Download or read book Damage free Femtosecond Structural Dynamics of Proteins in the Biologically Relevant Regime written by Olivier Paré-Labrosse and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the first part of this work, we present two techniques that we developed to improve the existing protein serial crystallography technique. By implementing the first technique that we call "chip mapping", we were able to decrease the time it takes to acquire enough data to reconstruct a single protein's structure by a factor five. The second technique called oscillation serial crystallography allowed us to decrease by one order of magnitude the number of crystals needed to reconstruct said protein structure. In the second part of this work, we use transient absorption spectroscopy to measure the population dynamics in carboxymyoglobin when excited with different laser peak powers. This allowed us to fit a population dynamics model as a function of peak power allowing us to study the protein's nonlinear absorption properties. We report for the first time the linear and nonlinear absorption cross section of carboxymyoglobin as, respectively, \mbox{$\sigma_0 = (1.07 \pm .02) \times 10^{-16}$ cm$^2$} and \mbox{$\sigma_0^{(2)} = (1.45 \pm .15)\times 10^{-19}$ cm$^4$/GW}. The latter part is an attempt at providing the threshold for excitation conditions to ensure that the structural dynamics of interest are studied under 1-photon excitation conditions, which are the most relevant to elucidating the biologically relevant protein response. To date, this essential condition has yet to be rigorously met in femtosecond time resolved x-ray studies of structural dynamics of biological systems. In that context, this thesis work provides the important criteria for next generation experiments. Dans la première partie de cette thèse, nous présentons deux techniques que nous avons développées afin d'améliorer les techniques existantes de cristallographie en série. En développement une première technique que nous appelons "chip mapping", nous avons pu diminuer par cinq le temps nécessaire pour acquérir assez de données pour reconstruire la structure d'une protéine. Une seconde technique appelée cristallographie en série avec oscillations nous a permis de diminuer par un ordre de grandeur la quantité de cristaux requise pour reconstruire la structure de protéine mentionnée ci-haut. Dans la seconde partie de cette thèse, nous utilisons la spectroscopie par absorption transitoire pour mesurer la dynamique des populations dans la carboxymyoglobine lorsque excitée avec des impulsions laser de différentes puissances. Avec ces données, nous avons pu construire un modèle décrivant l'évolution temporelle des différentes espèces présentes, ainsi que les interactions interespèces et leurs propriétés d'absorption non linéaires. Nous présentons pour la première fois les sections efficaces d'absorption linéaire et non linéaire de la carboxymyoglobine qui sont, respectivement, \mbox{$\sigma_0 = (1.07 \pm .02) \times 10^{-16}$ cm$^2$} et \mbox{$\sigma_0^{(2)} = (1.45 \pm .15)\times 10^{-19}$ cm$^4$/GW}. Afin de s'assurer d'étudier des protéines dans des conditions pertinentes à la biologie structurelle qui se doit d'être un régime linéaire où un seul photon est absorbé par un chromophore; cette dernière partie se veut une tentative de démontrer l'existance de limites dans les conditions d'excitation par impulsions laser lors d'expériences de dynamique structurelle sur des protéines. À notre connaissance, ces conditions essentielles ont été que très peu utilisées et discutées dans la littérature de dynamiques structurelles femtosecondes de systèmes biologiques. Dans ce contexte, cette thèse fournie des critères importants pour les futures générations d'expériences de ce type.
Download or read book X Ray Free Electron Laser written by Kiyoshi Ueda and published by MDPI. This book was released on 2018-07-04 with total page 457 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a printed edition of the Special Issue "X-Ray Free-Electron Laser" that was published in Applied Sciences
Download or read book X ray Free Electron Lasers written by Sébastien Boutet and published by Springer. This book was released on 2018-12-27 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt: The timely volume describes recent discoveries and method developments that have revolutionized Structural Biology with the advent of X-ray Free Electron Lasers. It provides, for the first time, a comprehensive examination of this cutting-edge technology. It discusses of-the-moment topics such as growth and detection of nanocrystals, Sample Delivery Techniques for serial femtosecond crystallography, data collection methods at XFELs, and more. This book aims to provide the readers with an overview of the new methods that have been recently developed as well as a prospective on new methods under development. It highlights the most important and novel Structural Discoveries made recently with XFELS, contextualized with a big-picture discussion of future developments.
