Download or read book Molecular Dynamics Simulations of Molecules Under Confined Geometry written by Xiang Yang Guo and published by . This book was released on 2020* with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: MCM41, ethanol-water, confinement, DPPC, fluorophilic, polyphile, molecular dynamics simulations, force field.
Download or read book Molecular Dynamics Simulations of Surface active Molecules Under Bulk and Confined Conditions written by Georgia Tsagkaropoulou and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Dynamics written by Lichang Wang and published by BoD – Books on Demand. This book was released on 2012-04-05 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This first book begins with a general description of underlying theories of molecular dynamics simulations and provides extensive coverage of molecular dynamics simulations in nanotechnology and energy. Coverage of this book includes: Recent advances of molecular dynamics theory Formation and evolution of nanoparticles of up to 106 atoms Diffusion and dissociation of gas and liquid molecules on silicon, metal, or metal organic frameworks Conductivity of ionic species in solid oxides Ion solvation in liquid mixtures Nuclear structures
Download or read book A Practical Introduction to the Simulation of Molecular Systems written by Martin J. Field and published by Cambridge University Press. This book was released on 2007-07-19 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through www.cambridge.org/9780521852524.
Download or read book Simulations of Molecules and Processes in the Synapse written by Kaihsu Tai and published by Kaihsu Tai. This book was released on 2002 with total page 110 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Effects of Confinement on Water Structure and Dynamics and on Proton Transport written by Pussana Hirunsit and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Classical molecular dynamics (MD) simulations are performed to study structural and dynamic properties of water confined within graphite surfaces. The surfaces are separated at distances varying between 7 and 14.5 Å and the water density is held constant at 1g/cc. Results at 298 K show the formation of a well-ordered structure constituted by water layers parallel to the graphite surfaces. The water molecules in the layers in contact with the surface have a tendency to orient their dipole parallel to the surface. Such ice-like structures may have different structural and dynamic properties than those of ice. The calculated mean square displacement reveals that the mobilities of the confined water at a separation of 8 Å become similar to that of low-temperature water (213 K) at the same density, although the structures of water are very different. The temperature at which the mobility of water confined at the separation of 7 Å would become similar to that of bulk low-temperature water was found to be 373K. With respect to the dynamics of confined water, a significant blue shift is observed in the intermolecular vibrational modes associated with the O···O···O bending and O···O stretching of molecules linked by hydrogen bonds. The analysis of the geometry of water clusters confined between two graphite surfaces has been performed using ab initio methods. The ab initio calculations yield two preferential orientations of water molecules which are; 1) one O-H bond points to the surface and the other is parallel; 2) both O-H bonds are parallel to the surface. These orientations agree with those found in our MD simulation results. The calculated energy barriers for proton transfer of the confined H3O-(H2O) complexes between two graphite model surfaces suggest that the confinement enhances the proton transfer at the separation 6-14.5 Å. When the confinement is high, at a separation of 4 Å, the barrier energies are extremely large. The confinement does not enhance proton transfer when the H3O-(H2O) complexes are located further from the surfaces by more than 8 Å. As a result, the barrier energies start to increase at the separation of 20 Å.
Download or read book Computer Simulation of Condensed Phases in Complex Geometries written by Martin Schoen and published by Springer Science & Business Media. This book was released on 2008-09-11 with total page 143 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecularly small confined phases play an important role in many scientific and engineering disciplines. For instance, the confining membrane of a living cell is known to affect the structure and transport of cellular water, which mediates the cell's metabolism and other biochemical processes. Transport of hazardous waste through the soil is strongly influenced by the adsorption of bulk phase molecules on the confining mineral _surfaces. Finally, molecularly thin confined fluid films play a prominent part in lubrication. These examples illustrate the broad range of natural and commercial processes to which the present subject pertains. Much experimental effort has been devoted to molecularly small confined phases, revealing the intriguing nature of such systems. Several sections of this book are therefore devoted to descriptions of experimental techniques. To date even the most refined experiments do not yield direct information about structure and processes on the molecular scale. Computer simulations, on the other hand, do give such information and therefore complement real laboratory experiments. Several sections of this book discuss the link between experiments and the corre sponding simulations.
Download or read book Molecular Simulation and Industrial Applications written by Keith E. Gubbins and published by Taylor & Francis. This book was released on 1996 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt: First published in 2004. Routledge is an imprint of Taylor & Francis, an informa company.
