Springer Series in Biophysics – serie

Molecular motors convert chemical energy (typically from ATP hydrolysis) to directed motion and mechanical work. Because of their dimension, the many small parts that make up molecular motors must operate at energies only a few times greater than those of the thermal baths.

Molecular motors convert chemical energy (typically from ATP hydrolysis) to directed motion and mechanical work. Because of their dimension, the many small parts that make up molecular motors must operate at energies only a few times greater than those of the thermal baths.

COVID-19 has brought us extensive research databases in the fields of biophysics, biology, and bioinformatics. To extract valuable structural bioinformatic information of SARS-CoV-2 structural and nonstructural proteins, it is necessary to work with large-scale datasets of molecular dynamics (MD) trajectories that need to be optimized.This monograph serves as a comprehensive guide to optimization-based MD studies of the molecular structures of SARS-CoV-2 proteins and RNA. The book begins by performing local optimization, taking into account the three-body movement and optimizing the noncovalent bonds of each molecular structure. The optimized structures reach a transition state that offers the best stability and lowest energy. The optimization process utilizes a hybrid strategy that combines mathematical optimization with various local search algorithms. This approach significantly reduces data volume while eliminating irrelevant bioinformatics data.To gain a thoroughunderstanding of molecular stability and the mechanism of action, it is essential to consider not only static NMR, X-ray, or cryo-EM structures but also dynamic information obtained through MD or Quantum Mechanics/Molecular Mechanics (QM/MM) simulations. These simulations capture the internal motions and dynamic processes of molecules. Furthermore, for each protein, the structural bioinformatics obtained from the optimized structure is validated by analyzing large-scale MD trajectory databases, which are openly and freely available online. The analysis includes key structural bioinformatics aspects such as salt bridge electrostatic interactions, hydrogen bonds, van der Waals interactions, and hydrophobic interactions specific to each SARS-CoV-2 molecular structure. The book also delves into discussions on drugs, vaccines, and the origins of the virus. Additionally, pandemic mathematical models, including those incorporating time delays, are explored.This book is particularly valuable for professionals working in practical computing roles within computational biochemistry, computational biophysics, optimization and molecular dynamics, structural bioinformatics, biological mathematics, and related fields. It serves as an accessible introduction to these disciplines and is also an excellent teaching resource for students.

COVID-19 has brought us extensive research databases in the fields of biophysics, biology, and bioinformatics. To extract valuable structural bioinformatic information of SARS-CoV-2 structural and nonstructural proteins, it is necessary to work with large-scale datasets of molecular dynamics (MD) trajectories that need to be optimized.This monograph serves as a comprehensive guide to optimization-based MD studies of the molecular structures of SARS-CoV-2 proteins and RNA. The book begins by performing local optimization, taking into account the three-body movement and optimizing the noncovalent bonds of each molecular structure. The optimized structures reach a transition state that offers the best stability and lowest energy. The optimization process utilizes a hybrid strategy that combines mathematical optimization with various local search algorithms. This approach significantly reduces data volume while eliminating irrelevant bioinformatics data.To gain a thoroughunderstanding of molecular stability and the mechanism of action, it is essential to consider not only static NMR, X-ray, or cryo-EM structures but also dynamic information obtained through MD or Quantum Mechanics/Molecular Mechanics (QM/MM) simulations. These simulations capture the internal motions and dynamic processes of molecules. Furthermore, for each protein, the structural bioinformatics obtained from the optimized structure is validated by analyzing large-scale MD trajectory databases, which are openly and freely available online. The analysis includes key structural bioinformatics aspects such as salt bridge electrostatic interactions, hydrogen bonds, van der Waals interactions, and hydrophobic interactions specific to each SARS-CoV-2 molecular structure. The book also delves into discussions on drugs, vaccines, and the origins of the virus. Additionally, pandemic mathematical models, including those incorporating time delays, are explored.This book is particularly valuable for professionals working in practical computing roles within computational biochemistry, computational biophysics, optimization and molecular dynamics, structural bioinformatics, biological mathematics, and related fields. It serves as an accessible introduction to these disciplines and is also an excellent teaching resource for students.

