides an extrapolation of new knowledge well beyond that covered in existing literature with regard to dealing with complicated forms and sets of data Addresses inspiring and innovative areas of research including environmental, power delivery and medical monitoring About the Editors: Emeritus Professor Gordon R. Jones - founder and former Director of the Centre for Intelligent Monitoring Systems (CIMS), former Head of the Department of Electrical Engineering and Electronics, and former Director of Electric Arcs Research Group at the University of Liverpool. He was awarded the IEEE Education, Science and Technology Achievement Medal (1999). Professor Joe W. Spencer - the present Director of CIMS at the University of Liverpool, having been Head of the Department of Electrical Engineering and Electronics at Liverpool. He is involved in operating a multi-million pound technology transfer unit (Sensor City, Liverpool) with whose establishment he played a major role and with which CIMS has major interactions.

The Role of Surface Modification on Bacterial Adhesion of Bio-implant Materials: Machining, Characterization, and Applications, explores the relationship between the surface roughness of artificial implants used for hard tissue replacement and their bacterial adhesion. It summarizes the reason for the failure of implants, the mechanisms of bacterial formation on implant surfaces, and the fundamental and established methods of implant surface modification techniques. It provides readers with an organized and rational representation about implant manufacturing and mechanical surface modification. It also explores the use of developed unidirectional abrasive flow finishing processes to finish biomaterials at the nano-level. It is an invaluable guide for academics, graduate students, biomaterial scientists, and manufacturing engineers researching implants, related infections, and implant manufacturing. Key Features: Explores implant related infections Discusses surface modification techniques Contains information on the mechanical finishing processes and complete guide on developed cutting edge unidirectional abrasive flow finishing technology

Humanhairisananocompositebiological?ber. Maintainingthehealth,feel,shine, color,softness,andoverallaestheticsofthehairishighlydesired. Haircarepr- ucts such as shampoos and conditioners, along with damaging processes such as chemical dyeing and permanent wave treatments, affect the maintenance and groomingprocessandareimportanttostudybecausetheyaltermanyhairprop- ties. Nanoscalecharacterizationofthecellularstructure,mechanicalproperties,and morphological, frictional,andadhesive properties(tribologicalproperties)ofhair areessentialtoevaluateanddevelopbettercosmeticproductsandtoadvancethe understandingofbiologicalandcosmeticscience. Theatomic/frictionforcemic- scope(AFM/FFM)andnanoindenterhavebecomeimportanttoolsforstudyingthe micro/nanoscalepropertiesofhumanhair. Inthisbook,wepresentacomprehensive review of structural, nanomechanical, and nanotribological properties of various hairandskinasafunctionofethnicity,damage,conditioningtreatment,andvarious environments. Variouscellularstructuresofhumanhairand?nesublamellarstr- turesofthecuticleareidenti?edandstudied. Nanomechanicalpropertiessuchas hardness,elasticmodulus,tensiledeformation,fatigue,creep,andscratchresistance arediscussed. Nanotribologicalpropertiessuchasroughness,friction,andadhesion are presented, as well as investigations of conditioner distribution, thickness, and bindinginteractions. Tounderstandtheelectrostaticchargebuilduponhair,surface potentialstudiesarealsopresented. Thebookshouldserveasareferencebookonthebiophysicsofhumanhairand hairtreatments. TheresearchreportedinthisbookwassupportedbyProcter&GambleCo. in Cincinnati,Ohio,andKobe,Japan. IwouldliketothankCarmenLaTorrewhohad assistedinvariouspublicationsonhairresearch. Iwouldalsoliketothankmywife Sudha,whohasbeenforbearingduringthepreparationofthisbook. Powell,OH BharatBhushan November2010 v Contents 1 Introduction-Human Hair, Skin, and Hair Care Products...1 1. 1 HumanHair ...1 1. 1. 1 TheCuticle ...3 1. 1. 2 TheCortexandMedulla...6 1. 2 Skin...7 1. 3 HairCare:CleaningandConditioningTreatments,andDamaging Processes ...10 1. 3. 1 CleaningandConditioningTreatments:Shampoo andConditioner...13 1. 3. 2 DamagingProcesses...18 1. 4 OrganizationoftheBook ...19 2 Experimental Methods...21 2. 1 ExperimentalApparatuses...23 2. 2 ExperimentalProcedure ...26 2. 2. 1 StructuralCharacterizationUsinganAFM...26 2. 2. 2 SurfacePotentialStudiesUsingAFM-Based KelvinProbeMicroscopy...29 2. 2. 3 NanomechanicalCharacterizationUsingNanoindentation ...30 2. 2. 4 InSituTensileDeformationCharacterizationUsingAFM ...32 2. 2. 5 Macroscale Tribological Characterization UsingaFrictionTestApparatus...33 2. 2. 6 Micro/nanotribologicalCharacterizationUsinganAFM...35 2. 3 HairandSkinSamples ...41 3 Structural Characterization Using an AFM ...45 3. 1 StructureofHairCrossSectionandLongitudinalSection ...45 3. 1. 1 CrossSectionofHair...45 3. 1. 2 LongitudinalSectionofHair...45 3. 2 StructureofVariousCuticleLayers...48 3. 2. 1 VirginHair...48 vii viii Contents 3. 2. 2 ChemicallyDamagedHair...50 3. 2. 3 Conditioner-TreatedHair...52 3. 2. 4 EffectofHumidityonMorphologyandCellularStructure ofHairSurface...54 3. 3 Summary...55 4 Nanomechanical Characterization Using Nanoindentation, Nanoscratch, and AFM...57 4. 1 Hardness,Young'sModulus,andCreep...