Download or read book Dynamics of Soft Matter written by VICTORIA GARCIA SAKAI and published by Springer Science & Business Media. This book was released on 2011-12-19 with total page 455 pages. Available in PDF, EPUB and Kindle. Book excerpt: Dynamics of Soft Matter: Neutron Applications provides an overview of neutron scattering techniques that measure temporal and spatial correlations simultaneously, at the microscopic and/or mesoscopic scale. These techniques offer answers to new questions arising at the interface of physics, chemistry, and biology. Knowledge of the dynamics at these levels is crucial to understanding the soft matter field, which includes colloids, polymers, membranes, biological macromolecules, foams, emulsions towards biological & biomimetic systems, and phenomena involving wetting, friction, adhesion, or microfluidics. Emphasizing the complementarities of scattering techniques with other spectroscopic ones, this volume also highlights the potential gain in combining techniques such as rheology, NMR, light scattering, dielectric spectroscopy, as well as synchrotron radiation experiments. Key areas covered include polymer science, biological materials, complex fluids and surface science.
Download or read book Homology Molecular Modeling written by Rafael Trindade Maia and published by BoD – Books on Demand. This book was released on 2021-03-10 with total page 147 pages. Available in PDF, EPUB and Kindle. Book excerpt: Homology modeling is an extremely useful and versatile technique that is gaining more and more space and demand in research in computational and theoretical biology. This book, “Homology Molecular Modeling - Perspectives and Applications”, brings together unpublished chapters on this technique. In this book, 7 chapters are intimately related to the theme of molecular modeling, carefully selected and edited for academic and scientific readers. It is an indispensable read for anyone interested in the areas of bioinformatics and computational biology. Divided into 4 sections, the reader will have a didactic and comprehensive view of the theme, with updated and relevant concepts on the subject. This book was organized from researchers to researchers with the aim of spreading the fascinating area of molecular modeling by homology.
Download or read book Time resolved Macromolecular Crystallography written by Royal Society (Great Britain) and published by Oxford [England] ; New York : Oxford University Press. This book was released on 1992 with total page 194 pages. Available in PDF, EPUB and Kindle. Book excerpt: The papers presented in this volume report the striking progress X-ray diffraction has facilitated in the study of structural molecular biology. Coupled with the revival of the Laue method, the advent of high-intensity synchrotron radiation sources has made possible the rapid collection of X-ray crystallography data, thereby allowing protein and virus crystallography to progress from studies of equilibrium structures to time-resolved studies of structures at reaction stages. The book also details the many recent technological developments in physics, chemistry and biochemistry that have been critical for the full exploitation of the synchrotron Laue method in the study of dynamic events in crystals. Necessary future developments are discussed.
Download or read book Beyond the Molecular Frontier written by National Research Council and published by National Academies Press. This book was released on 2003-03-19 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemistry and chemical engineering have changed significantly in the last decade. They have broadened their scopeâ€"into biology, nanotechnology, materials science, computation, and advanced methods of process systems engineering and controlâ€"so much that the programs in most chemistry and chemical engineering departments now barely resemble the classical notion of chemistry. Beyond the Molecular Frontier brings together research, discovery, and invention across the entire spectrum of the chemical sciencesâ€"from fundamental, molecular-level chemistry to large-scale chemical processing technology. This reflects the way the field has evolved, the synergy at universities between research and education in chemistry and chemical engineering, and the way chemists and chemical engineers work together in industry. The astonishing developments in science and engineering during the 20th century have made it possible to dream of new goals that might previously have been considered unthinkable. This book identifies the key opportunities and challenges for the chemical sciences, from basic research to societal needs and from terrorism defense to environmental protection, and it looks at the ways in which chemists and chemical engineers can work together to contribute to an improved future.
