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  • Protein Structure Prediction / Patrice Koehl -- Molecular Modeling of Biomembranes: A How-to Approach / Allison N. Dickey and Roland Faller -- Introduction to Electron Paramagnetic Resonance Spectroscopy / Marcin Brynda -- Theory and Applications of Biomolecular NMR Spectroscopy / James B. Ames -- FRET and Its Biological Application as a Molecular Ruler / Jie Zheng -- Introduction to Modern Techniques in Mass Spectrometry / Caroline S. Chu and Carlito B. Lebrilla -- Transmission Electron Microscopy and Computer-Aided Image Processing for 3D Structural Analysis of Macromolecules / Dominik J. Green and R. Holland Cheng -- Raman Spectroscopy of Living Cells / Tyler Weeks and Thomas Huser.
  • When quantum mechanics was first proposed a century ago, nobody could have anticipated how deeply it would affect our lives. Today, we are connected and powered through devices whose existence is predicated on the basic principles of this strange physics. Not even the biological sciences have escaped its reach. As scientists query the deepest mysteries of the living world, the physical scales probed and the types of questions asked are increasingly blurring the lines between biology and physics. The hybrid field of biophysics represents the new frontier of the 21st century. The ribosome has been at the heart of three Nobel Prizes. Understanding its essential nature and how it interacts with other proteins and nucleic acids to control protein synthesis has been one of the central foundations in our understanding of the biology at the molecular level. With the advent of atomic scale structures, methods to visualize and separate individual molecules, and the computational power to model the complex interactions of over a million atoms at once, our understanding of how gene expression is controlled at the level of protein translation is now deeply ensconced in the biophysical realm. This book provides a premier resource to a wide audience, whether it be the general reader seeking a broad view of the field, a clinician interested in the role of protein translation in human disease, the bench researcher looking for state-of-the-art technologies, or computational scientists involved in cutting edge molecular modeling.
  • Biophysics for the life sciences v. 1-, 2013-, Springer
  • This book can be used to provide insight into this important application of biophysics for those who are planning a career in protein therapeutic development, and for those outside this area who are interested in understanding it better. The initial chapters describe the underlying theory, and strengths and weaknesses of the different techniques commonly used during therapeutic development. The majority of the chapters discuss the applications of these techniques, including case studies, across the product lifecycle from early discovery, where the focus is on identifying targets, and screening for potential drug product candidates, through expression and purification, large scale production, formulation development, lot-to-lot comparability studies, and commercial support including investigations.
  • "The volume is intended as an introduction to the physical principles governing the main processes that occur in photosynthesis, with emphasis on the light reactions and electron transport chain. A unique feature of the photosynthetic apparatus is the fact that the molecular structures are known in detail for essentially all of its major components. The availability of this data has allowed their functions to be probed at a very fundamental level to discover the design principles that have guided evolution. Other volumes on photosynthesis have tended to focus on single components or on a specific set of biophysical techniques, and the authors' goal is to provide new researchers with an introduction to the overall field of photosynthesis. The book is divided into sections, each dealing with one of the main physical processes in photosynthetic energy conversion. Each section has several chapters each describing the role that a basic physical property, such as charge or spin, plays in governing the process being discussed. The chapters proceed in an orderly fashion from a quantum mechanical description of early processes on an ultrafast timescale to a classical treatment of electron transfer and catalysis on a biochemical timescale culminating in evolutionary principles on a geological timescale."--Publisher's website.
  • Structured RNAs are everywhere, functioning throughout gene expression with key roles ranging from catalysis to regulation. New functional RNAs are being discovered all the time; in fact, it is now clear that a much greater fraction of eukaryotic genomes is devoted to coding for RNA than protein. Many of these RNAs must traverse complex energy landscapes to find their functional three-dimensional structures. Along the way, they may encounter native and non-native folding intermediates, chaperone proteins, and assemble with partner proteins. This volume, written by experts in the field, discusses the current understanding of the biophysical principles that govern RNA folding, with featured RNAs including the ribosomal RNAs, viral RNAs, and self-splicing introns. In addition to the fundamental features of RNA folding, the central experimental and computational approaches in the field are presented with an emphasis on their individual strengths and limitations, and how they can be combined to be more powerful than any method alone; these approaches include NMR, single molecule fluorescence, site-directed spin labeling, structure mapping, comparative sequence analysis, graph theory, course-grained 3D modeling, and more. This volume will be of interest to professional researchers and advanced students entering the field of RNA folding.
