Computational Modeling And Simulations Of Biomolecular Systems

Computational Modeling And Simulations Of Biomolecular Systems
Author: Benoit Roux
Publisher: World Scientific
Total Pages: 209
Release: 2021-08-23
Genre: Computers
ISBN: 9811232776

This textbook originated from the course 'Simulation, Modeling, and Computations in Biophysics' that I have taught at the University of Chicago since 2011. The students typically came from a wide range of backgrounds, including biology, physics, chemistry, biochemistry, and mathematics, and the course was intentionally adapted for senior undergraduate students and graduate students. This is not a highly technical book dedicated to specialists. The objective is to provide a broad survey from the physical description of a complex molecular system at the most fundamental level, to the type of phenomenological models commonly used to represent the function of large biological macromolecular machines.The key conceptual elements serving as building blocks in the formulation of different levels of approximations are introduced along the way, aiming to clarify as much as possible how they are interrelated. The only assumption is a basic familiarity with simple mathematics (calculus and integrals, ordinary differential equations, matrix linear algebra, and Fourier-Laplace transforms).

Water in Biological and Chemical Processes

Water in Biological and Chemical Processes
Author: Biman Bagchi
Publisher: Cambridge University Press
Total Pages: 383
Release: 2013-11-14
Genre: Medical
ISBN: 1107037298

A unified overview of the dynamical properties of water and its unique and diverse role in biological and chemical processes.

Biological Water

Biological Water
Author: Gertz I. Likhtenshtein
Publisher: Springer Nature
Total Pages: 523
Release: 2021-10-21
Genre: Science
ISBN: 3030825035

This book embraces all physiochemical aspects of the structure and molecular dynamics of water, focusing on its role in biological objects, e.g. living cells and tissue, and in the formation of functionally active structures of biological molecules and their ensembles. Water is the single most abundant chemical found in all living things. It offers a detailed look into the latest modern physical methods for studying the molecular structure and dynamics of the water and provides a critical analysis of the existing literature data on the properties of water in biological objects. Water as a chemical reagent and as a medium for the formation of conditions for enzymatic catalysis is a core focus of this book. Although well suited for active researchers, the book as a whole, as well as each chapter on its own, can be used as fundamental reference material for graduate and undergraduate students throughout chemistry, physics, biophysics and biomedicine.

Spectroscopy and Modeling of Biomolecular Building Blocks

Spectroscopy and Modeling of Biomolecular Building Blocks
Author: Jean-Pierre Schermann
Publisher: Elsevier
Total Pages: 499
Release: 2007-10-16
Genre: Science
ISBN: 0080558224

Spectroscopy and Modeling of Biomolecular Building Blocks presents an overview of recent advances in the intertwining of the following research fields: photon and electron spectroscopy, quantum chemistry, modelling and mass-spectrometry. The coupling of these disciplines offers a new point of view to the understanding of isolated elementary building blocks of biomolecules and their assemblies. It allows the unambiguous separation between intrinsic properties of biomolecular systems and those induced by the presence of their environment. The first chapters provide background in modelling (I), frequency-resolved spectroscopy using microwave, infrared and UV photons, time-resolved spectroscopy in the femtosecond domain and energy-resolved electron spectroscopy (II) and production of gas-phase neutral and ionic biomolecular species, mass-spectrometry, ion mobility and BIRD techniques (III). Chapter IV is devoted to case studies of gas-phase experimental investigations coupled to quantum or classical calculations. The topics are structural studies of nucleobases and oligonucleotides, peptides and proteins, sugars; neuromolecules; non-covalent complexes; chiral systems, interactions of low-energy electrons with biomolecules in the radiation chemistry context and very large gas-phase biomolecular systems. The fifth chapter concerns the link between gas-phase and liquid-phase. Different treatments of solvation are illustrated through examples pointing out the influence of progressive addition of water molecules upon properties of nucleobases, peptides, sugars and neuromolecules. - Offer a new perspective to the understanding of isolated elementary building blocks of bio molecules - Includes case studies of experimental investigations coupled to quantum or classical calculations

Radiation Damage in Biomolecular Systems

Radiation Damage in Biomolecular Systems
Author: Gustavo García Gómez-Tejedor
Publisher: Springer Science & Business Media
Total Pages: 508
Release: 2012-01-05
Genre: Science
ISBN: 9400725639

