Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes
Author: Adam Liwo
Publisher: Springer
Total Pages: 849
Release: 2018-12-19
Genre: Technology & Engineering
ISBN: 3319958437

This book provides a comprehensive overview of modern computer-based techniques for analyzing the structure, properties and dynamics of biomolecules and biomolecular processes. It is organized in four main parts; the first one deals with methodology of molecular simulations; the second one with applications of molecular simulations; the third one introduces bioinformatics methods and the use of experimental information in molecular simulations; the last part reports on selected applications of molecular quantum mechanics. This second edition has been thoroughly revised and updated to include the latest progresses made in the respective field of research.

Membrane Hydration

Membrane Hydration
Author: E. Anibal Disalvo
Publisher: Springer
Total Pages: 295
Release: 2015-10-05
Genre: Science
ISBN: 3319190601

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.

Biomembrane Simulations

Biomembrane Simulations
Author: Max L. Berkowitz
Publisher: CRC Press
Total Pages: 335
Release: 2019-04-30
Genre: Science
ISBN: 1351060295

Due to recent advancements in the development of numerical algorithms and computational hardware, computer simulations of biological membranes, often requiring use of substantial computational resources, are now reaching a mature stage. Since molecular processes in membranes occur on a multitude of spatial and time scales, molecular simulations of membranes can also serve as a testing ground for use of multi-scale simulation techniques. This book addresses some of the important issues related to understanding properties and behavior of model biological membranes and it Shows how simulations improve our understanding of biological membranes and makes connections with experimental results. Presents a careful discussion of the force fields used in the membrane simulations including detailed all-atom fields and coarse-grained fields. Presents a continuum description of membranes. Discusses a variety of issues such as influence of membrane surfaces on properties of water, interaction between membranes across water, nanoparticle permeation across the membrane, action of anesthetics and creation of inhomogeneous regions in membranes. Discusses important methodological issues when using simulations to examine phenomena such as pore creation and permeation across membranes. Discusses progress recently achieved in modeling bacterial membranes. It will be a valuable resource for graduate students, researchers and instructors in biochemistry, biophysics, pharmacology, physiology, and computational biology.

Permeability and Stability of Lipid Bilayers

Permeability and Stability of Lipid Bilayers
Author: E. Anibal Disalvo
Publisher: CRC Press
Total Pages: 298
Release: 2017-12-14
Genre: Science
ISBN: 1351425382

This book presents a comprehensive and coherent picture of how molecules diffuse across a liquid that is, on average, only two molecules thick. It begins by characterizing bilayers structurally, using X-ray diffraction, and then mechanically by measuring elastic moduli and mechanisms of failure. Emphasis is placed on the stability and mechanical properties of plant membranes that are subject to very large osmotic and thermal stresses. Using this information, the transport of molecules of increasing complexity across bilayers is analyzed.

Computer Simulation of Liquids

Computer Simulation of Liquids
Author: M. P. Allen
Publisher: Oxford University Press
Total Pages: 641
Release: 2017
Genre: Computers
ISBN: 0198803192

This is the second edition of a widely used practical guide to computer simulations of liquids. The technique uses a model for the way molecules interact, to predict how large numbers of them behave in liquid state. This essential introduction to this rapidly growing field is complete with illustrative computer code.

Index Medicus

Index Medicus
Author:
Publisher:
Total Pages: 2002
Release: 2004
Genre: Medicine
ISBN:

Vols. for 1963- include as pt. 2 of the Jan. issue: Medical subject headings.

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.

Hydration Processes in Biology

Hydration Processes in Biology
Author: Marie-Claire Bellissent-Funel
Publisher: IOS Press
Total Pages: 456
Release: 1999
Genre: Medical
ISBN: 9789051994391

The interaction of water at organic surfaces or interfaces is of fundamental and technological interest and importance in chemistry, physics and biology. Progress towards an in-depth, molecular interpretation of the structure and dynamics of interfacial water needs a range of novel experimental and simulation techniques. We are now reaching the stage at which we understand, at the molecular level, the mutual perturbation at a macromolecule/water interface. The aims of this book are to provide with a comprehensive background to the properties of bulk water at the microscopic level and with a substantial account of the theoretical and experimental contributions which have been done to understand the role of water in various systems from some model systems to the more complex ones such as the biological systems.

Lipid Bilayers

Lipid Bilayers
Author: J. Katsaras
Publisher: Springer Science & Business Media
Total Pages: 304
Release: 2013-06-29
Genre: Science
ISBN: 366204496X

Provides the reader with an up to date insight of the current state of the art in the field of lipid bilayer research and the important insights derived for the understanding of the complex and varied behaviour of biological membranes and its function.