This book highlights key findings generated during the past years from the main disciplines that constitute Physical Virology, from theoretical physics and simulations to material sciences and vaccines development to structural biology.

This book highlights key findings generated during the past years from the main disciplines that constitute Physical Virology, from theoretical physics and simulations to material sciences and vaccines development to structural biology.

The 4th International Symposium on Mechanobiology (ISMB) organized by the Australian Society for Mechanobiology (AuSMB) took place at the Sydney Nanoscience Hub at the University of Sydney, Australia, from the 6th to the 9th of November 2022. This conference started in 2011 with the founding of the Society in Shanghai, China, and has occurred every three years also visiting Okayama (2014) and more recently Singapore (2017). This is the first time this conference was held in Australia.The primary purpose of the 4th International Symposium on Mechanobiology (ISMB) was to act as a forum for dissemination of cutting-edge research and innovation in the field of mechanobiology. It brought together 200+ delegates from both the Australian and International communities (students, scientists, clinicians, engineers and stakeholders from academia, industry and other organisations) working in the broader field of mechanobiology to discuss new and exciting advances in the field. This collection reflects the diverse and multidisciplinary nature of mechanobiology research spanning length scales and organ systems.Chapter 4 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

The 4th International Symposium on Mechanobiology (ISMB) organized by the Australian Society for Mechanobiology (AuSMB) took place at the Sydney Nanoscience Hub at the University of Sydney, Australia, from the 6th to the 9th of November 2022. This conference started in 2011 with the founding of the Society in Shanghai, China, and has occurred every three years also visiting Okayama (2014) and more recently Singapore (2017). This is the first time this conference was held in Australia.The primary purpose of the 4th International Symposium on Mechanobiology (ISMB) was to act as a forum for dissemination of cutting-edge research and innovation in the field of mechanobiology. It brought together 200+ delegates from both the Australian and International communities (students, scientists, clinicians, engineers and stakeholders from academia, industry and other organisations) working in the broader field of mechanobiology to discuss new and exciting advances in the field. This collection reflects the diverse and multidisciplinary nature of mechanobiology research spanning length scales and organ systems.Chapter 4 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

In recent years, extensive research on stochastic processes such as neuron networks, molecular motors, dynamics models, anomalous diffusion, and disordered media has led to the development of various methods for applying the Classical and Quantum Smoluchowski Equation to these phenomena.

In recent years, extensive research on stochastic processes such as neuron networks, molecular motors, dynamics models, anomalous diffusion, and disordered media has led to the development of various methods for applying the Classical and Quantum Smoluchowski Equation to these phenomena. This book focuses on presenting the solution to the Fokker-Planck equation using the Crank-Nicholson formalism. This method is particularly effective for handling systems with numerous interactions, requiring vector and matrix-oriented approaches suitable for implementation in Matlab. Among the topics treated in the book are: Dynamics of protons in DNA, Photosynthesis and the quantum mechanochemical model, Entanglement, coherence and decoherence, Excitons in the Fenna-Mathews-Olson complex, and Energy exchange between cells.The author has made an incredible work in facilitating the understanding of these complex topics. This book includes a brief and clear explanation of the Quantum theory and also includes code to build useful software to use in research environments. This volume is particularly helpful for graduate students in physics and biology interested in understanding biological processes with the use of quantum physics tools.

This monograph discusses the physical phenomena encountered in the heat transfer in living tissues and mathematical models. It also considers all the relevant information regarding heat transfer in humans, animals and plants in nature and medicine from the whole body down to cellular and sub-cellular models.Effects of the high or low temperature on the biological systems at the different levels - cells, tissues and organisms - as well a role of the blood circulation and the structure of the vascular network on the heat transfer are considered.The classic Pennes bioheat equation, a number of the non-Fourier heat transfer models (including the single-phase-lag and dual-phase-lag models), the porous media models, the models based on the fractional differential equations, the discrete vascular models are analyzed and discussed at length.This book is particularly interesting for graduate students, postdoctoral fellows and researching working on heat transfer in biological systems.

