Download or read book Expanding the Space time Resolution of Molecular Dynamics Studies of Condensed Phases for Ionic Liquids Polymers and Bio molecules written by Chang Yun Son and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular dynamics (MD) simulations have grown rapidly, providing molecular details to understand the mechanisms of biomolecular processes and the design principles of materials properties, which can ul- timately foster new experiments to investigate with better understanding of the underlying physics. Recent development of new hardware architectures for massive parallel computing and new simulation techniques vastly extended the scope of computational studies in chemistry, physics, biology and materials science. However, a brute-force simulation studies of condensed phase systems with large number of atoms are still challenging due to the complexity of these systems, which requires essentially multi-scale approach in both time and space domains. In this dissertation, we study a wide range of complex condensed phase systems -- ranging from ionic liquids (ILs), polymers, bio-mimicking surfactants and biomolecular proton pumps -- with the state of art hardware architectures including the use of graphical processing units (GPUs) and simulation algorithms such as metadynamics and Markov state models. We have developed a general framework to build a first-principles, non-polarizable united atom force fields, which provides accurate and cost-effective description of neat ILs, ionic liquid crystals and polymer/IL mixtures that are in excellent agreement to the experiments without any implicit parametrization. Extensive unrestrained MD simulations are performed to characterize the self-assembly of synthetic six-tailed amphiphiles, which aided the struc- tural assignment of the liquid crystalline phases observed with small angle X-ray scattering experiments. Lastly, we investigate the hydration level change in an internal cavity of the transmembrane protein cy- tochrome c oxidase (CcO), an enzyme that generates proton concentration gradient across membrane. The computed energetic and kinetic features for the cavity wetting transition suggest that reversible hydration level change of the cavity can be a key factor that regulates the branching of proton transfer events and therefore contributes to the vectorial efficiency of proton transport. The studies in this dissertation highlight how one can incorporate recent advances of computational chemistry to expand the molecular understanding in complex systems to a space-time resolution that was unreachable in the past.
Download or read book Algorithmic Improvements and Applications of Molecular Dynamics Simulations to Probe Condensed Phase Systems written by Shanmuga Sundaram Venkatesan and published by . This book was released on 2019 with total page 116 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular dynamics (MD) simulation studies were considered in this study in the fields of phosphonium based ionic liquids (PBILs) and heterogeneous (solid/liquid) zeolite systems. A new generation of ionic liquids (ILs) called phase-separable ionic liquids (PSILs) are able to dissolve cellulose and lignin, a necessary step, for conversion of biomass to fuels and chemicals with co-solvents and are immiscible with water or saline solutions. Molecular simulations on these systems will provide insights of phase behavior and dissolution phenomenon. The knowledge of interfacial phase behavior of ionic liquids/solvent systems is critical for materials discovery for designing efficient dissolution processes. Transition zone from miscible to immiscible behavior was observed for alkyl chain lengths varying from 6 to 8. Emulsion phase was observed for [P8888]+ ion. Result from molecular dynamics (MD) simulations shows excellent agreement with experimental data for both chloride and acetate anions. These contributions will be helpful in modeling PBILs system for cellulose dissolution, liquid-liquid extraction and biomass studies. Another important aspect in biofuel conversion is glucose isomerization step using zeolites. Zeolites are crystalline solids that have wide applications in industrial areas for its hydrocarbon conversion, adsorption of molecules. In this study, we report MD simulation studies on glucose solution diffusion into zeolite structure as a function of temperature and pressure. Development of united-atom force field for PBILs, for phosphonium cation with anions of chloride and acetate, is considered in this study. Force field parameterization was considered for these ionic liquids with a variation of alkyl chain length in phosphonium ion with chloride and acetate anions. Performance of force field parameters was analyzed by calculating properties such as density and viscosity at various temperature and compared with available experimental data. Efficient algorithm techniques were developed in molecular simulations that will reduce computational load in calculating non-bonded interactions. We introduce theory of local sample (TLS) in calculating non-bonded interactions acting on atoms. Another algorithmic improvement in MD simulations is calculating force acting on atoms based on previous time steps, that achieves up to 50 % reduction in computational time.
Download or read book Scientific and Technical Aerospace Reports written by and published by . This book was released on 1981 with total page 1370 pages. Available in PDF, EPUB and Kindle. Book excerpt: Lists citations with abstracts for aerospace related reports obtained from world wide sources and announces documents that have recently been entered into the NASA Scientific and Technical Information Database.
