Download or read book Synthetic Biology written by Luc Brunsveld and published by Royal Society of Chemistry. This book was released on 2017-11-29 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: Leading researchers draw on the recent literature in Synthetic Biology, from both dedicated journals and broader sources, making this an essential reference to any library supporting this research in this emerging field.

Download or read book Mesoscale Chemistry written by National Research Council and published by National Academies Press. This book was released on 2015-08-06 with total page 229 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last few decades great strides have been made in chemistry at the nanoscale, where the atomic granularity of matter and the exact positions of individual atoms are key determinants of structure and dynamics. Less attention, however, has been paid to the mesoscale-it is at this scale, in the range extending from large molecules (10 nm) through viruses to eukaryotic cells (10 microns), where interesting ensemble effects and the functionality that is critical to macroscopic phenomenon begins to manifest itself and cannot be described by laws on the scale of atoms and molecules alone. To further explore how knowledge about mesoscale phenomena can impact chemical research and development activities and vice versa, the Chemical Sciences Roundtable of the National Research Council convened a workshop on mesoscale chemistry in November 2014. With a focus on the research on chemical phenomena at the mesoscale, participants examined the opportunities that utilizing those behaviors can have for developing new catalysts, adding new functionality to materials, and increasing our understanding of biological and interfacial systems. The workshop also highlighted some of the challenges for analysis and description of mesoscale structures. This report summarizes the presentations and discussion of the workshop.

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.

Download or read book Bulletin of the Atomic Scientists written by and published by . This book was released on 1961-05 with total page 88 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Bulletin of the Atomic Scientists is the premier public resource on scientific and technological developments that impact global security. Founded by Manhattan Project Scientists, the Bulletin's iconic "Doomsday Clock" stimulates solutions for a safer world.

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.

Download or read book Computational Pharmaceutics written by Defang Ouyang and published by John Wiley & Sons. This book was released on 2015-07-20 with total page 350 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular modeling techniques have been widely used in drug discovery fields for rational drug design and compound screening. Now these techniques are used to model or mimic the behavior of molecules, and help us study formulation at the molecular level. Computational pharmaceutics enables us to understand the mechanism of drug delivery, and to develop new drug delivery systems. The book discusses the modeling of different drug delivery systems, including cyclodextrins, solid dispersions, polymorphism prediction, dendrimer-based delivery systems, surfactant-based micelle, polymeric drug delivery systems, liposome, protein/peptide formulations, non-viral gene delivery systems, drug-protein binding, silica nanoparticles, carbon nanotube-based drug delivery systems, diamond nanoparticles and layered double hydroxides (LDHs) drug delivery systems. Although there are a number of existing books about rational drug design with molecular modeling techniques, these techniques still look mysterious and daunting for pharmaceutical scientists. This book fills the gap between pharmaceutics and molecular modeling, and presents a systematic and overall introduction to computational pharmaceutics. It covers all introductory, advanced and specialist levels. It provides a totally different perspective to pharmaceutical scientists, and will greatly facilitate the development of pharmaceutics. It also helps computational chemists to look for the important questions in the drug delivery field. This book is included in the Advances in Pharmaceutical Technology book series.

Download or read book Fuzziness written by Monika Fuxreiter and published by Springer Science & Business Media. This book was released on 2012-03-07 with total page 210 pages. Available in PDF, EPUB and Kindle. Book excerpt: Detailed characterization of fuzzy interactions will be of central importance for understanding the diverse biological functions of intrinsically disordered proteins in complex eukaryotic signaling networks. In this volume, Peter Tompa and Monika Fuxreiter have assembled a series of papers that address the issue of fuzziness in molecular interactions. These papers provide a broad overview of the phenomenon of fuzziness and provide compelling examples of the central role played by fuzzy interactions in regulation of cellular signaling processes and in viral infectivity. These contributions summarize the current state of knowledge in this new field and will undoubtedly stimulate future research that will further advance our understanding of fuzziness and its role in biomolecular interactions.

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

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

Download or read book The Art of Molecular Dynamics Simulation written by D. C. Rapaport and published by Cambridge University Press. This book was released on 2004-04 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt: First time paperback of successful physics monograph. Copyright © Libri GmbH. All rights reserved.