  • Field Potential Generation and Current Source Density Analysis / L. Stan Leung -- Current Source Density Analysis of Ongoing Neural Activity: Theory and Application / Yonghong Chen, Mukesh Dhamala, Anil Bollimunta, Charles E. Schroeder, Mingzhou Ding -- The Juxtacellular Recording-Labeling Technique / Didier Pinault -- Neural Recording Using Digital Telemetry / André A. Fenton, Kathryn J. Jeffery, James G. Donnett -- Large-Scale Neural Ensembles in Mice: Methods for Recording and Data Analysis / Hui Kuang, Joe Z. Tsien -- Behavioral Correlates of Neuronal Activity Recorded as Single-Units: Promises and Pitfalls as Illustrated by the Rodent Head Direction Cell Signal / Robert W. Stackman -- Event-Related Potentials of the Cerebral Cortex / Steven L. Bressler -- Multisite Spike-Field Coherence, Theta Rhythmicity, and Information Flow Within Papez's Circuit / Zimbul Albo, Gonzalo Viana Prisco, Robert P. Vertes -- Cognitively Relevant Recoding in Hippocampus: Beneficial Feedback of Ensemble Codes in a Closed Loop Paradigm / Robert E. Hampson, John D. Simeral, Theodore W. Berger, Dong Song, Rosa H. Chan, Vasilis Z. Marmarelis, Sam A. Deadwyler -- An Intact Septo-Hippocampal Preparation for Investigating the Mechanisms of Hippocampal Oscillation / Romain Goutagny, Jesse Jackson, Sylvain Williams -- Targeted Modulation of Neural Circuits: A New Treatment Strategy for Neuropsychiatric Disease / Helen S. Mayberg, Paul E. Holtzheimer.
  • Pt. 1. Fluorescence spectroscopy: basics and advanced approaches. Basics of fluorescence spectroscopy in biosciences / M. Hof, V. Fidler and R. Hutterer -- Pulse and phase fluorometries: an objective comparison / B. Valeur -- Non-exponential fluorescence of electronically coupled donors contains distance information / S. Kalinin, M. Isaksson and L.B.-Å. Johansson -- Fluorescence nanotomography: recent progress, constraints and opportunities / O.J. Rolinski and D.J.S. Birch -- Solvent relaxation as a tool for probing micro-polarity and -fluidity / J. Sýkora, R. Hutterer and M. Hof -- Total internal reflection fluorescence microscopy: applications in biophysics / N.L. Thompson and J.K. Pero -- Single molecule spectroscopy: basics and applications / J. Enderlein --Pt. 2. Application of fluorescence spectroscopy to biological membranes. Raft microdomains in model membranes as revealed by fluorescence quenching / G. Duportail -- The lateral structure of lipid membranes as seen by fluorescence microscopy / L.A. Bagatolli -- Pt. 3. Application of fluorescence spectroscopy to protein studies. Protein dynamics and protein folding dynamics revealed by time-resolved fluorescence / A. Saxena, J.B. Upgaonkar and G. Krishnamoorthy -- Time-resolved fluorescence and two-photon FCS investigation of the interaction of HIV-1 nucleocapsid protein with hairpin loop oligonucleotides / J. Azoulay ... [et al.] -- Pt. 4. Application of fluorescence spectroscopy to DNA and drug delivery. Fluorescence techniques in non-viral gene therapy / N. Adjimatera, A.P. Neal and I.S. Blagbrough -- Fluorescence applications in targeted drug delivery / K. Bryl and M. Langner -- Pt. 5. Fluorescence spectroscopy in cells: FCS and quantum dots. Fluorescence correlations spectroscopy in cell biology / B. Brock -- Fluorescence quantum dots: properties and applications / M.R. Warnement and S.J. Rosenthal -- Heat stress of cancer cells: fluorescence imaging of structural changes with quantum dots 605 and alexa 488.
