Physical Chemical Understanding Of Membrane Partitioning And Permeation At An Atomic Resolution

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Physical-chemical Understanding of Membrane Partitioning and Permeation at an Atomic Resolution

Author : Tahani Ossman
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (128 download)

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Book Synopsis Physical-chemical Understanding of Membrane Partitioning and Permeation at an Atomic Resolution by : Tahani Ossman

Download or read book Physical-chemical Understanding of Membrane Partitioning and Permeation at an Atomic Resolution written by Tahani Ossman and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The mechanism of interaction between drugs or any xenobiotic and membrane is one of thekey factors that affect its biological of action, and so its therapeutic activity. A thoroughrationalization of the relationship between the intrinsic properties of the xenobiotics and theirmechanism of interaction with membranes can now be assessed with atomistic details.Molecular dynamics (MD) is a powerful research tool to study xenobiotics-membraneinteractions, which can access time and space scales that are not simultaneously accessibleby experimental methods. Semi-quantitative molecular and thermodynamic descriptions ofthese interactions can be provided using in silico model of lipid bilayers, often in agreementwith experimental measurements.The main goal of our investigation consisted to get in depth insight into the mechanisms ofinteraction/partitioning/insertion/crossing with/in/into/through membrane and drug deliveryusing MD. In this thesis, we have focused on both drugs used in renal transplantation (e.g.,antivirals, immunosuppressants) and antioxidants, which can also be used to protect organsalong the transplantation processes. We have provided a series of clues showing that MDsimulations can tackle the delicate process of drug passive permeation.Both, unbiased and biased MD (z-constraint) simulations have been used to elucidate thexenobiotics-membrane interactions (i.e., positioning and orientation) and to evaluate crossingenergies, diffusion coefficients, and permeability coefficients. These findings led us to drawqualitative structure-permeability relationships (SPR). We have carefully analyzed how thechemical and physical properties of xenobiotics affect the mechanism of interactions andthus permeability. The robustness of these MD-based methodologies has been determinedto qualitatively predict these pharmacological parameters. Hydrophobic compounds showeda favorable partitioning into the lipid bilayer and relatively low Gibbs energy of crossing thecenter of membrane (Î”Gcross). Hydrophilic or charged compounds showed partitioning closeto membrane surface, in interaction with the polar head groups and water molecules; this hasbeen shown to dramatically increase Î”Gcross. Amphiphilic compounds are intermediatecompounds in terms of membrane insertion/positioning/crossing. It clearly appears that theyshould be analyzed case by case, an analysis for which MD simulations could be particularlysupportive. Also the influence of size at predicting permeation has been studied (i.e.,relatively large drugs were tested). The molecular size has shown no significant influence onÎ”Gcross whereas diffusion coefficients were significantly affected, depending on themembrane regions.

Free Energy Calculations

Author : Christophe Chipot
Publisher : Springer Science & Business Media
ISBN 13 : 3540384472
Total Pages : 528 pages
Book Rating : 4.5/5 (43 download)

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Book Synopsis Free Energy Calculations by : Christophe Chipot

Download or read book Free Energy Calculations written by Christophe Chipot and published by Springer Science & Business Media. This book was released on 2007-01-08 with total page 528 pages. Available in PDF, EPUB and Kindle. Book excerpt: Free energy constitutes the most important thermodynamic quantity to understand how chemical species recognize each other, associate or react. Examples of problems in which knowledge of the underlying free energy behaviour is required, include conformational equilibria and molecular association, partitioning between immiscible liquids, receptor-drug interaction, protein-protein and protein-DNA association, and protein stability. This volume sets out to present a coherent and comprehensive account of the concepts that underlie different approaches devised for the determination of free energies. The reader will gain the necessary insight into the theoretical and computational foundations of the subject and will be presented with relevant applications from molecular-level modelling and simulations of chemical and biological systems. Both formally accurate and approximate methods are covered using both classical and quantum mechanical descriptions. A central theme of the book is that the wide variety of free energy calculation techniques available today can be understood as different implementations of a few basic principles. The book is aimed at a broad readership of graduate students and researchers having a background in chemistry, physics, engineering and physical biology.

