Enhancements To Implicit Solvent Modeling Of Peptides In Water And In Lipid Bilayers

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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.

Computational Modeling of Membrane Bilayers

Author : V. Sundararajan
Publisher : Academic Press
ISBN 13 : 0080879705
Total Pages : 493 pages
Book Rating : 4.0/5 (88 download)

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Book Synopsis Computational Modeling of Membrane Bilayers by : V. Sundararajan

Download or read book Computational Modeling of Membrane Bilayers written by V. Sundararajan and published by Academic Press. This book was released on 2011-08-29 with total page 493 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current Topics in Membranes provides a systematic, comprehensive, and rigorous approach to specific topics relevant to the study of cellular membranes. Each volume is a guest edited compendium of membrane biology. *Discusses the current stat of electrostatics in biomolecular simulations and future directions *Includes information on time and length scales in lipid bilayer simulations *Includes a chapter on the nature of lipid rafts

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.

Peptide-Lipid Interactions

Author : Sidney A. Simon
Publisher : Academic Press
ISBN 13 : 0080925855
Total Pages : 606 pages
Book Rating : 4.0/5 (89 download)

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Book Synopsis Peptide-Lipid Interactions by : Sidney A. Simon

Download or read book Peptide-Lipid Interactions written by Sidney A. Simon and published by Academic Press. This book was released on 2002-11-13 with total page 606 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains a comprehensive overview of peptide-lipid interactions by leading researchers. The first part covers theoretical concepts, experimental considerations, and thermodynamics. The second part presents new results obtained through site-directed EPR, electron microscopy, NMR, isothermal calorimetry, and fluorescence quenching. The final part covers problems of biological interest, including signal transduction, membrane transport, fusion, and adhesion. Key Features * world-renowned experts * state-of-the-art experimental methods * monolayers, bilayers, biological membranes * theoretical aspects and computer simulations * rafts * synaptic transmission * membrane fusion * signal transduction

COSMO-RS

Author : Andreas Klamt
Publisher : Elsevier
ISBN 13 : 0080455530
Total Pages : 247 pages
Book Rating : 4.0/5 (84 download)

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Book Synopsis COSMO-RS by : Andreas Klamt

Download or read book COSMO-RS written by Andreas Klamt and published by Elsevier. This book was released on 2005-07-26 with total page 247 pages. Available in PDF, EPUB and Kindle. Book excerpt: The COSMO-RS technique is a novel method for predicting the thermodynamic properties of pure and mixed fluids which are important in many areas, ranging from chemical engineering to drug design. COSMO-RS, From Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design is about this novel technology, which has recently proven to be the most reliable and efficient tool for the prediction of vapour-liquid equilibria. In contrast to group contribution methods, which depend on an extremely large number of experimental data, COSMO-RS calculates the thermodynamic data from molecular surface polarity distributions, resulting from quantum chemical calculations of the individual compounds in the mixture. In this book, the author cleverly combines a vivid overview of the partly demanding theoretical steps with a deeper analysis of their scientific background and justification. Aimed at theoretical chemists, computational chemists, physical chemists, chemical engineers, thermodynamicists as well as students,academic and industrial experts, COSMO-RS, From Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design provides a novel viewpoint to anyone looking to gain more insight into the theory and potential of the unique method, COSMO-RS. - The only book currently available on COSMO-RS technique - Provides a novel viewpoint for the scientific understanding and for the practical quantitative treatment of fluid phase thermodynamics - Includes illustrative examples of the COSMOtherm program

Amber 2021

Author : David A. Case
Publisher : University of California, San Francisco
ISBN 13 :
Total Pages : 959 pages
Book Rating : 4./5 ( download)

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Book Synopsis Amber 2021 by : David A. Case

Download or read book Amber 2021 written by David A. Case and published by University of California, San Francisco. This book was released on 2021-06-13 with total page 959 pages. Available in PDF, EPUB and Kindle. Book excerpt: Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful framework for many common calculations. The term Amber is also used to refer to the empirical force fields that are implemented here. It should be recognized, however, that the code and force field are separate: several other computer packages have implemented the Amber force fields, and other force fields can be implemented with the Amber programs. Further, the force fields are in the public domain, whereas the codes are distributed under a license agreement. The Amber software suite is divided into two parts: AmberTools21, a collection of freely available programs mostly under the GPL license, and Amber20, which is centered around the pmemd simulation program, and which continues to be licensed as before, under a more restrictive license. Amber20 represents a significant change from the most recent previous version, Amber18. (We have moved to numbering Amber releases by the last two digits of the calendar year, so there are no odd-numbered versions.) Please see https://ambermd.org for an overview of the most important changes. AmberTools is a set of programs for biomolecular simulation and analysis. They are designed to work well with each other, and with the “regular” Amber suite of programs. You can perform many simulation tasks with AmberTools, and you can do more extensive simulations with the combination of AmberTools and Amber itself. Most components of AmberTools are released under the GNU General Public License (GPL). A few components are in the public domain or have other open-source licenses. See the README file for more information.

Experimental Approaches of NMR Spectroscopy

Author : The Nuclear Magnetic Resonance Society of Japan
Publisher : Springer
ISBN 13 : 9811059667
Total Pages : 634 pages
Book Rating : 4.8/5 (11 download)

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Book Synopsis Experimental Approaches of NMR Spectroscopy by : The Nuclear Magnetic Resonance Society of Japan

Download or read book Experimental Approaches of NMR Spectroscopy written by The Nuclear Magnetic Resonance Society of Japan and published by Springer. This book was released on 2017-11-23 with total page 634 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the advanced developments in methodology and applications of NMR spectroscopy to life science and materials science. Experts who are leaders in the development of new methods and applications of life and material sciences have contributed an exciting range of topics that cover recent advances in structural determination of biological and material molecules, dynamic aspects of biological and material molecules, and development of novel NMR techniques, including resolution and sensitivity enhancement. First, this book particularly emphasizes the experimental details for new researchers to use NMR spectroscopy and pick up the potentials of NMR spectroscopy. Second, the book is designed for those who are involved in either developing the technique or expanding the NMR application fields by applying them to specific samples. Third, the Nuclear Magnetic Resonance Society of Japan has organized this book not only for NMR members of Japan but also for readers worldwide who are interested in using NMR spectroscopy extensively.