  • ch. 1. Basic definitions -- ch. 2. General properties of Fourier transforms -- ch. 3. Discrete Fourier transform -- ch. 4. Fast Fourier transform (FFT) -- ch. 5. Other integral transforms -- ch. 6. Fourier transform spectroscopy (FTS) -- ch. 7. Nuclear magnetic resonance (NMR) spectrometry -- ch. 8. Ion cyclotron resonance (ICR) mass spectrometry -- ch. 9. Diffraction and Fourier transform -- ch. 10. Uncertainty principle -- ch. 11. Processing of signal and spectrum -- ch. 12. Fourier self-deconvolution (FSD) -- ch. 13. Linear prediction.
  • FRET and FLIM techniques 2009., ScienceDirect
  • Introduction -- 1. Environmental and Occupationally Encountered Electromagnetic Fields / Kjell Hansson Mild and Ben Greenebaum -- 2. Endogenous Electric Fields in Animals / Richard Nuccitelli -- 3. Dielectric Properties of Biological Materials / Camelia Gabriel -- 4. Magnetic Properties of Biological Material / Jon Dobson -- 5. Interaction of Direct Current and Extremely Low-Frequency / Electric Fields with Biological Materials and Systems / Frank S. Barnes -- 6. Magnetic Field Effects on Free Radical Reactions in Biology / Stefan Engström -- 7. Signals, Noise, and Thresholds / James C. Weaver and Martin Bier -- 8. Biological Effects of Static Magnetic Fields / Shoogo Ueno and Tsukasa Shigemitsu -- 9. The Ion Cyclotron Resonance Hypothesis / A.R. Liboff -- 10. Computational Methods for Predicting Field Intensity and Temperature Change / James C. Lin and Paolo Bernardi -- 11. Experimental EMF Exposure Assessment / Sven Kühn and Niels Kuster -- 12. Electromagnetic Imaging of Biological Systems / William T. Joines, Qing H. Liu, and Gary Ybarra.
  • v. 1. -- Part I. Sample preparation and sample pretreatment -- ch. 1. Collection and preparation of gaseous samples / Douglas A. Lane -- ch. 2. Sample collection and preparation of liquid and solids / Brian M. Cullum, Tuan Vo-Dinh -- Part II. Methods 1: Optical spectroscopy -- ch. 3. Basics of optical spectroscopy / Martin Hof -- ch. 4. Instrumentation / Valdas Sablinskas -- ch. 5. Measurement techniques / Gerald Steiner -- ch. 6. Applications / Valdas Sablinskas, Gerald Steiner, Martin Hof -- Part III. Methods 2: Nuclear magnetic resonance spectroscopy -- ch. 7. An Introduction to solution, solid-state, and imaging NMR spectroscopy / Leslie G. Butler -- ch. 8. Solution NMR spectroscopy / Gary E. Martin, Chad E. Hadden, David J. Russell -- ch. 9. Solid-state NMR / Steven P. Brown, Lyndon Emsley -- Part IV. Methods 3: Mass spectrometry -- ch. 10. Mass spectrometry / Michael Przybylski, Wolfgang Weinmann, Thilo A. Fligge -- Part V. Methods 4: Elemental analysis -- ch. 11. X-ray fluorescence analysis / K. Janssens -- ch. 12. Atomic absorption spectrometry (AAS) and atomic emission spectrometry (AES) / Erwin Rosenberg, Ulrich Panne -- Part VI. Methods 5: Surface analysis techniques -- ch. 13. Surface analysis techniques / A. Macková, S.A. Morton, C.G.H. Walker, K. Volka -- v. 2. -- Part VII. Applications 1: Bioanalysis -- ch. 14. Bioanalysis / Willem M. Albers, Arto Annila, Nicholas J. Goddard, Gabor Patonay, Erkki Soini -- Part VIII. Applications 2: Environmental analysis -- ch. 15. LC-MS in environmental analysis / H.Fr. Schröder -- ch. 16. Gas chromatography/ion trap mass spectrometry (GC/ITMS) for environmental analysis / Michel Sablier, Toshihiro Fujii -- Part IX. Application 3: Process control -- ch. 17. Optical spectroscopy / John Green -- ch. 18. NMR / Loring A. Weisenberger -- ch. 19. Process mass spectrometry / Christian Hassell -- ch. 20. Elemental analysis / J.S. Crighton -- Part X. Hyphenated techniques -- ch. 21. Hyphenated techniques for chromatographic detection / John C. Fetzer -- Part XI. General data treatment: data bases/spectral libraries -- ch. 22. Optical spectroscopy / Steffen Thiele, Reiner Salzer -- ch. 23. Nuclear magnetic resonance spectroscopy / Wolfgang Robien -- ch. 24. Mass spectrometry / Antony N. Davies.