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 Ionic Liquids in Separation Technology written by Antonia Perez De Los Rios and published by Elsevier. This book was released on 2014-08-08 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ionic Liquids in Separation Technology reports on the most important fundamental and technological advances in separation processes using ionic liquids. It brings together the latest developments in this fascinating field, supplements them with numerous practical tips, and thus provides those working in both research and industry with an indispensable source of information. The book covers fundamental topics of physical, thermal, and optical properties of ionic liquids, including green aspects. It then moves on to contexts and applications, including separation of proteins, reduction of environmental pollutants, separation of metal ions and organic compounds, use in electrochromic devices, and much more. For the specialist audience the book serves as a recompilation of the most important knowledge in this field, whereas for starting researchers in ionic liquid separation technology the book is a great introduction to the field. First book in the marketplace dedicated to ionic liquids in separation technology Contributions from scientists in academia and researchers in industry ensure the coverage of both scientific fundamentals and industrial applications Covers a broad collection of applications in separation technology which makes the book a single source of information Includes many practical tips for researchers in industry and scientists who apply ionic liquids in their work
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 Structures and Interactions of Ionic Liquids written by Suojiang Zhang and published by Springer. This book was released on 2013-12-20 with total page 201 pages. Available in PDF, EPUB and Kindle. Book excerpt: Structures, Bonding and Hydrogen Bonds, by Kun Dong, Qian Wang, Xingmei Lu, Suojiang Zhang Aggregation in System of Ionic Liquids, by Jianji Wang, Huiyong Wang Dissolution of Biomass Using Ionic Liquids, by Hui Wang, Gabriela Gurau, Robin D. Rogers Effect of the Structures of Ionic Liquids on Their Physical-Chemical Properties, by Yu-Feng Hu, Xiao-Ming Peng Microstructure study of Ionic liquids by spectroscopy, by Haoran Li Structures and Thermodynamic Properties of Ionic Liquids, by Tiancheng Mu, Buxing Han
Download or read book Beyond the Molecular Frontier written by National Research Council and published by National Academies Press. This book was released on 2003-03-19 with total page 238 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemistry and chemical engineering have changed significantly in the last decade. They have broadened their scopeâ€"into biology, nanotechnology, materials science, computation, and advanced methods of process systems engineering and controlâ€"so much that the programs in most chemistry and chemical engineering departments now barely resemble the classical notion of chemistry. Beyond the Molecular Frontier brings together research, discovery, and invention across the entire spectrum of the chemical sciencesâ€"from fundamental, molecular-level chemistry to large-scale chemical processing technology. This reflects the way the field has evolved, the synergy at universities between research and education in chemistry and chemical engineering, and the way chemists and chemical engineers work together in industry. The astonishing developments in science and engineering during the 20th century have made it possible to dream of new goals that might previously have been considered unthinkable. This book identifies the key opportunities and challenges for the chemical sciences, from basic research to societal needs and from terrorism defense to environmental protection, and it looks at the ways in which chemists and chemical engineers can work together to contribute to an improved future.
Download or read book The Structure of Ionic Liquids written by Ruggero Caminiti and published by Springer Science & Business Media. This book was released on 2013-11-09 with total page 202 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume describes the most recent findings on the structure of ILs interpreted through cutting-edge experimental and theoretical methods. Research in the field of ionic liquids (ILs) keeps a fast and steady pace. Since these new-generation molten salts first appeared in the chemistry and physics landscape, a large number of new compounds has been synthesized. Most of them display unexpected behaviour and possess stunning properties. The coverage in this book ranges from the mesoscopic structure of ILs to their interaction with proteins. The reader will learn how diffraction techniques (small and large angle X-Ray and neutron scattering, powder methods), X-Ray absorption spectroscopies (EXAFS/XANES), optical methods (IR, RAMAN), NMR and calorimetric methods can help the study of ILs, both as neat liquids and in mixtures with other compounds. It will enable the reader to choose the best method to suit their experimental needs. A detailed survey of theoretical methods, both quantum-chemical and classical, and of their predictive power will accompany the exposition of experimental ones. This book is a must read for postgraduate students, for post-docs, and for researchers who are interested in understanding the structural properties of ILs.
Download or read book Protein Simulations written by Valerie Daggett and published by Elsevier. This book was released on 2003-11-26 with total page 477 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function. * Force Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations
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 Molten Salts and Ionic Liquids written by Marcelle Gaune-Escard and published by John Wiley & Sons. This book was released on 2012-07-06 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: For many years, the related fields of molten salts and ionic liquids have drifted apart, to their mutual detriment. Both molten salts and ionic liquids are liquid salts containing only ions - all that is different is the temperature! Both fields involve the study of Coulombic fluids for academic and industrial purposes; both employ the same principles; both require skilled practitioners; both speak the same language; all then that is truly different is their semantics, and how superficial is that? The editors of this book, recognising that there was so much knowledge, both empirical and theoretical, which can be passed from the molten salt community to the ionic liquid community, and vice versa, organised a landmark meeting in Tunisia, designed to bridge the gap and heal the rift. Leaders from both communities met for a week for a mutual exchange, with a high tutorial content intermixed with cutting edge findings. This volume is a condensate of the principal offerings of that week, and emphasises the success which was achieved. Indeed, four future biannual meetings, under the title of “EUCHEM Conferences on Molten Salts and Ionic Liquids”, have now been planned as a direct result of this meeting of minds. Topics discussed in this volume include structure, dynamics, electrochemistry, interfacial and thermodynamic properties, spectroscopy, synthesis, and theoretical studies. Experimental and theoretical methods for investigating these data are elaborated, as are techniques for data collection and analysis. This book represents the first serious discussion on the transfer of these methods and techniques between the differing temperature regimes, and is a major contribution to the future of both fields.