The second edition of the book published by Springer in 2006, Optical Polarization in Biomedical Applications concerns the optical methods exploring a unique feature of light —its polarization—for quantitative tissue characterization. The new edition will introduce new topics and expand on existing, cutting-edge developments in this field. Particular attention is paid to recent theoretical and instrumental advances in Mueller polarimetry and their potential clinical applications, a discussion of the principles and concepts of optical tissue clearing, orbital angular momentum, and quantum entangled photons in tissue polarization optics, polarization encoding and symbolic mapping of DNA sequences, and machine learning for pathology signature extraction.Some polarization-sensitive optical methods have already found clinical application, while others are still in the research phase but could become breakthrough technologies in various medical fields in the near future. Recent developments in Stokes-Muller polarimetry have led to extensive ex vivo and in vivo studies of various tissues. Important advances have been made in the field of matrix Mueller algebra for post-processing of diagnostic data, in the extension of the polarization Monte Carlo method to the study of scattering anisotropic media for the purpose of simulating the interaction of polarized light with tissue, and in the search for optimal optical markers for certain types of pathologies. These results are of interest to optical engineers, researchers, students, and clinicians seeking new, revolutionary approaches to solving diagnostic problems by assessing the presence of microstructural features to determine tissue integrity and in the development of new polarimetric technologies.

Parkinson’s disease (PD), the second most common neurodegenerative disorder in human. The cause of PD is believed to involve genetic factors. At least 6 pathogenic genes have been associated with familial PD. α-Synuclein (αS) is the main component of the Lewy bodies that accumulate in the brains of people with PD. Misfolding of the αS protein has been implicated in the molecular chain of events leading to PD. This book studies wild type (WT) αS proteins and their (8) αS(1-140)-mutants by optimization and Molecular Dynamics (MD). In this book our systematic MD study of a wider range of mutants would provide some answers for genetic factors. Numerous bindings of some segments of αS are also MD studied. Some fibrils leaded by aS misfolding are MD studied too.This book is particularly valuable for professionals working in computing roles within computational biochemistry/biophysics, bioinformatics, etc. It serves as an accessible introduction and is an excellent resource for students.

This book covers a broad area of STEM discipline, and is written as a textbook for  biology, bioengineering, physical chemistry, electrical engineering, and computer science students. It includes muscle biomechanics, viscoelasticity, chemical kinetics, system analysis, analog and digital electronics, methods for interfacing the experimental apparatus to a computer, programming computers to carry out experiments, and mathematics needed for these operations. Emphasis is given to the essentials, so that a beginner can understand the content, yet the principles can be applied to a variety of advanced systems. This book also includes exercise questions for important equations to be verified. Trying to solve a problem by oneself fosters good thinking, creativity, and independence, which would be essential for exploration of science. You can start from any chapter based on your interest and need and jump around chapters as necessary.

This book is dedicated to the channels and pores that belong to an eclectic and ubiquitous class of unconventional - perhaps at times strange - pore-forming molecules, which nevertheless play fundamental roles in various organisms. These non-canonical channels may take on various and sometimes complex architectures, such as large beta-barrels or lipid-containing pores. They may originate from bacteria, viruses or intracellular organelles. For some of them, the physiologically relevant substrate may indeed be ions, and for others folded polypeptides. Some are released by cells in a soluble form that has the ability to insert into biological membranes to exert its permeabilizing effect. Many of these unconventional pores have been investigated by electrophysiology, which, by its virtue of focusing on a few or even a single unit, has provided invaluable insight into the mechanisms and structure-function relationships of these remarkable membrane entities. The chapters of this book highlight a representative set of these interesting investigations.

This book is dedicated to the channels and pores that belong to an eclectic and ubiquitous class of unconventional - perhaps at times strange - pore-forming molecules, which nevertheless play fundamental roles in various organisms.