  • Structure of matter -- Nuclear transformations -- Production of x-rays -- Clinical radiation generators -- Interactions of ionizing radiation -- Measurement of ionizing radiation -- Quality of x-ray beams -- Measurement of absorbed dose -- Dose distribution and scatter analysis -- A system of dosimetric calculations -- Treatment planning i : isodose distributions -- Treatment planning ii : patient data acquisition, treatment verification, and -- Inhomogeneity corrections -- Treatment planning iii: field shaping, skin dose, and field separation -- Electron beam therapy -- Low-dose-rate brachytherapy: rules of implantation and dose specification -- Radiation protection -- Quality assurance -- Total body irradiation -- Three-dimensional conformal radiation therapy -- Intensity-modulated radiation therapy -- Stereotactic radiotherapy and radiosurgery -- Stereotactic body radiation therapy -- High-dose-rate brachytherapy -- Prostate implants: technique, dosimetry, and treatment planning -- Intravascular brachytherapy -- Image-guided radiation therapy -- Proton beam therapy.
  • Mechanosensitivity of cells from various tissues -- Mechanotransduction in the Nematode Caenorhabditis elegans -- Mechanically mediated crosstalk in heart -- Swelling-and stretch-activated chloride channels in the heart: regulation and function -- Role of stretch-activated channels in the heart: action potential and Ca2+ transients -- Isolated cardiomyocytes: mechanosensitivity of action potential, membrane current and ion concentration -- Mechano-electric feedback in the heart: evidence from intracellular microelectrode recordings on multicellular preparations and single cells from healthy and diseased tissue -- The Role of mechanosensitive fibroblasts in the heart -- Mechanical modulation of intracellular ion concentrations: mechanisms and electrical consequences -- Stretch-induced slow force response in mammalian ventricular myocardium -- The Na+/H+ exchanger as the main protagonist following myocardial stretch: the Anrep effect and myocardial hypertrophy -- Mechano-electric feedback and atrial arrhythmias -- The Role of mechano-electrical feedback in the cholinergic atrial fibrillation initiation --; Mechanosensitive cation channels of leech neurons -- Mechanosensitivity of primary afferent nociceptors in the pain pathway -- Stimulus-secretion coupling in the osmoreceptive prolactin cell of the tilapia -- Stretch-inactivated channels in skeletal muscle -- Stretch-activated cation channels and the myogenic response of small arteries -- Mechanobiology of bone tissue and bone cells -- Functional roles of mechanosensitive ion channels, ss1 integrins and kinase cascades in chondrocyte mechanotransduction -- Enigmatic roles of the epithelial sodium channel (ENaC) in articular chondrocytes and osteoblasts: mechanotransduction, sodium transport or extracellular sodium sensing?
  • The three-dimensional structure of proteins. -- Liquid chromatography of biomolecules. -- Mass spectrometry. -- X-ray structural analysis. -- Protein infrared spectroscopy. -- Electron microscopy. -- Scanning probe microscopy. -- Biophysical nanotechnology. -- Proteomics: high throughput protein functional analysis. -- Ion mobility spectrometry. -- Ø-value analysis. -- Evolutionary computer programming. -- Conclusions.
  • This volume of the series Biophysics for the Life Sciences focuses on the conceptual framework and major research tools of contemporary molecular biophysics. It is designed to enable non-specialists -both students and professionals in other fields - to understand how these approaches can be used across the biosciences and in medicine, agriculture, biotechnology, pharmaceutical development and other fields. The scope of this volume is appropriate for advanced undergraduate and graduate courses in biophysics and biophysical chemistry. The book begins with an overview of the development of molecular biophysics and a brief survey of structural, physical, and chemical principles. Subsequent chapters written by experts present, with examples, the major experimental methods: optical spectroscopy, X-ray and neutron diffraction and scattering, nuclear magnetic resonance, electron paramagnetic resonance, mass spectrometry, and single molecule methods. The relationship between the biophysical properties of biological macromolecules and their roles as molecular machines is emphasized throughout and illustrated with three examples DNA helicases, rotary motor ATPases, and myosin.The concluding chapter discusses future prospects in X-ray and neutron scattering, mass spectrometry, and pharmaceutical development.