Download or read book Molecular Dynamics Simulations of Thermodynamic Properties of Selected Polymeric and Biological Molecules written by Liangxu Xie and published by . This book was released on 2017-01-26 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation, "Molecular Dynamics Simulations of Thermodynamic Properties of Selected Polymeric and Biological Molecules" by Liangxu, Xie, 谢良旭, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Molecular dynamics (MD) simulations have been widely applied to study equilibrium and dynamical properties of macromolecular systems. In this thesis MD simulations are applied to important macromolecular processes, including conformation transformation in macromolecular systems and enzymatic catalysis, molecular details of which are inaccessible to experimental methods. A fundamental investigation of macromolecular processes is presented in this dissertation. Different computational methods, such as integrated tempering sampling (ITS), umbrella sampling (US), and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, have been applied to study conformation changes of macromolecules including those in an enzyme catalyzed reaction. Three representative topics are investigated in this dissertation: (1) structural and dynamic relaxation behavior of polyelectrolytes confined in metal-organic framework (MOF) MIL-53(Al); (2) switch of peptide conformations between α-helix and β-hairpin states; and (3) chorismate rearrangement reaction catalyzed by ―isochorismate-pyruvate lyase from Pseudomonas aeruginosa‖ (PchB). Conformation and dynamical properties of polyelectrolytes threaded in MOF are investigated by MD simulations. A polymer threaded inside MOF was reported to have augmented conductivity and high ion-exchange kinetics. Basic understanding of confinement effect on polyelectrolytes is critical for designing novel polyelectrolyte MOF composites. Three polyelectrolytes, sodium polyacrylate acid, sodium poly (4-vinylbenzonic acid), and polydiallyldimethylammonium chloride (PDADMA), have been introduced into MIL-53(Al) channels to elucidate the confinement effect with variation of charged groups and molecular structures. Quantitative analysis demonstrates that confinement effects include (1) increasing order and size of polyelectrolytes, (2) enabling uniform counter-ion distribution, and (3) changing dynamic relaxation and configurational entropy of polyelectrolytes in the polyelectrolyte MIL-53(Al) composites. To efficiently sample conformation transformations of peptide, the ITS method has been used to investigate secondary structure transformation process of peptides. Proteins undergo conformational changes to fulfill their functions. Secondary structure changes between α-helix and β-hairpin, an essential feature of proteins, is explored by the ITS method. Results demonstrate that ITS can widely sample peptide conformational space, without prior knowledge of the structure or the use of a bias potential. The obtained free energy landscape is used reliably to characterize conformations changes of the peptide between α-helix and β-hairpin states. Finally, chorismate mutate reaction has been a central topic of the enzyme catalysis for decades. This reaction has attracted studies using the QM/MM scheme. However, it is still unclear whether the reaction is enthalpy driven or entropy driven. In this dissertation, the free energy changes of reaction in water are compared to corresponding enzymatic reaction catalyzed by PchB. This reaction is also studied by long timescale US simulations to illustrate the enthalpy/entropy scheme in this enzyme. Comparing the uncatalyzed reaction with the catalyzed reaction in PchB, we conclude that both enthalpy and entropy contribute to catalysis. The stable structure of bound chorismate and the enthalpy/
Download or read book A Molecular Simulation Study on Micelle Fragmentation and Wetting in Nano confined Channels written by Mona Habibi and published by . This book was released on 2014 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: We performed coarse-grained molecular-dynamics (MD) simulations to study the structural and dynamical properties of surfactant micelles in equilibrium and under Poiseuille-like flow in a nano-confined geometry. We used the MARTINI force-field to model the interactions between water molecules, counter-ions, and sodium dodecyl sulfate (SDS) surfactants. SDS surfactant was chosen as the standard model because of its potential application in drug delivery systems. First, we focused on the self-assembly of SDS in equilibrium. To form stable spherical mi- celles, we ran simulations in the isothermal-isobaric ensemble (NPT) on a system of free SDS surfactants, counter-ions and water molecules. We studied the aggregation number, shape and radius of the SDS micelles in equilibrium. These results agree well with all-atom simulations of SDS. Second, we studied the spreading of a spherical micelle on a solid surface over various interaction strengths in a system consisting of a spherical SDS micelle, and counter-ions in the vicinity of a surface and water molecules. The interaction energies between walls and surfac- tants were parameterized at three distinct levels corresponding to non-, low-, and high-wetting walls surfaces. The wetting properties of the surfaces were determined by calculating the con- tact angles of the micelle on the surface in equilibrium. We calculated the contact angle from Young's equation through measuring the surfaces tension of wall-water, wall-SDS, and water- SDS. As the micelle interacts with the surface, it either forms a cap, a bulb-shape structure, or detaches itself and floats away on high-, low-, and non-wetting surfaces respectively. Third, we explored the effect of flow, confinement, and wetting on SDS micelles when the micelle is forced through a channel slightly smaller than its equilibrium size. We performed simulations on micellar solutions confined in a die geometry in the isothermal ensemble (NVT). We show that the flowing micelle adopts different shapes to pass through the channel. Inside the channel, the micelle may fragment into smaller micelles. We demonstrate that in addition to the flow rate, the wettability of the channel surface dictates whether the micelle fragments and determines the size of daughter micelles.