Drug-Membrane Interactions

Author : Joachim K. Seydel
Publisher : John Wiley & Sons
ISBN 13 : 3527616497
Total Pages : 367 pages
Book Rating : 4.5/5 (276 download)

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Book Synopsis Drug-Membrane Interactions by : Joachim K. Seydel

Download or read book Drug-Membrane Interactions written by Joachim K. Seydel and published by John Wiley & Sons. This book was released on 2009-07-10 with total page 367 pages. Available in PDF, EPUB and Kindle. Book excerpt: Barrier, reservoir, target site - those are but some of the possible functions of biological lipid membranes in the complex interplay of drugs with the organism. A detailed knowledge of lipid membranes and of the various modes of drug-membrane interaction is therefore the prerequisite for a better understanding of drug action. Many of today's pharmaceuticals are amphiphilic or catamphiphilic, enabling them to interact with biological membranes. Crucial membrane properties are surveyed and techniques to elucidate drug-membrane interactions presented, including computer-aided predictions. Effects of membrane interaction on drug action and drug distribution are discussed, and numerous examples are given. This unique reference volume builds on the authors' long experience in the study of drug-membrane interaction. Recommended reading for everyone involved in pharmaceutical research.

Absorption and Drug Development

Author : Alex Avdeef
Publisher : John Wiley & Sons
ISBN 13 : 0471450251
Total Pages : 313 pages
Book Rating : 4.4/5 (714 download)

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Book Synopsis Absorption and Drug Development by : Alex Avdeef

Download or read book Absorption and Drug Development written by Alex Avdeef and published by John Wiley & Sons. This book was released on 2003-09-19 with total page 313 pages. Available in PDF, EPUB and Kindle. Book excerpt: Many times drugs work fine when tested outside the body, but when they are tested in the body they fail. One of the major reasons a drug fails is that it cannot be absorb by the body in a way to have the effect it was intended to have. Permeability, Solubility, Dissolution, and Charged State of Ionizable Molecules: Helps drug discovery professionals to eliminate poorly absorbable molecules early in the drug discovery process, which can save drug companies millions of dollars. Extensive tabulations, in appendix format, of properties and structures of about 200 standard drug molecules.

Membrane Hydration

Author : E. Anibal Disalvo
Publisher : Springer
ISBN 13 : 3319190601
Total Pages : 295 pages
Book Rating : 4.3/5 (191 download)

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Book Synopsis Membrane Hydration by : E. Anibal Disalvo

Download or read book Membrane Hydration written by E. Anibal Disalvo and published by Springer. This book was released on 2015-10-05 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is about the importance of water in determining the structure, stability and responsive behavior of biological membranes. Water confers to lipid membranes unique features in terms of surface and mechanical properties. The analysis of the hydration forces, plasticiser effects, controlled hydration, formation of microdomains of confined water suggests that water is an active constituent in a water-lipid system. The chapters describe water organization at the lipid membrane–water interphase, the water penetration, the long range water structure in the presence of lipid membranes by means of X-ray and neutron scattering, general polarization, fluorescent probes, ATR-FTIR and near infrared spectroscopies, piezo electric methods, computer simulation and surface thermodynamics. Permeation, percolation, osmotic stress, polarization, protrusion, sorption, hydrophobicity, density fluctuations are treated in detail in self-assembled bilayers. Studies in lipid monolayers show the correlation of surface pressure with water activity and its role in peptide and enzyme interactions. The book concludes with a discussion on anhydrobiosis and the effect of water replacement in microdomains and its consequence for cell function. New definitions of lipid/water interphases consider water not only as a structural-making solvent but as a mediator in signalling metabolic activity, modulating protein insertion and enzymatic activity, triggering oscillatory reactions and functioning of membrane bound receptors. Since these effects occur at the molecular level, membrane hydration appears fundamental to understand the behavior of nano systems and confined environments mimicking biological systems. These insights in structural, thermodynamical and mechanical water properties give a base for new paradigms in membrane structure and function for those interested in biophysics, physical chemistry, biology, bio and nano medicine, biochemistry, biotechnology and nano sciences searching for biotechnological inputs in human health, food industry, plant growing and energy conversion.