  • Structure of Matter -- Radioactive Decay -- Kinetics of Radioactive Decay -- Statistics of Radiation Counting -- Production of Radionuclides -- Interaction of Radiation with Matter -- Gas-Filled Detectors -- Scintillation and Semiconductor Detectors -- Gamma Cameras -- Performance Parameters of Gamma Cameras -- Digital Computers in Nuclear Medicine -- Single Photon Emission Computed Tomography -- Positron Emission Tomography -- Internal Radiation Dosimetry -- Radiation Biology -- Radiation Regulations and Protection.
  • Terminology, the standard human, and scaling -- Statics of the body -- Motion -- Mechanical properties of the body -- Muscles -- Metabolism: energy, heat, work, and power -- Fluid pressure, fluid flow in the body, and motion in fluids -- Cardiovascular system -- Lungs and breathing -- Sound, speech, and hearing -- Light, eyes, and vision -- Electrical and magnetic properties -- Feedback and control -- Appendix A. Symbols and units -- Appendix B. Locator of major anatomical and anthropometric information -- Appendix C. Differential equations -- Appendix D. Similar model systems -- Appendix E. Biophysics of the human body.
  • Star polymer surface passivation for single-molecule detection / Jürgen Groll and Martin Moeller -- Azide-specific labeling of biomolecules by Staudinger-Bertozzi ligation: phosphine derivatives of fluorescent probes suitable for single-molecule fluorescence spectroscopy / Anirban Chakraborty ... [et al.] -- Preparation of fluorescent pre-mRNA substrates for an smFRET study of pre-mRNA splicing in yeast / John Abelson, Haralambos Hadjivassiliou and Christine Guthrie -- Nanovesicle trapping for studying weak protein interactions by single-molecule FRET / Jaime J. Benítez, Aaron M. Keller and Peng Chen -- Droplet confinement and fluorescence measurement of single molecules / Lori S. Goldner, Ana M. Jofre and Jianyong Tang -- Single-molecule fluorescence spectroscopy using phospholipid bilayer nanodiscs / Abhinav Nath ... [et al.] -- Single-molecule spectroscopy using microfluidic platforms / Samuel Kim and Richard N. Zare -- Detection of protein-protein interactions in the live cell plasma membrane by quantifying prey redistribution upon bait micropatterning / Julian Weghuber ... [et al.] -- Analysis of complex single-molecule FRET time trajectories / Mario Blanco and Nils G. Walter -- Single-molecule fluorescence studies of intrinsically disordered proteins / Allan Chris M. Ferreon ... [et al.] -- Measuring the energetic coupling of tertiary contacts in RNA folding using single molecule fluorescence resonance energy transfer / Max Greenfield and Daniel Herschlag -- A highly purified, fluorescently labeled in vitro translation system for single-molecule studies of protein synthesis / Jingyi Fei ... [et al.] -- Watching individual proteins acting on single molecules of DNA / Ichiro Amitani ... [et al.] -- DNA curtains for high-throughput single-molecule optical imaging / Eric C. Greene ... [et al.] -- Scanning FCS for the characterization of protein dynamics in live cells / Zdenĕk Petrás̆ek, Jonas Ries and Petra Schwille -- Observing protein interactions and their stoichiometry in living cells by brightness analysis of fluorescence fluctuation experiments / Yan Chen ... [et al.] -- Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes / Arjin Raj and Sanjay Tyagi -- Single mRNA tracking in live cells / Hye Yoon Park, Adina R. Buxbaum and Robert H. Singer -- Single-molecule sequencing: sequence methods to enable accurate quantitation / Christopher Hart ... [et al.] -- Real-time DNA sequencing from single polymerase molecules / Jonas Korlach ... [et al.].
