Molecular dynamic calculations on fluid systems. by Owen David Moorhouse

Cover of: Molecular dynamic calculations on fluid systems. | Owen David Moorhouse

Published in [Toronto] .

Written in English

Read online


  • Molecular dynamics,
  • Fluid dynamics,
  • Viscosity

Edition Notes

Book details

ContributionsToronto, Ont. University. Theses (M.Sc.)
LC ClassificationsLE3 T525 MSC 1968 M66
The Physical Object
Pagination[132 leaves]
Number of Pages132
ID Numbers
Open LibraryOL17319344M

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Introduces Molecular dynamic calculations on fluid systems. book innovative system of molecular units for molecular dynamics calculations, and provides conventional units as well. Features a thorough, mathematical presentation that fosters understanding and mastery of all topics covered. Explains how to solve the exercises in its appended "Answers" section.

Elsevier, - Computers - pages 2 Reviews The aim of this book is to examine some of the important aspects of recent progress in the use of molecular simulation /5(2). This book, authored by a well-known researcher and expositor in meteorology, focuses on the direct link between molecular dynamics, turbulence theory, fluid mechanics and non equilibrium statistical mechanics, it is relevant to the fields of applied mathematics, physics and atmospheric sciences, and focuses on fluid flow and turbulence, as well as on temperature, radiative transfer and by: The method is a molecular dynamics version of the Gibbs-Ensemble Monte Carlo technique, which has been developed some years ago for the direct simulation of phase equilibria in fluid systems.

For molecular systems, we simply build the molecules out of site-site potentials of the form of Eq. (3) or similar. Typically, a single-molecule quantum-chemical calculation may be used to estimate the electron density throughout the molecule, which may then be mod-elled by a distribution of partial charges via Size: KB.

Molecular simulations include a broad range of methodologies such as Monte Carlo, Brownian dynamics, lattice dynamics, and molecular dynamics (MD). Features of this book: •. Journal of Dynamic Systems, Molecular dynamic calculations on fluid systems. book, and Control is used to improve the accuracy of fluid flow calculations in the slip flow regime where the continuum assumption of zero fluid velocity at the surface is inaccurate because fluid “slip” occurs.

Molecular dynamics techniques are used to study impacts of individual gas atoms upon solid. Fluid power is one domain within the field of system dynamics, just as mechanical translational, mechanical rotational and electronic net-works are system dynamic domains. Fluid power systems can be an-alyzed with the same mathematical tools used to describe spring-mass-damper or inductor-capacitor-resistor systems.

Like the other domains. Thermophysical Properties of Fluid Systems. Accurate thermophysical properties are available for several fluids. These data include the following. In a molecular dynamics simulation, one often wishes to explore the macroscopic properties of a system through microscopic simulations, for example, to calculate changes in the binding free energy of a particular drug candidate, or to examine the energetics and mechanisms of conformational change.

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system.

Understanding the fine balance between changes of entropy and enthalpy and the competition between a guest and water molecules in molecular binding is crucial in fundamental studies and practical applications. Experiments provide measurements. However, illustrating the binding/unbinding processes gives a complete picture of molecular recognition not directly available.

Molecular dynamics (MD) is a simulation methodology in which the movement of system particles is calculated in a certain period of time and the system evolution is investigated. It can be used in the studies of equilibrium and dynamic properties of a system. Molecular dynamics studies of polar/nonpolar fluid mixtures: I.

Mixtures of Lennard-Jones and Stockmayer fluids; The mobility of adsorbed species in zeolites: A molecular dynamics simulation of xenon in silicalit; A new local states method for the calculation of free energies in {Monte Carlo} simulations of lattice models.

Rheology and Fluid Dynamics; View All Topics; The Journal of Chemical Physics. Gaussian basis sets for accurate calculations on molecular systems in gas and condensed phases J. Chem The basis can therefore be used in first principles molecular dynamics simulations and is well suited for linear scaling calculations.

Article Metrics. The effect of cut-off distance used in molecular dynamics (MD) simulations on fluid properties was studied systematically in both canonical (NVT) and isothermal–isobaric (NPT) ensembles.

Results show that the cut-off distance in the NVT ensemble plays little role in determining the equilibrium structure of fluid if the ensemble has a high. Statistical Mechanics explores the physical properties of matter based on the dynamic behavior of its microscopic constituents.

After a historical introduction, this book presents chapters about thermodynamics, ensemble theory, simple gases theory, Ideal Bose and Fermi systems, statistical mechanics of interacting systems, phase transitions, and computer simulations.

An introduction to the rapidly evolving methodology of electronic excited states For academic researchers, postdocs, graduate and undergraduate students, Quantum Chemistry and Dynamics of Excited States: Methods and Applications reports the most updated and accurate theoretical techniques to treat electronic excited states.

From methods to deal with stationary calculations through time. Incremental viscosity by non-equilibrium molecular dynamics and the Eyring model. The Journal of Chemical Physics, Vol.

Issue. 19, p. On the calculation by molecular dynamics of the shear viscosity of a simple fluid. Mol. Phys., 26 [] Nosé, S. and Klein, M. Constant pressure molecular dynamics for molecular systems.

Molecular dynamics simulations have been carried out on CO 2 – [bmim][PF 6] mixtures using a refined atomistic potential model for the ionic liquid, at different concentrations of CO expansion in volume as a function of added CO 2 was found to agree well with experiments at all but the highest concentration.

Significant concentration dependent differences in the radial distribution. A methodology for the determination of the solid-fluid contact angle, to be employed within molecular dynamics (MD) simulations, is developed and systematically applied. The calculation of the contact angle of a fluid drop on a given surface, averaged over an equilibrated MD trajectory, is divided in three main steps: (i) the determination of the fluid molecules that constitute the interface.