Since the discovery of X-rays and radioactivity, ionizing radiations have been widely applied in medicine both for diagnostic and therapeutic purposes. The risks associated with radiation exposure and handling led to the parallel development of the field of radiation protection. Pioneering experiments done by Sanche and co-workers in 2000 showed that low-energy secondary electrons, which are abundantly generated along radiation tracks, are primarily responsible for radiation damage through successive interactions with the molecular constituents of the medium. Apart from ionizing processes, which are usually related to radiation damage, below the ionization level low-energy electrons can induce molecular fragmentation via dissociative processes such as internal excitation and electron attachment. This prompted collaborative projects between different research groups from European countries together with other specialists from Canada, the USA and Australia. This book summarizes the advances achieved by these research groups after more than ten years of studies on radiation damage in biomolecular systems. An extensive Part I deals with recent experimental and theoretical findings on radiation induced damage at the molecular level. It includes many contributions on electron and positron collisions with biologically relevant molecules. X-ray and ion interactions are also covered. Part II addresses different approaches to radiation damage modelling. In Part III biomedical aspects of radiation effects are treated on different scales. After the physics-oriented focus of the previous parts, there is a gradual transition to biology and medicine with the increasing size of the object studied. Finally, Part IV is dedicated to current trends and novel techniques in radiation reserach and the applications hence arising. It includes new developments in radiotherapy and related cancer therapies, as well as technical optimizations of accelerators and totally new equipment designs, giving a glimpse of the near future of radiation-based medical treatments.

Water and Ions in Biological Systems

Water and Ions in Biological Systems
Author: Alberte Pullman
Publisher: Springer
Total Pages: 848
Release: 1985-07
Genre: Science
ISBN:

As the First International Conference on Water and Ions in Biological Systems (Bucharest, June 25-27, 1980) was appreciated as a success, a second one was organized in the fall of the year 1982 under the sponsorship of the United Nations Educational, Scientific and Cultural Organization (UNESCO), the Romanian Academy of Medical Sciences, the Romanian Biophysical Society (Union of Societies for Medical Sciences in the Socialist Republic of Romania) and in co operation with the International Union for Pure and Applied Bio physics (IUPAB). The responsibility for the scientific program and organization of the Second Conference on Water fell on an International Scientific Committee which included Prof. J. Tigyi (Pees), President of the UNESCO Expert Committee on Biophysics, Prof. K. Wuthrich, Secretary General of IUPAB and Prof. H. Eisenberg, (member of the IUPAB Council) under the guidance of an Executive Board whose members were Prof. J. Jaz (representative of UNESCO), Prof. B. Pullman (Vice President of IUPAB) and Prof. V. Vasilescu (President of the Romanian Biophysical Society). The Meeting was attended by more than 250 specialists including 150 Romanian participants and others from Bulgaria, Czechoslovakia, England, the Federal Republic of Germany, the German Democratic Republic, Greece, Hungary, India, Israel, Italy, Japan, the Netherlands, Nigeria, Poland, Sweden, Switzerland, USSR, USA, Venezuela, Yugoslavia. The proceedings of the Conference took place in the Medical Faculty of Bucharest. The theoretical and practical importance of the Meeting was pointed out by the speakers, among whom were Prof.

Biomolecular Simulations

Biomolecular Simulations
Author: Massimiliano Bonomi
Publisher: Humana
Total Pages: 581
Release: 2020-08-14
Genre: Science
ISBN: 9781493996100

This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.

Radiation Damage in Biomolecular Systems

Radiation Damage in Biomolecular Systems
Author: Gustavo García Gómez-Tejedor
Publisher: Springer Science & Business Media
Total Pages: 508
Release: 2012-01-04
Genre: Science
ISBN: 9400725647

Since the discovery of X-rays and radioactivity, ionizing radiations have been widely applied in medicine both for diagnostic and therapeutic purposes. The risks associated with radiation exposure and handling led to the parallel development of the field of radiation protection. Pioneering experiments done by Sanche and co-workers in 2000 showed that low-energy secondary electrons, which are abundantly generated along radiation tracks, are primarily responsible for radiation damage through successive interactions with the molecular constituents of the medium. Apart from ionizing processes, which are usually related to radiation damage, below the ionization level low-energy electrons can induce molecular fragmentation via dissociative processes such as internal excitation and electron attachment. This prompted collaborative projects between different research groups from European countries together with other specialists from Canada, the USA and Australia. This book summarizes the advances achieved by these research groups after more than ten years of studies on radiation damage in biomolecular systems. An extensive Part I deals with recent experimental and theoretical findings on radiation induced damage at the molecular level. It includes many contributions on electron and positron collisions with biologically relevant molecules. X-ray and ion interactions are also covered. Part II addresses different approaches to radiation damage modelling. In Part III biomedical aspects of radiation effects are treated on different scales. After the physics-oriented focus of the previous parts, there is a gradual transition to biology and medicine with the increasing size of the object studied. Finally, Part IV is dedicated to current trends and novel techniques in radiation reserach and the applications hence arising. It includes new developments in radiotherapy and related cancer therapies, as well as technical optimizations of accelerators and totally new equipment designs, giving a glimpse of the near future of radiation-based medical treatments.