Molecular Modeling and Simulation

Author : Tamar Schlick
Publisher : Springer Science & Business Media
ISBN 13 : 0387224645
Total Pages : 669 pages
Book Rating : 4.3/5 (872 download)

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Book Synopsis Molecular Modeling and Simulation by : Tamar Schlick

Download or read book Molecular Modeling and Simulation written by Tamar Schlick and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 669 pages. Available in PDF, EPUB and Kindle. Book excerpt: Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text

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

Theory of Solutions

Author : John G. Kirkwood
Publisher : CRC Press
ISBN 13 : 9780677010304
Total Pages : 320 pages
Book Rating : 4.0/5 (13 download)

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Book Synopsis Theory of Solutions by : John G. Kirkwood

Download or read book Theory of Solutions written by John G. Kirkwood and published by CRC Press. This book was released on 2001-12 with total page 320 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Molecular and Cellular Biophysics

Author : Meyer B. Jackson
Publisher : Cambridge University Press
ISBN 13 : 9780521624411
Total Pages : 536 pages
Book Rating : 4.6/5 (244 download)

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Book Synopsis Molecular and Cellular Biophysics by : Meyer B. Jackson

Download or read book Molecular and Cellular Biophysics written by Meyer B. Jackson and published by Cambridge University Press. This book was released on 2006-01-12 with total page 536 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular and Cellular Biophysics provides advanced undergraduate and graduate students with a foundation in the basic concepts of biophysics. Students who have taken physical chemistry and calculus courses will find this book an accessible and valuable aid in learning how these concepts can be used in biological research. The text provides a rigorous treatment of the fundamental theories in biophysics and illustrates their application with examples. Conformational transitions of proteins are studied first using thermodynamics, and subsequently with kinetics. Allosteric theory is developed as the synthesis of conformational transitions and association reactions. Basic ideas of thermodynamics and kinetics are applied to topics such as protein folding, enzyme catalysis and ion channel permeation. These concepts are then used as the building blocks in a treatment of membrane excitability. Through these examples, students will gain an understanding of the general importance and broad applicability of biophysical principles to biological problems.

Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs

Author : Sumit Sharma
Publisher : Elsevier
ISBN 13 : 0128169559
Total Pages : 368 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs by : Sumit Sharma

Download or read book Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs written by Sumit Sharma and published by Elsevier. This book was released on 2019-08-09 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs presents the three major software packages used for the molecular dynamics simulation of nanocomposites. The book explains, in detail, how to use each of these packages, also providing real-world examples that show when each should be used. The latter two of these are open-source codes which can be used for modeling at no cost. Several case studies how each software package is used to predict various properties of nanocomposites, including metal-matrix, polymer-matrix and ceramic-matrix based nanocomposites. Properties explored include mechanical, thermal, optical and electrical properties. This is the first book that explores methodologies for using Materials Studio, Lammps and Gromacs in the same place. It will be beneficial for students, researchers and scientists working in the field of molecular dynamics simulation. - Gives a detailed explanation of basic commands and modules of Materials Studio, Lammps and Gromacs - Shows how Materials Studio, Lammps and Gromacs predict mechanical, thermal, electrical and optical properties of nanocomposites - Uses case studies to show which software should be used to solve a variety of nanoscale modeling problems

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.

Progress in Clinical and Biological Research

Author : George J. Brewer
Publisher :
ISBN 13 : 9780845151426
Total Pages : 520 pages
Book Rating : 4.1/5 (514 download)

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Book Synopsis Progress in Clinical and Biological Research by : George J. Brewer

Download or read book Progress in Clinical and Biological Research written by George J. Brewer and published by . This book was released on 1988 with total page 520 pages. Available in PDF, EPUB and Kindle. Book excerpt:

AB INITIO Molecular Orbital Theory

Author : Warren J. Hehre
Publisher : Wiley-Interscience
ISBN 13 :
Total Pages : 572 pages
Book Rating : 4.:/5 (319 download)

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Book Synopsis AB INITIO Molecular Orbital Theory by : Warren J. Hehre

Download or read book AB INITIO Molecular Orbital Theory written by Warren J. Hehre and published by Wiley-Interscience. This book was released on 1986-03-24 with total page 572 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book addresses the formulation of theoretical molecular orbital models starting from quantum mechanics, and compares them to experimental results. It draws on a series of models that have already received widespread application and are available for new applications.

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.

Computational Modeling of Membrane Bilayers

Author : V. Sundararajan
Publisher : Academic Press
ISBN 13 : 0080920500
Total Pages : 493 pages
Book Rating : 4.0/5 (89 download)

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Book Synopsis Computational Modeling of Membrane Bilayers by : V. Sundararajan

Download or read book Computational Modeling of Membrane Bilayers written by V. Sundararajan and published by Academic Press. This book was released on 2011-08-29 with total page 493 pages. Available in PDF, EPUB and Kindle. Book excerpt: Current Topics in Membranes provides a systematic, comprehensive, and rigorous approach to specific topics relevant to the study of cellular membranes. Each volume is a guest edited compendium of membrane biology. Discusses the current state of electrostatics in biomolecular simulations and future directions Includes information on time and length scales in lipid bilayer simulations Includes a chapter on the nature of lipid rafts