This volume brings together information on membrane organization and dynamics from a variety of spectroscopic, microscopic and simulation approaches, spanning a broad range of time scales. The implication of such dynamic information on membrane function in health and disease is a topic of contemporary interest. The chapters cover various aspects of membrane lipid and protein dynamics, explored using a battery of experimental and theoretical approaches. The synthesis of information and knowledge gained by utilizing multiple approaches will provide the reader with a comprehensive understanding of the underlying membrane dynamics and function, which will help to develop robust dynamic models for the understanding of membrane function in healthy and diseased states.  In the last few years, crystal structures of an impressive number of membrane proteins have been reported, thanks to tremendous advances in membrane protein crystallization techniques. Some of these recently solved structures belong to the G protein-coupled receptor (GPCR) family, which are particularly difficult to crystallize due to their intrinsic flexibility. Nonetheless, these static structures do not provide the necessary information to understand the function of membrane proteins in the complex membrane milieu. This volume will address the dynamic nature of membrane proteins within the membrane and will provide the reader with an up-to date overview of the theory and practical approaches that can be used.  This volume will be invaluable to researchers working in a wide range of scientific areas, from biochemistry and molecular biology to biophysics and protein science. Students of these fields will also find this volume very useful. This book will also be of great use to those who are interested in the dynamic nature of biological processes.

This volume brings together information on membrane organization and dynamics from a variety of spectroscopic, microscopic and simulation approaches, spanning a broad range of time scales. The implication of such dynamic information on membrane function in health and disease is a topic of contemporary interest. The chapters cover various aspects of membrane lipid and protein dynamics, explored using a battery of experimental and theoretical approaches. The synthesis of information and knowledge gained by utilizing multiple approaches will provide the reader with a comprehensive understanding of the underlying membrane dynamics and function, which will help to develop robust dynamic models for the understanding of membrane function in healthy and diseased states.  In the last few years, crystal structures of an impressive number of membrane proteins have been reported, thanks to tremendous advances in membrane protein crystallization techniques. Some of these recently solved structures belong to the G protein-coupled receptor (GPCR) family, which are particularly difficult to crystallize due to their intrinsic flexibility. Nonetheless, these static structures do not provide the necessary information to understand the function of membrane proteins in the complex membrane milieu. This volume will address the dynamic nature of membrane proteins within the membrane and will provide the reader with an up-to date overview of the theory and practical approaches that can be used.  This volume will be invaluable to researchers working in a wide range of scientific areas, from biochemistry and molecular biology to biophysics and protein science. Students of these fields will also find this volume very useful. This book will also be of great use to those who are interested in the dynamic nature of biological processes.

Writing or editing a book on a very topical field of science is always a great challenge,since by the time the book is published some of the newest and latest findings might be obsolete compared with results reported in the most current issues of various high-level journals. Nevertheless,stimulating good books describe complicated systems and int- relationships and provide a broad spectrum of material for talented researchers who may find new inspiration from a joint presentation of correlated data. Of course,an editor cannot rank his own book. However,in this case,the contrib- ing authors have high scientific standards and well-known achievements which speak for themselves. Transmembrane signaling has many different forms and biochemical and biophysical details. However,the final outcome of transmembrane signaling at the cellular level elucidates some cellular functions, which are at the center of se- defense, alimentation, escape reactions, etc. Transmembrane signaling can be studied best in the immune system,in particular in lymphocytes,the main cel- lar carriers of immune defense.The different chapters are independent studies, written by well-known experts in their particular fields. Some chapters include the authors' very recent data, generalized, on the one hand, to provide und- standable material for those who are interested in the field but not experts. On the other hand,the current data and novel efforts to unify biochemical and bioph- ical events in a physiological description provide interesting reading for experts as well.