FLUID PRESSURE The cause of fluid pressure Section described the dynamic behaviour of molecules in a liquid or gas. When a molecule rebounds from any confining boundary, a force equal to the rate of change of momentum of that molecule is exerted upon the boundary.

If the area of the solid/fluid boundary is large compared to. Computer simulations of inhomogeneous soft matter systems often require accurate methods for computing the local pressure.

We present a simple derivation, based on the virial relation, of two equivalent expressions for the local (atomistic) pressure in a molecular dynamics simulation. Molecular Dynamics. Molecular Dynamics (MD) is an atomistic simulation method for studying nanoscale phenomenon in wide range of materials like metals, ceramics and biological molecules.

The method typically describes the forces between atoms, using interatomic potentials and tracks the trajectories of as they move due to the attractive and repulsive forces between neighboring atoms. Instead, a shear rate can be imposed at the wall, which allows the calculation of wall material properties by means of an iterative method.

The remaining fluid region will be computed by a spectral hp method. We present MD simulations of a Couette flow, and the results of the developed boundary conditions from the wall fluid interaction. We present results of molecular dynamics simulations of lipid bilayers under a high transverse electrical field aimed at investigating their electroporation.

Several systems are studied, namely 1), a bare bilayer, 2), a bilayer containing a peptide nanotube channel, and 3), a. A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress.

In this formulation the MD cell shape and size can change according to dynamical equations given by this Lagrangian. This new MD technique is well suited to the study of structural transformations in solids. Molecular dynamics calculation of electrostatic potential differences has the ability to provide a significant advantage over these continuum models, in that it can in principle describe biomolecular systems without system-specific empirical parametrisation (e.g., choice of a permittivity constant for a specific system of biomolecules Abstract.

A molecular dynamics version of the Gibbs ensemble calculation is proposed. This calculation is based on an extended Hamiltonian formalism that treats the temperature, volume, and the coupling of a single particle to the rest of the system as continuous dynamical degrees of freedom with their own equations of motion.

@article{osti_, title = {Molecular-dynamics calculations of the velocity autocorrelation function: hard-sphere results}, author = {Erpenbeck, J J and Wood, W W}, abstractNote = {The velocity autocorrelation function for the hard-sphere fluid is computed for ten values of the volume ranging from 25 to times the close-packed volume V/sub 0/ for systems of from to hard spheres.

Firstly, thermodynamic results of real gases can be used to fit the parameters of the interaction potentials that later will be used in Molecular Dynamics simulation of systems at high densities.

Revised thermodynamic and dynamical properties of the hard sphere (HS) system are obtained from extensive molecular dynamics calculations carried out with large system sizes (number of particles, N) and long te formulas for the compressibility factor of the HS solid and fluid branches are proposed, which represent the metastable region and take into account its divergence at close.

The image depicts a hydraulic fluid additive molecule. In a recent blog, “A nanoscale view of hydraulic fluids,” we related how researchers at the University of California, Merced and the Milwaukee School of Engineering are working to better understand the fundamentals of hydraulics fluids on the molecular level, and how that might lead to more-efficient fluid-power systems.

The Lennard-Jones potential (also termed the LJ potential or potential) is an intermolecular pair the intermolecular potentials, the Lennard-Jones potential has a central role as water among real fluids: It is the potential that has been studied most extensively and most is considered as archetype model for simple yet realistic intermolecular interactions.

A nonequilibrium molecular dynamics (NEMD) code was developed and verified by comparing a micro Poiseuille flow with the classical Navier–Stokes solution with nonslip wall boundary conditions.

Liquid argon fluids in a platinum nanotube were simulated to characterize the homogeneous fluid. Calculation of viscosities of branched alkanes from to MPa by molecular dynamics methods using COMPASS force field. Fluid Phase Equilibria, DOI: / A recent () book by (Daivis and Todd) discusses use of the SLLOD method and non-equilibrium MD (NEMD) thermostatting generally, for both simple and complex fluids, e.g.

molecular systems. The latter can be tricky to do correctly. A large number of molecules are usually required to model atomic walls in molecular dynamics simulations.

A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time.

The infinite repetition of unit cell structures within the atomic wall causes the periodicity of the force acting on a fluid molecule from the wall molecules.

LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. Full Text Analysis of dynamic decomposition for barium dimethyl-naphthalene-sulfonate on an Al3Mg (0 0 1) surface from ab-initio molecular dynamics by Zhong, Jun and Li.

Diffusion coefficient calculation. According to the Einstein relation, the self-diffusion coefficient of water, D, can be estimated numerically with the finite difference express 30 (∣r(t 2)−r(t 0)∣ 2 − ∣r(t 1)−r(t 0)∣ 2)∕(t 2 −t 1)=2nD, where r(t 0), r(t 1), and r(t 2) are the positions of water oxygen at time “zero,” 1, and 2 ps, respectively; ⋯ denotes the.been simulated on the molecular level.

Molecular dynamics simulation can provide the. Prediction of Gas Hydrates Equilibria Using Molecular Dynamics Simulation, Mamatha Sudhakar,Chemical equilibrium, pages. In this thesis, Molecular Dynamic (MD) Simulation will be used for the prediction of methane and ethane gas hydrate equilibrium.Molecular mechanics force fields • Today, we’ll focus on molecular mechanics force fields, which are often used for molecular simulations • These are more toward the physics-based, all-atom end (i.e., the more “realistic” force fields) – Represent physical forces .

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