Download or read book Controlling the Quantum World written by National Research Council and published by National Academies Press. This book was released on 2007-06-21 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: As part of the Physics 2010 decadal survey project, the Department of Energy and the National Science Foundation requested that the National Research Council assess the opportunities, over roughly the next decade, in atomic, molecular, and optical (AMO) science and technology. In particular, the National Research Council was asked to cover the state of AMO science, emphasizing recent accomplishments and identifying new and compelling scientific questions. Controlling the Quantum World, discusses both the roles and challenges for AMO science in instrumentation; scientific research near absolute zero; development of extremely intense x-ray and laser sources; exploration and control of molecular processes; photonics at the nanoscale level; and development of quantum information technology. This book also offers an assessment of and recommendations about critical issues concerning maintaining U.S. leadership in AMO science and technology.
Download or read book Structural DNA Nanotechnology written by Nadrian C. Seeman and published by Cambridge University Press. This book was released on 2015 with total page 269 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by the founder of the field, this is a comprehensive and accessible introduction to structural DNA nanotechnology.
Download or read book Physical Biology of the Cell written by Rob Phillips and published by Garland Science. This book was released on 2012-10-29 with total page 1089 pages. Available in PDF, EPUB and Kindle. Book excerpt: Physical Biology of the Cell is a textbook for a first course in physical biology or biophysics for undergraduate or graduate students. It maps the huge and complex landscape of cell and molecular biology from the distinct perspective of physical biology. As a key organizing principle, the proximity of topics is based on the physical concepts that
Download or read book Macromolecular Crystallography written by Charles W. Carter and published by Gulf Professional Publishing. This book was released on 1997 with total page 756 pages. Available in PDF, EPUB and Kindle. Book excerpt: Annotation Accurate molecular structures is vital for rational drug design and for structure based functional studies directed toward the development of effective therapeutic agents and drugs. Crystallography can reliably predict structure, both in terms of folding and atomic details of bonding. * Phases * Map interpretation and refinement * Analysis and software.
Download or read book Visualizing Chemistry written by National Research Council and published by National Academies Press. This book was released on 2006-06-01 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientists and engineers have long relied on the power of imaging techniques to help see objects invisible to the naked eye, and thus, to advance scientific knowledge. These experts are constantly pushing the limits of technology in pursuit of chemical imagingâ€"the ability to visualize molecular structures and chemical composition in time and space as actual events unfoldâ€"from the smallest dimension of a biological system to the widest expanse of a distant galaxy. Chemical imaging has a variety of applications for almost every facet of our daily lives, ranging from medical diagnosis and treatment to the study and design of material properties in new products. In addition to highlighting advances in chemical imaging that could have the greatest impact on critical problems in science and technology, Visualizing Chemistry reviews the current state of chemical imaging technology, identifies promising future developments and their applications, and suggests a research and educational agenda to enable breakthrough improvements.
Download or read book Methods in Molecular Biophysics written by Nathan R. Zaccai and published by Cambridge University Press. This book was released on 2017-05-18 with total page 710 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current techniques for studying biological macromolecules and their interactions are based on the application of physical methods, ranging from classical thermodynamics to more recently developed techniques for the detection and manipulation of single molecules. Reflecting the advances made in biophysics research over the past decade, and now including a new section on medical imaging, this new edition describes the physical methods used in modern biology. All key techniques are covered, including mass spectrometry, hydrodynamics, microscopy and imaging, diffraction and spectroscopy, electron microscopy, molecular dynamics simulations and nuclear magnetic resonance. Each method is explained in detail using examples of real-world applications. Short asides are provided throughout to ensure that explanations are accessible to life scientists, physicists and those with medical backgrounds. The book remains an unparalleled and comprehensive resource for graduate students of biophysics and medical physics in science and medical schools, as well as for research scientists looking for an introduction to techniques from across this interdisciplinary field.