Biological membranes have long been identified as key elements in a wide variety of cellular processes including cell defense communication, photosynthesis, signal transduction, and motility;

Technical advancements are basic elements in our life. In biophysical studies, new applications and improvements in well-established techniques are being implemented every day. This book deals with advancements produced not only from a technical point of view, but also from new approaches that are being taken in the study of biophysical samples, such as nanotechniques or single-cell measurements. This book constitutes a privileged observatory for reviewing novel applications of biophysical techniques that can help the reader enter an area where the technology is progressing quickly and where a comprehensive explanation is not always to be found.

This book assembles chapters from experts in the Biophysics of RNA to provide a broadly accessible snapshot of the current status of this rapidly expanding field. The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, highlighting just one example of a large number of non-protein coding RNAs. Because non-protein coding RNAs outnumber protein coding genes in mammals and other higher eukaryotes, it is now thought that the complexity of organisms is correlated with the fraction of their genome that encodes non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic transposons, higher-level organization of eukaryotic chromosomes, and gene expression itself are found to largely be directed by non-protein coding RNAs. The biophysical study of these RNAs employs X-ray crystallography, NMR, ensemble and single molecule fluorescence spectroscopy, optical tweezers, cryo-electron microscopy, and other quantitative tools. This emerging field has begun to unravel the molecular underpinnings of how RNAs fulfill their multitude of roles in sustaining cellular life.The physical and chemical understanding of RNA biology that results from biophysical studies is critical to our ability to harness RNAs for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.

All living cells are able to detect and translate environmental stimuli into biologically meaningful signals. Sensations of touch, hearing, sight, taste, smell or pain are essential to the survival of all living organisms. The importance of sensory input for the existence of life thus justifies the effort made to understand its molecular origins. Sensing with Ion Channels focuses on ion channels as key molecules enabling biological systems to sense and process the physical and chemical stimuli that act upon cells in their living environment. Its aim is to serve as a reference to ion channel specialists and as a source of new information to non specialists who want to learn about the structural and functional diversity of ion channels and their role in sensory physiology.

The investigation of molecules as individuals has grown rapidly in recent years, and in the process has uncovered molecular properties not normally accessible by ensemble experiments. In particular, the direct characterization of biologically important molecules such as enzymes, molecular motors, or receptors and entire signaling complexes in action, for example in a live biological cell, yielded un- pected insights. Common approaches for studying single molecules include the electrical detection of ion channels in membranes, the measurement of the dynamics of (bio)chemical reactions between individual molecules, the imaging of individual molecules by scanning probe techniques or by fluorescence correlation spectr- copy, and the direct monitoring of single molecules by optical microscopies, to mention a few. The application of these techniques in physics, chemistry, and bi- ogy has opened new areas of nanotechnology. This book provides a representative selection of recent developments in the rapidly evolving field of single molecule techniques of importance in life sciences and will have future impact on the quan- tative description of biological processes. The editors of this book hope that the chapters, written by leading scientists in the field, will attract students and scientists from different disciplines, provide them with an authentic insight into this young field of research, allow them to evaluate experimental methods and results, and thereby give them support for their own research. Lausanne Rudolf Rigler September 2007 Horst Vogel v Contents 1 Nanophotonics and Single Molecules. . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 W. E. Moerner, P. James Schuck, David P.

Biological membranes have long been identified as key elements in a wide variety of cellular processes including cell defense communication, photosynthesis, signal transduction, and motility; thus they emerge as primary targets in both basic and applied research. This book brings together in a single volume the most recent views of experts in the area of protein–lipid interactions, providing an overview of the advances that have been achieved in the field in recent years, from very basic aspects to specialized technological applications. Topics include the application of X-ray and neutron diffraction, infrared and fluorescence spectroscopy, and high-resolution NMR to the understanding of the specific interactions between lipids and proteins within biological membranes, their structural relationships, and the implications for the biological functions that they mediate. Also covered in this volume are the insertion of proteins and peptides into the membrane and the concomitant formation of definite lipid domains within the membrane.