  • Single-molecule measurement techniques are providing fundamental information on the structure and function of biomolecules and are becoming an indispensable tool to understand how proteins work. During the last two decades, this field has grown at an almost exponential rate in terms of biological and biophysical applications. Single-molecule techniques have opened new fields of science that are at the crossroads of several disciplines such as biology, physics, chemistry, material science and computer science. These methods are often the approach of choice to clarify and better understand the structure and function of single proteins. This volume consists of up-to-date and comprehensive reviews of important and timely applications of different biological problems tackled by single-molecule methods; it also covers basic principles of operation, experiment and theory.In Single-molecule Studies of Proteins, expert researchers discuss the successful application of single-molecule techniques to a wide range of biological events, such as the imaging and mapping of cell surface receptors, the analysis of the unfolding and folding pathways of single proteins, the analysis interaction forces between biomolecules, the study of enzyme catalysis or the visualization of molecular motors in action. The chapters are aimed at established investigators and post-doctoral researchers in the life sciences wanting to pursue research in the various areas in which single-molecule approaches are important; this volume also remains accessible to advanced graduate students seeking similar research goals.
  • Transient kinetics, flourescence, and FRET in studies of initiation and translation in bacteria / Pohl Milon ... [et al.] -- Binding of mRNA to the bacterial translation initiation complex / Sean M. Studer and Simpson Joseph -- Real-time dynamics of ribosome-ligand interaction by time-resolved chemical probing methods / Attilio Fabbretti ... [et al] -- Overexpression and purification of mammalian mitochondrial translational initiation factor 2 and initiation factor 3 / Domenick G. Grasso ... [et al.] -- In vitro studies of archaeal translational initiation / Dario Benelli and Paola Londei -- Reconstitution of yeast translation initiation / Michael G. Acker ... [et al.] -- Assembly and analysis of eukaryotic translation initiation complexes / Andrey V. Pisarev -- Reconstitution of mammalian 48S ribosomal translation initiation complex / Romit Majumdar, Jayanta Chaudhuri, and Umadas Maitra -- Biophysical approach to studies of Cap-elF4E interaction by synthetic cap analogs / Anna Niedzwiecka ... [et al.] -- Biophysical studies of the translation initiation pathway with immobilized mRNA analogs / John E. G. McCarthy, Steven Marsden, and Tobias von der Haar -- Protection-based assays to measure aminoacyl-tRNA binding to translation initiation factors / Yves Mechulam ... [et al.] -- NMR methods for studying protein-protein interactions involved in translation initiation / Assen Marintchev, Dominique Frueh, and Gerhard Wagner -- Structural methods for studying IRES function / Jeffrey S. Kieft ... [et al.].
  • Ultrahigh-resolution optical coherence tomography using femtosecond lasers /J. G. Fujimoto ... [et al.] --Two-photon laser scanning microscopy /A. Nimmerjahn, P. Theer, F. Helmchen --Femtosecond lasers in ophthalmology: surgery and imaging /J. F. Bille --Ultrafast peptide and protein dynamics by vibrational spectroscopy /P. Hamm --Photosynthetic light-harvesting /T. Pullerits, T. Polivka, V. Sundström --Primary photosynthetic energy conversion in bacterial reaction centers /W. Zinth, J. Wachtveitl --Ultrafast primary reactions in the photosystems of oxygen-evolving organisms /A. R. Holzwarth --Primary photochemistry in the photoactive yellow protein: the prototype xanthopsin /D. S. Larsen, R. van Grondelle, K. J. Hellingwerf --Structure based kinetics by time-resolved X-ray crystallography /M. Schmidt --Primary reactions in retinal proteins /R. Diller --Ultrashort laser pulses in single molecule spectroscopy /E. Houstein, P. Schwille.
  • A number of techniques to study ion channels have been developed since the electrical basis of excitability was first discovered. Ion channel biophysicists have at their disposal a rich and ever-growing array of instruments and reagents to explore the biophysical and structural basis of sodium channel behavior. Armed with these tools, researchers have made increasingly dramatic discoveries about sodium channels, culminating most recently in crystal structures of voltage-gated sodium channels from bacteria. These structures, along with those from other channels, give unprecedented insight into the structural basis of sodium channel function. This volume of the Handbook of Experimental Pharmacology will explore sodium channels from the perspectives of their biophysical behavior, their structure, the drugs and toxins with which they are known to interact, acquired and inherited diseases that affect sodium channels and the techniques with which their biophysical and structural properties are studied.
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