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

Download or read book Classical And Quantum Dynamics In Condensed Phase Simulations Proceedings Of The International School Of Physics written by Bruce J Berne and published by World Scientific. This book was released on 1998-06-17 with total page 881 pages. Available in PDF, EPUB and Kindle. Book excerpt: The school held at Villa Marigola, Lerici, Italy, in July 1997 was very much an educational experiment aimed not just at teaching a new generation of students the latest developments in computer simulation methods and theory, but also at bringing together researchers from the condensed matter computer simulation community, the biophysical chemistry community and the quantum dynamics community to confront the shared problem: the development of methods to treat the dynamics of quantum condensed phase systems.This volume collects the lectures delivered there. Due to the focus of the school, the contributions divide along natural lines into two broad groups: (1) the most sophisticated forms of the art of computer simulation, including biased phase space sampling schemes, methods which address the multiplicity of time scales in condensed phase problems, and static equilibrium methods for treating quantum systems; (2) the contributions on quantum dynamics, including methods for mixing quantum and classical dynamics in condensed phase simulations and methods capable of treating all degrees of freedom quantum-mechanically.

Download or read book Linear Dichroism and Circular Dichroism written by Bengt Nordén and published by Royal Society of Chemistry. This book was released on 2019-05-02 with total page 305 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an introduction to optical anisotropy (linear dichroism, LD) and optical activity (circular dichroism, CD) as techniques for the study of structures and interactions of molecules in solution. The book covers the use of these techniques for both small and large molecular systems with particular emphasis being placed on proteins and nucleic acids. CD is a well-established technique and this book aims to explain how it can be used simply and effectively for new entrants to the field as well as covering more advanced techniques for experts. LD is often seen as a rather exotic method intended only for experienced spectroscopists. This book demonstrates that it is an approach with real utility that may be used by both students and scientists from graduate level onwards to give simple answers, which are not available from any other technique, to structural and kinetic questions. Much of the emphasis is on flow orientation of samples in solution phase. The book first describes the techniques and the information they can provide; it then goes on to give specific details on how to actually implement them, including a wide range of examples showing how LD and CD can help with * protein and nucleic acid secondary structure elucidation; * analysis of the formation and rearrangements of fibrous proteins and membrane proteins; * identification of the absolute configuration of small molecules; * determination of the orientation of small molecules in anisotropic media; * assignment of transition moment polarizations; * investigation of binding strengths and geometries of ligand-macromolecule complexes; * 3-D structure determination from LD, molecular replacement and MD modeling. The advantages of combined LD/CD studies are also outlined with examples of DNA/drug complexes and protein insertion into membranes. Taken together the book represents a comprehensive text on the theory and application of LD and CD in the chemical and biological sciences.

Download or read book Intermolecular and Surface Forces written by Jacob N. Israelachvili and published by Academic Press. This book was released on 2011-07-22 with total page 708 pages. Available in PDF, EPUB and Kindle. Book excerpt: Intermolecular and Surface Forces describes the role of various intermolecular and interparticle forces in determining the properties of simple systems such as gases, liquids and solids, with a special focus on more complex colloidal, polymeric and biological systems. The book provides a thorough foundation in theories and concepts of intermolecular forces, allowing researchers and students to recognize which forces are important in any particular system, as well as how to control these forces. This third edition is expanded into three sections and contains five new chapters over the previous edition. - Starts from the basics and builds up to more complex systems - Covers all aspects of intermolecular and interparticle forces both at the fundamental and applied levels - Multidisciplinary approach: bringing together and unifying phenomena from different fields - This new edition has an expanded Part III and new chapters on non-equilibrium (dynamic) interactions, and tribology (friction forces)

Download or read book New Algorithms for Macromolecular Simulation written by B. Leimkuhler and published by Springer Science & Business Media. This book was released on 2006-02-10 with total page 390 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.

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.

Download or read book Molecular Dynamics written by Ben Leimkuhler and published by Springer. This book was released on 2015-05-18 with total page 461 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the mathematical underpinnings of algorithms used for molecular dynamics simulation, including both deterministic and stochastic numerical methods. Molecular dynamics is one of the most versatile and powerful methods of modern computational science and engineering and is used widely in chemistry, physics, materials science and biology. Understanding the foundations of numerical methods means knowing how to select the best one for a given problem (from the wide range of techniques on offer) and how to create new, efficient methods to address particular challenges as they arise in complex applications. Aimed at a broad audience, this book presents the basic theory of Hamiltonian mechanics and stochastic differential equations, as well as topics including symplectic numerical methods, the handling of constraints and rigid bodies, the efficient treatment of Langevin dynamics, thermostats to control the molecular ensemble, multiple time-stepping, and the dissipative particle dynamics method.