The Giant Vesicle Book

Author : Rumiana Dimova
Publisher : CRC Press
ISBN 13 : 1351648551
Total Pages : 1144 pages
Book Rating : 4.3/5 (516 download)

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Book Synopsis The Giant Vesicle Book by : Rumiana Dimova

Download or read book The Giant Vesicle Book written by Rumiana Dimova and published by CRC Press. This book was released on 2019-11-19 with total page 1144 pages. Available in PDF, EPUB and Kindle. Book excerpt: Giant vesicles are widely used as a model membrane system, both for basic biological systems and for their promising applications in the development of smart materials and cell mimetics, as well as in driving new technologies in synthetic biology and for the cosmetics and pharmaceutical industry. The reader is guided to use giant vesicles, from the formation of simple membrane platforms to advanced membrane and cell system models. It also includes fundamentals for understanding lipid or polymer membrane structure, properties and behavior. Every chapter includes ideas for further applications and discussions on the implications of the observed phenomena towards understanding membrane-related processes. The Giant Vesicle Book is meant to be a road companion, a trusted guide for those making their first steps in this field as well as a source of information required by experts. Key Features • A complete summary of the field, covering fundamental concepts, practical methods, core theory, and the most promising applications • A start-up package of theoretical and experimental information for newcomers in the field • Extensive protocols for establishing the required preparations and assays • Tips and instructions for carefully performing and interpreting measurements with giant vesicles or for observing them, including pitfalls • Approaches developed for investigating giant vesicles as well as brief overviews of previous studies implementing the described techniques • Handy tables with data and structures for ready reference

Structure and Dynamics of Confined Polymers

Author : John J. Kasianowicz
Publisher : Springer Science & Business Media
ISBN 13 : 9781402006975
Total Pages : 46 pages
Book Rating : 4.0/5 (69 download)

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Book Synopsis Structure and Dynamics of Confined Polymers by : John J. Kasianowicz

Download or read book Structure and Dynamics of Confined Polymers written by John J. Kasianowicz and published by Springer Science & Business Media. This book was released on 2002-07-31 with total page 46 pages. Available in PDF, EPUB and Kindle. Book excerpt: Polymers are essential to biology because they can have enough stable degrees of freedom to store the molecular code of heredity and to express the sequences needed to manufacture new molecules. Through these they perform or control virtually every function in life. Although some biopolymers are created and spend their entire career in the relatively large free space inside cells or organelles, many biopolymers must migrate through a narrow passageway to get to their targeted destination. This suggests the questions: How does confining a polymer affect its behavior and function? What does that tell us about the interactions between the monomers that comprise the polymer and the molecules that confine it? Can we design and build devices that mimic the functions of these nanoscale systems? The NATO Advanced Research Workshop brought together for four days in Bikal, Hungary over forty experts in experimental and theoretical biophysics, molecular biology, biophysical chemistry, and biochemistry interested in these questions. Their papers collected in this book provide insight on biological processes involving confinement and form a basis for new biotechnological applications using polymers. In his paper Edmund DiMarzio asks: What is so special about polymers? Why are polymers so prevalent in living things? The chemist says the reason is that a protein made of N amino acids can have any of 20 different kinds at each position along the chain, resulting in 20 N different polymers, and that the complexity of life lies in this variety.

Physical Biology of the Cell

Author : Rob Phillips
Publisher : Garland Science
ISBN 13 : 1134111584
Total Pages : 1089 pages
Book Rating : 4.1/5 (341 download)

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Book Synopsis Physical Biology of the Cell by : Rob Phillips

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

Research Awards Index

Author :
Publisher :
ISBN 13 :
Total Pages : 1230 pages
Book Rating : 4.:/5 (3 download)

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Book Synopsis Research Awards Index by :

Download or read book Research Awards Index written by and published by . This book was released on 1980 with total page 1230 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Methods in Membrane Lipids

Author : Alex M. Dopico
Publisher : Springer Science & Business Media
ISBN 13 : 1588296628
Total Pages : 1265 pages
Book Rating : 4.5/5 (882 download)

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Book Synopsis Methods in Membrane Lipids by : Alex M. Dopico

Download or read book Methods in Membrane Lipids written by Alex M. Dopico and published by Springer Science & Business Media. This book was released on 2007-08-30 with total page 1265 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents a compendium of methodologies for the study of membrane lipids, varying from traditional lab bench experimentation to computer simulation and theoretical models. The volume provides a comprehensive set of techniques for studying membrane lipids with a strong biophysical emphasis. It compares the various available techniques including the pros and cons as seen by the experts.