Writing or editing a book on a very topical field of science is always a great challenge,since by the time the book is published some of the newest and latest findings might be obsolete compared with results reported in the most current issues of various high-level journals. Nevertheless,stimulating good books describe complicated systems and int- relationships and provide a broad spectrum of material for talented researchers who may find new inspiration from a joint presentation of correlated data. Of course,an editor cannot rank his own book. However,in this case,the contrib- ing authors have high scientific standards and well-known achievements which speak for themselves. Transmembrane signaling has many different forms and biochemical and biophysical details. However,the final outcome of transmembrane signaling at the cellular level elucidates some cellular functions, which are at the center of se- defense, alimentation, escape reactions, etc. Transmembrane signaling can be studied best in the immune system,in particular in lymphocytes,the main cel- lar carriers of immune defense.The different chapters are independent studies, written by well-known experts in their particular fields. Some chapters include the authors' very recent data, generalized, on the one hand, to provide und- standable material for those who are interested in the field but not experts. On the other hand,the current data and novel efforts to unify biochemical and bioph- ical events in a physiological description provide interesting reading for experts as well.

Technical advancements are basic elements in our life. In biophysical studies, new applications and improvements in well-established techniques are being implemented every day. This book deals with advancements produced not only from a technical point of view, but also from new approaches that are being taken in the study of biophysical samples, such as nanotechniques or single-cell measurements. This book constitutes a privileged observatory for reviewing novel applications of biophysical techniques that can help the reader enter an area where the technology is progressing quickly and where a comprehensive explanation is not always to be found.

The 2006 Nobel Prize in Physiology or Medicine was awarded to the discoverers of RNA interference, Andrew Fire and Craig Mello. This prize, which follows “RNA” Nobels for splicing and RNA catalysis, highlights just one class of recently discovered non-protein coding RNAs. Remarkably, non-coding RNAs are thought to outnumber protein coding genes in mammals by perhaps as much as four-fold. In fact, it appears that the complexity of an organism correlates with the fraction of its genome devoted to non-protein coding RNAs. Essential biological processes as diverse as cell differentiation, suppression of infecting viruses and parasitic tra- posons, higher-level organization of eukaryotic chromosomes, and gene expression are found to be largely directed by non-protein coding RNAs. Currently, bioinformatic, high-throughput sequencing, and biochemical approaches are identifying an increasing number of these RNAs. Unfortunately, our ability to characterize the molecular details of these RNAs is significantly lacking. The biophysical study of these RNAs is an emergent field that is unraveling the molecular underpinnings of how RNA fulfills its multitude of roles in sustaining cellular life. The resulting understanding of the physical and chemical processes at the molecular level is critical to our ability to harness RNA for use in biotechnology and human therapy, a prospect that has recently spawned a multi-billion dollar industry.

The investigation of molecules as individuals has grown rapidly in recent years, and in the process has uncovered molecular properties not normally accessible by ensemble experiments. In particular, the direct characterization of biologically important molecules such as enzymes, molecular motors, or receptors and entire signaling complexes in action, for example in a live biological cell, yielded un- pected insights. Common approaches for studying single molecules include the electrical detection of ion channels in membranes, the measurement of the dynamics of (bio)chemical reactions between individual molecules, the imaging of individual molecules by scanning probe techniques or by fluorescence correlation spectr- copy, and the direct monitoring of single molecules by optical microscopies, to mention a few. The application of these techniques in physics, chemistry, and bi- ogy has opened new areas of nanotechnology. This book provides a representative selection of recent developments in the rapidly evolving field of single molecule techniques of importance in life sciences and will have future impact on the quan- tative description of biological processes. The editors of this book hope that the chapters, written by leading scientists in the field, will attract students and scientists from different disciplines, provide them with an authentic insight into this young field of research, allow them to evaluate experimental methods and results, and thereby give them support for their own research. Lausanne Rudolf Rigler September 2007 Horst Vogel v Contents 1 Nanophotonics and Single Molecules. . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 W. E. Moerner, P. James Schuck, David P.