Download or read book Bridging the Time Scales written by Peter Nielaba and published by Springer Science & Business Media. This book was released on 2007-10-13 with total page 498 pages. Available in PDF, EPUB and Kindle. Book excerpt: The behaviour of many complex materials extends over time- and lengthscales well beyond those that can normally be described using standard molecular dynamics or Monte Carlo simulation techniques. As progress is coming more through refined simulation methods than from increased computer power, this volume is intended as both an introduction and a review of all relevant modern methods that will shape molecular simulation in the forthcoming decade. Written as a set of tutorial reviews, the book will be of use to specialists and nonspecialists alike.
Download or read book Giant Molecules written by A. I?U. Grosberg and published by World Scientific. This book was released on 2011 with total page 347 pages. Available in PDF, EPUB and Kindle. Book excerpt: ?? Giant molecules are important in our everyday life. But, as pointed out by the authors, they are also associated with a culture. What Bach did with the harpsichord, Kuhn and Flory did with polymers. We owe a lot of thanks to those who now make this music accessible ??Pierre-Gilles de GennesNobel Prize laureate in Physics(Foreword for the 1st Edition, March 1996)This book describes the basic facts, concepts and ideas of polymer physics in simple, yet scientifically accurate, terms. In both scientific and historic contexts, the book shows how the subject of polymers is fascinating, as it is behind most of the wonders of living cell machinery as well as most of the newly developed materials. No mathematics is used in the book beyond modest high school algebra and a bit of freshman calculus, yet very sophisticated concepts are introduced and explained, ranging from scaling and reptations to protein folding and evolution. The new edition includes an extended section on polymer preparation methods, discusses knots formed by molecular filaments, and presents new and updated materials on such contemporary topics as single molecule experiments with DNA or polymer properties of proteins and their roles in biological evolution.
Download or read book Visualizing Chemistry written by National Research Council and published by National Academies Press. This book was released on 2006-06-01 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: Scientists and engineers have long relied on the power of imaging techniques to help see objects invisible to the naked eye, and thus, to advance scientific knowledge. These experts are constantly pushing the limits of technology in pursuit of chemical imagingâ€"the ability to visualize molecular structures and chemical composition in time and space as actual events unfoldâ€"from the smallest dimension of a biological system to the widest expanse of a distant galaxy. Chemical imaging has a variety of applications for almost every facet of our daily lives, ranging from medical diagnosis and treatment to the study and design of material properties in new products. In addition to highlighting advances in chemical imaging that could have the greatest impact on critical problems in science and technology, Visualizing Chemistry reviews the current state of chemical imaging technology, identifies promising future developments and their applications, and suggests a research and educational agenda to enable breakthrough improvements.
Download or read book Modeling and Simulation in Polymers written by Purushottam D. Gujrati and published by John Wiley & Sons. This book was released on 2010-03-30 with total page 564 pages. Available in PDF, EPUB and Kindle. Book excerpt: Filling a gap in the literature and all set to become the standard in this field, this monograph begins with a look at computational viscoelastic fluid mechanics and studies of turbulent flows of dilute polymer solutions. It then goes on discuss simulations of nanocomposites, polymerization kinetics, computational approaches for polymers and modeling polyelectrolytes. Further sections deal with tire optimization, irreversible phenomena in polymers, the hydrodynamics of artificial and bacterial flagella as well as modeling and simulation in liquid crystals. The result is invaluable reading for polymer and theoretical chemists, chemists in industry, materials scientists and plastics technologists.
Download or read book Physics of Surfaces and Interfaces written by Harald Ibach and published by Springer Science & Business Media. This book was released on 2006-11-18 with total page 653 pages. Available in PDF, EPUB and Kindle. Book excerpt: This graduate-level textbook covers the major developments in surface sciences of recent decades, from experimental tricks and basic techniques to the latest experimental methods and theoretical understanding. It is unique in its attempt to treat the physics of surfaces, thin films and interfaces, surface chemistry, thermodynamics, statistical physics and the physics of the solid/electrolyte interface in an integral manner, rather than in separate compartments. It is designed as a handbook for the researcher as well as a study-text for graduate students. Written explanations are supported by 350 graphs and illustrations.