The Biophysics of Cell Membranes

Author : Richard M. Epand
Publisher : Springer
ISBN 13 : 9811062447
Total Pages : 224 pages
Book Rating : 4.8/5 (11 download)

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Book Synopsis The Biophysics of Cell Membranes by : Richard M. Epand

Download or read book The Biophysics of Cell Membranes written by Richard M. Epand and published by Springer. This book was released on 2017-09-25 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume focuses on the modulation of biological membranes by specific biophysical properties. The readers are introduced to emerging biophysical approaches that mimick specific states (like membrane lipid asymmetry, membrane curvature, lipid flip-flop, lipid phase separation) that are relevant to the functioning of biological membranes. The first chapter describes innovative methods to mimic the prevailing asymmetry in biological membranes by forming asymmetrical membranes made of monolayers with different compositions. One of the chapters illustrates how physical parameters, like curvature and elasticity, can affect and modulate the interactions between lipids and proteins. This volume also describes the sensitivity of certain ion channels to mechanical forces and it presents an analysis of how cell shape is determined by both the cytoskeleton and the lipid domains in the membrane. The last chapter provides evidence that liposomes can be used as a minimal cellular model to reconstitute processes related to the origin of life. Each topic covered in this volume is presented by leading experts in the field who are able to present clear, authoritative and up-to-date reviews. The novelty of the methods proposed and their potential for a deeper molecular description of membrane functioning are particularly relevant experts in the areas of biochemistry, biophysics and cell biology, while also presenting clear and thorough introductions, making the material suitable for students in these fields as well.

Lipid Domains

Author :
Publisher : Academic Press
ISBN 13 : 0128033274
Total Pages : 393 pages
Book Rating : 4.1/5 (28 download)

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Book Synopsis Lipid Domains by :

Download or read book Lipid Domains written by and published by Academic Press. This book was released on 2015-06-08 with total page 393 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current Topics in Membranes is targeted toward scientists and researchers in biochemistry and molecular and cellular biology, providing the necessary membrane research to assist them in discovering the current state of a particular field and in learning where that field is heading. This volume offers an up to date presentation of current knowledge in the field of Lipid Domains. Written by leading experts Contains original material, both textual and illustrative, that should become a very relevant reference material The material is presented in a very comprehensive manner Both researchers in the field and general readers should find relevant and up-to-date information

Understanding Molecular Simulation

Author : Daan Frenkel
Publisher : Elsevier
ISBN 13 : 0080519989
Total Pages : 661 pages
Book Rating : 4.0/5 (85 download)

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Book Synopsis Understanding Molecular Simulation by : Daan Frenkel

Download or read book Understanding Molecular Simulation written by Daan Frenkel and published by Elsevier. This book was released on 2001-10-19 with total page 661 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text. Since the first edition only five years ago, the simulation world has changed significantly -- current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on: Transition path sampling and diffusive barrier crossing to simulaterare events Dissipative particle dynamic as a course-grained simulation technique Novel schemes to compute the long-ranged forces Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations Multiple-time step algorithms as an alternative for constraints Defects in solids The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules Parallel tempering for glassy Hamiltonians Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.

A Research Agenda for Transforming Separation Science

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309491703
Total Pages : 115 pages
Book Rating : 4.3/5 (94 download)

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Book Synopsis A Research Agenda for Transforming Separation Science by : National Academies of Sciences, Engineering, and Medicine

Download or read book A Research Agenda for Transforming Separation Science written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2019-10-30 with total page 115 pages. Available in PDF, EPUB and Kindle. Book excerpt: Separation science plays a critical role in maintaining our standard of living and quality of life. Many industrial processes and general necessities such as chemicals, medicines, clean water, safe food, and energy sources rely on chemical separations. However, the process of chemical separations is often overlooked during product development and this has led to inefficiency, unnecessary waste, and lack of consensus among chemists and engineers. A reevaluation of system design, establishment of standards, and an increased focus on the advancement of separation science are imperative in supporting increased efficiency, continued U.S. manufacturing competitiveness, and public welfare. A Research Agenda for Transforming Separation Science explores developments in the industry since the 1987 National Academies report, Separation and Purification: Critical Needs and Opportunities. Many needs stated in the original report remain today, in addition to a variety of new challenges due to improved detection limits, advances in medicine, and a recent emphasis on sustainability and environmental stewardship. This report examines emerging chemical separation technologies, relevant developments in intersecting disciplines, and gaps in existing research, and provides recommendations for the application of improved separation science technologies and processes. This research serves as a foundation for transforming separation science, which could reduce global energy use, improve human and environmental health, and advance more efficient practices in various industries.