Download or read book Physics of and Science with X Ray Free Electron Lasers written by J. Hastings and published by IOS Press. This book was released on 2020-12-18 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many X-Ray Free-Electron Lasers (X-FELs) have been designed, built and commissioned since the first lasing of the Linac Coherent Light Source in the hard and soft X-ray regions, and great progress has been made in improving their performance and extending their capabilities. Meanwhile, experimental techniques to exploit the unique properties of X-FELs to explore atomic and molecular systems of interest to physics, chemistry, biology and the material sciences have also been developed. As a result, our knowledge of atomic and molecular science has been greatly extended. Nevertheless, there is still much to be accomplished, and the potential for discovery with X-FELs is still largely unexplored. The next generation of scientists will need to be well versed in both particle beams/FEL physics and X-ray photon science. This book presents material from the Enrico Fermi summer school: Physics of and Science with X-Ray Free-Electron Lasers, held at the Enrico Fermi International School of Physics in Varenna, Italy, from 26 June - 1 July 2017. The lectures presented at the school were aimed at introducing graduate students and young scientists to this fast growing and exciting scientific area, and subjects covered include basic accelerator and FEL physics, as well as an introduction to the main research topics in X-FEL-based biology, atomic molecular optical science, material sciences, high-energy density physics and chemistry. Bridging the gap between accelerator/FEL physicists and scientists from other disciplines, the book will be of interest to all those working in the field.
Download or read book Three dimensional Electron Microscopy of Macromolecular Assemblies written by Joachim Frank and published by Oxford University Press. This book was released on 2006 with total page 427 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cryoelectron microscopy of biological molecules is among the hottest growth areas in biophysics and structural biology at present, and Frank is arguably the most distinguished practitioner of this art. CryoEM is likely over the next few years to take over much of the structural approaches currently requiring X-ray crystallography, because one can now get good and finely detailed images of single molecules down to as little as 200,000 MW, covering a substantial share of the molecules of greatest biomedical research interest. This book, the successor to an earlier work published in 1996 with Academic Press, is a natural companion work to our forthcoming book on electron crystallography by Robert Glaeser, with contributions by six others, including Frank. A growing number of workers will employ CryoEM for structural studies in their own research, and a large proportion of biomedical researchers will have a growing interest in understanding what the capabilities and limits of this approach are.
Download or read book Handbook of Single Molecule Biophysics written by Peter Hinterdorfer and published by Springer Science & Business Media. This book was released on 2009-12-24 with total page 634 pages. Available in PDF, EPUB and Kindle. Book excerpt: This handbook describes experimental techniques to monitor and manipulate individual biomolecules, including fluorescence detection, atomic force microscopy, and optical and magnetic trapping. It includes single-molecule studies of physical properties of biomolecules such as folding, polymer physics of protein and DNA, enzymology and biochemistry, single molecules in the membrane, and single-molecule techniques in living cells.
Download or read book Dielectric Relaxation in Biological Systems written by Valerica Raicu and published by OUP Oxford. This book was released on 2015-07-23 with total page 451 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of dielectric properties of biological systems and their components is important not only for fundamental scientific knowledge but also for its applications in medicine, biology, and biotechnology. The associated technique - known as dielectric spectroscopy - has enabled researchers to quickly and accurately acquire time- or frequency-spectra of permittivity and conductivity and permitted the derivation and testing of realistic electrical models for cells and organelles. This text covers the theoretical basis and practical aspects of the study of dielectric properties of biological systems, such as water, electrolyte and polyelectrolytes, solutions of biological macromolecules, cells suspensions and cellular systems. The authors' combined efforts provide a comprehensive and cohesive book that takes advantage of the expertise of multiple scientists involved in cutting-edge research in the specific sub-fields of bio-dielectric spectroscopy while maintaining its self-consistency through numerous discussions. The first six chapters cover theoretical, methodological and experimental aspects of relaxation and dispersion in biological dielectrics at molecular, cellular and cellular aggregate level. Applications are presented in the following chapters which are organized in the order of increased complexity, beginning with pure water, amino acids and proteins, continuing with vesicles and simple cells such as erythrocytes, and then with more complex, organelle-containing cells and cellular aggregates. Due to its broad coverage, the text could be used as a reference book by researchers, and as a textbook for upper-level undergraduate classes and graduate classes in (bio) physics, medical physics, quantitative biology, and engineering.