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 Molecular Dynamics Simulation in Arbitrary Geometries for Nanoscale Fluid Mechanics written by Graham Bruce Macpherson and published by . This book was released on 2008 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Simulations of nanoscale systems where fluid mechanics plays an important role are required to help design and understand nano-devices and biological systems. A simulation method which hybridises molecular dynamics (MD) and continuum computational fluid dynamics (CFD) is demonstrated to be able to accurately represent the relevant physical phenomena and be computationally tractable. An MD code has been written to perform MD simulations in systems where the geometry is described by a mesh of unstructured arbitrary polyhedral cells that have been spatially decomposed into irregular portions for parallel processing. The MD code that has been developed may be used for simulations on its own, or may serve as the MD component of a hybrid method. The code has been implemented using OpenFOAM, an open source C++ CFD toolbox (www.openfoam.org) . Two key enabling components are described in detail. 1) Parallel generation of initial configurations of molecules in arbitrary geometries. 2) Calculation of intermolecular pair forces, including between molecules that lie on mesh portions assigned to different, and possibly non-neighbouring processors. To calculate intermolecular forces, the spatial relationship of mesh cells is calculated once at the start of the simulation and only the molecules contained in cells that have part of their surface closer than a cut-off distance are required to interact. Interprocessor force calculations are carried out by creating local copies of molecules from other processors in a layer around the processor in question. The process of creating these copied molecules is described in detail. A case study of flow in a realistic nanoscale mixing channel, where the geometry is drawn and meshed using engineering CAD tools, is simulated to demonstrate the capabilities of the code for complex simulations.
Download or read book Dynamics in Geometrical Confinement written by Friedrich Kremer and published by Springer. This book was released on 2014-06-03 with total page 365 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the dynamics of low molecular weight and polymeric molecules when they are constrained under conditions of geometrical confinement. It covers geometrical confinement in different dimensionalities: (i) in nanometer thin layers or self supporting films (1-dimensional confinement) (ii) in pores or tubes with nanometric diameters (2-dimensional confinement) (iii) as micelles embedded in matrices (3-dimensional) or as nanodroplets. The dynamics under such conditions have been a much discussed and central topic in the focus of intense worldwide research activities within the last two decades. The present book discusses how the resulting molecular mobility is influenced by the subtle counterbalance between surface effects (typically slowing down molecular dynamics through attractive guest/host interactions) and confinement effects (typically increasing the mobility). It also explains how these influences can be modified and tuned, e.g. through appropriate surface coatings, film thicknesses or pore diameters. "Dynamics in Confinement" sums up the present state-of-the-art and introduces to the analytical methods of choice for the study of dynamics in nanometer-scale confinement.
Download or read book Molecular Dynamics written by Perla Balbuena and published by Elsevier. This book was released on 1999-04-22 with total page 971 pages. Available in PDF, EPUB and Kindle. Book excerpt: The latest developments in quantum and classical molecular dynamics, related techniques, and their applications to several fields of science and engineering. Molecular simulations include a broad range of methodologies such as Monte Carlo, Brownian dynamics, lattice dynamics, and molecular dynamics (MD). Features of this book: • Presents advances in methodologies, introduces quantum methods and lists new techniques for classical MD • Deals with complex systems: biomolecules, aqueous solutions, ice and clathrates, liquid crystals, polymers • Provides chemical reactions, interfaces, catalysis, surface phenomena and solids Although the book is not formally divided into methods and applications, the chapters are arranged starting with those that discuss new algorithms, methods and techniques, followed by several important applications.
Download or read book Nonequilibrium Molecular Dynamics written by Billy D. Todd and published by Cambridge University Press. This book was released on 2017-03-10 with total page 371 pages. Available in PDF, EPUB and Kindle. Book excerpt: This coherent collection of theory, algorithms, and illustrative results presents the field of nonequilibrium molecular dynamics in detail.
Download or read book Molecular Dynamics written by Lichang Wang and published by BoD – Books on Demand. This book was released on 2012-04-11 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Dynamics is a two-volume compendium of the ever-growing applications of molecular dynamics simulations to solve a wider range of scientific and engineering challenges. The contents illustrate the rapid progress on molecular dynamics simulations in many fields of science and technology, such as nanotechnology, energy research, and biology, due to the advances of new dynamics theories and the extraordinary power of today's computers. This second book begins with an introduction of molecular dynamics simulations to macromolecules and then illustrates the computer experiments using molecular dynamics simulations in the studies of synthetic and biological macromolecules, plasmas, and nanomachines. Coverage of this book includes: Complex formation and dynamics of polymers Dynamics of lipid bilayers, peptides, DNA, RNA, and proteins Complex liquids and plasmas Dynamics of molecules on surfaces Nanofluidics and nanomachines
Download or read book Molecular Modelling for Beginners written by Alan Hinchliffe and published by John Wiley & Sons. This book was released on 2003-09-26 with total page 436 pages. Available in PDF, EPUB and Kindle. Book excerpt: Eletric Charges and Their Properties. The Forces Between Molecules. Balls on Springs. Molecular Mechanics. The Molecular Potential Energy Surface. A Molecular Mechanics Calculation. Quick Guide to Statical Thermodynamics. Molecular Dynamics. Monte Carlo. Introduction to Quantum Modelling. Quantum Gases. One-Electron Atoms. The Orbital Model. Simple Molecules. The HF-LCAO Model. HF-LCAO Examples. Semi-Empirical Models. Electron Correlation. Destiny Functional Theory and the Kohn-Sham LCAO Equations. Miscellany.