Molecular Simulations

Author : Saman Alavi
Publisher : John Wiley & Sons
ISBN 13 : 3527341056
Total Pages : 342 pages
Book Rating : 4.5/5 (273 download)

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Book Synopsis Molecular Simulations by : Saman Alavi

Download or read book Molecular Simulations written by Saman Alavi and published by John Wiley & Sons. This book was released on 2020-06-29 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides hands-on knowledge enabling students of and researchers in chemistry, biology, and engineering to perform molecular simulations This book introduces the fundamentals of molecular simulations for a broad, practice-oriented audience and presents a thorough overview of the underlying concepts. It covers classical mechanics for many-molecule systems as well as force-field models in classical molecular dynamics; introduces probability concepts and statistical mechanics; and analyzes numerous simulation methods, techniques, and applications. Molecular Simulations: Fundamentals and Practice starts by covering Newton's equations, which form the basis of classical mechanics, then continues on to force-field methods for modelling potential energy surfaces. It gives an account of probability concepts before subsequently introducing readers to statistical and quantum mechanics. In addition to Monte-Carlo methods, which are based on random sampling, the core of the book covers molecular dynamics simulations in detail and shows how to derive critical physical parameters. It finishes by presenting advanced techniques, and gives invaluable advice on how to set up simulations for a diverse range of applications. -Addresses the current need of students of and researchers in chemistry, biology, and engineering to understand and perform their own molecular simulations -Covers the nitty-gritty ? from Newton's equations and classical mechanics over force-field methods, potential energy surfaces, and probability concepts to statistical and quantum mechanics -Introduces physical, chemical, and mathematical background knowledge in direct relation with simulation practice -Highlights deterministic approaches and random sampling (eg: molecular dynamics versus Monte-Carlo methods) -Contains advanced techniques and practical advice for setting up different simulations to prepare readers entering this exciting field Molecular Simulations: Fundamentals and Practice is an excellent book benefitting chemist, biologists, engineers as well as materials scientists and those involved in biotechnology.

Membrane Biological Reactors

Author : Faisal I. Hai
Publisher : IWA Publishing
ISBN 13 : 1780400659
Total Pages : 484 pages
Book Rating : 4.7/5 (84 download)

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Book Synopsis Membrane Biological Reactors by : Faisal I. Hai

Download or read book Membrane Biological Reactors written by Faisal I. Hai and published by IWA Publishing. This book was released on 2013-11-01 with total page 484 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years the MBR market has experienced unprecedented growth. The best practice in the field is constantly changing and unique quality requirements and management issues are regularly emerging. Membrane Biological Reactors: Theory, Modeling, Design, Management and Applications to Wastewater Reuse comprehensively covers the salient features and emerging issues associated with the MBR technology. The book provides thorough coverage starting from biological aspects and fundamentals of membranes, via modeling and design concepts, to practitioners’ perspective and good application examples. Membrane Biological Reactors focuses on all the relevant emerging issues raised by including the latest research from renowned experts in the field. It is a valuable reference to the academic and professional community and suitable for undergraduate and postgraduate teaching in Environmental Engineering, Chemical Engineering and Biotechnology. Editors: Faisal I. Hai, University of Wollongong, Australia Kazuo Yamamoto, University of Tokyo, Japan Chung-Hak Lee, Seoul National University, Korea.

Coarse-Graining of Condensed Phase and Biomolecular Systems

Author : Gregory A. Voth
Publisher : CRC Press
ISBN 13 : 1420059564
Total Pages : 492 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Coarse-Graining of Condensed Phase and Biomolecular Systems by : Gregory A. Voth

Download or read book Coarse-Graining of Condensed Phase and Biomolecular Systems written by Gregory A. Voth and published by CRC Press. This book was released on 2008-09-22 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exploring recent developments in the field, Coarse-Graining of Condensed Phase and Biomolecular Systems examines systematic ways of constructing coarse-grained representations for complex systems. It explains how this approach can be used in the simulation and modeling of condensed phase and biomolecular systems. Assembling some of the most influential, world-renowned researchers in the field, this book covers the latest developments in the coarse-grained molecular dynamics simulation and modeling of condensed phase and biomolecular systems. Each chapter focuses on specific examples of evolving coarse-graining methodologies and presents results for a variety of complex systems. The contributors discuss the minimalist, inversion, and multiscale approaches to coarse-graining, along with the emerging challenges of coarse-graining. They also connect atomic-level information with new coarse-grained representations of complex systems, such as lipid bilayers, proteins, peptides, and DNA.