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Molecular dynamics at constant temperature and pressureDecker, Mike W. 02 November 1995 (has links)
Molecular dynamics is a technique in which the
trajectories of a group of particles are calculated as a
function of time by integrating the equations of motion. In
this thesis we study the use of molecular dynamics for atoms
in a crystal.
A model is introduced which describes interactions of a
physical system with an external heat reservoir in molecular
dynamics simulations. This is accomplished by the addition
of a "virtual variable" to the Hamiltonian which is used to
scale time. Aspects of this model are discussed and
examples are presented for a simple system.
Similarly, a constant pressure model is introduced in
which additional virtual volume variables are added to the
Hamiltonian. The volume and shape of the molecular dynamics
cell are now free to vary. Simple examples are discussed.
Aspects of the computer programs and the algorithms are
explained. Particular attention is focused on the methods
used to integrate the equations of motion and to calculate
the coulomb interactions.
Examples of simulations using a zirconium oxide crystal
are presented. We study the effects of heat bath and
pressure bath simulations, both separately and in
combination. Various features of the behavior are
investigated with the primary focus on phase changes,
numerical errors, and parameters describing the heat and
pressure baths. / Graduation date: 1996
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Dynamics of double-walled carbon nanotube oscillatorsWong, Lai-ho. January 2005 (has links)
Thesis (Ph. D.)--University of Hong Kong, 2006. / Title proper from title frame. Also available in printed format.
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An Analysis of Prominent Water Models by Molecular Dynamics SimulationsJohnson, Quentin Ramon 20 April 2010 (has links)
Water is the most common solvent for most biological reactions, therefore it is vital that we fully understand water and all its properties. The complex hydrogen bonding network that water forms can influence protein-protein and protein-substrate interactions and can slow protein conformational shifts. Here, I examine an important property of water known as energetic roughness. The network of interactions between individual water molecules affect the energy landscape of proteins by altering the underlying energetic roughness. I have attributed this roughness to the making and breaking of hydrogen bonds as the network of hydrogen bonds constantly adopts new conformations. Through a novel computational approach I have analyzed five prominent water models and have determined their inherent roughness to be between 0.43 and 0.62 kcal/mol.
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Molecular dynamics simulation of montmorillonite and mechanical and thermodynamic properties calculationsAtilhan, Selma 15 May 2009 (has links)
Nanocomposites refer to the materials in which the defining characteristic size of
inclusions is in the order of 10-100nm. There are several types of nanoparticle inclusions
with different structures: metal clusters, fullerenes particles and molybdenum selenide,
Our research focus is on polymer nanocomposites with inorganic clay particles as
inclusions, in particular we used sodium montmorillonite polymer nanocomposite.
In our study, modeling and simulations of sodium montmorillonite (Na+-MMT) is
currently being investigated as an inorganic nanocomposite material. Na+-MMT clay
consists of platelets, one nanometer thick with large lateral dimensions, which can be
used to achieve efficient reinforcement of polymer matrices. This nanocomposite has
different applications such as a binder of animal feed, a plasticizing agent in cement,
brick and ceramic, and a thickener and stabilizer of latex and rubber adhesives.
In this study, sodium montmorillonite called Na+-MMT structure is built with the
bulk system and the layered system which includes from 1 to 12 layers by using Crystal
Builder of Cerius2. An isothermal and isobaric ensemble is used for calculation of
thermodynamic properties such as specific heat capacities and isothermal expansion
coefficients of Na+-MMT. A canonical ensemble which holds a fixed temperature,
volume and number of molecules is used for defining exfoliation kinetics of layered
structures and surface formation energies for Na+-MMT layered structures are calculated
by using a canonical ensemble. Mechanical properties are used to help characterize and
identify the Na+-MMT structure. Several elastic properties such as compliance and
stiffness matrices, Young's, shear, and bulk modulus, volume compressibility, Poisson's
ratios, Lamé constants, and velocities of sound are calculated in specified directions. Another calculation method is the Vienna Ab-initio Simulation Package (VASP). VASP
is a complex package for performing ab-initio quantum-mechanical calculations and
molecular dynamic (MD) simulations using pseudopotentials and a plane wave basis set.
Cut off energy is optimized for the unit cell of Na+-MMT by using different cut off
energy values. Experimental and theoretical cell parameters are compared by using cell
shape and volume optimization and root mean square (RMS) coordinate difference is
calculated for variation of cell parameters. Cell shape and volume optimization are done
for calculating optimum expansion or compression constant.
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Molecular dynamic modeling and simulation for polymers /Harrell, Anthony F. January 2003 (has links) (PDF)
Thesis (M.Sc.)--Naval Postgraduate School, September 2003. / Includes bibliographical references.
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Molecular dynamic modeling and simulation for polymers /Harrell, Anthony F. January 2003 (has links) (PDF)
Thesis (M.S. in Mechanical Engineering)--Naval Postgraduate School, September 2003. / Thesis advisor(s): Young W. Kwon. Includes bibliographical references (p. 49-50). Also available online.
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Combined crystallographic and cryo-electron microscopic analysis of adeno-associated virus type 2Bhatia, Smita. Chapman, Michael S., January 2003 (has links)
Thesis (Ph. D.)--Florida State University, 2003. / Advisor: Dr. Michael S. Chapman, Florida State University, College of Arts and Sciences, Institute of Molecular Biophysics. Title and description from dissertation home page (viewed Mar. 11, 2004). Includes bibliographical references.
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A theoretical analysis of experimental open quantum dynamicsModi, Kavan Kishore, 1978- 25 September 2012 (has links)
In recent years there has been a significant development of the dynamical map formalism for initially correlated states of a system and its environment. Based on some of these results, we study quantum process tomography for initially correlated states of the system and the environment. This is beyond the usual assumption that the state of the system and the environment are initially uncorrelated. Since quantum process tomography is an experimental procedure, we wind up having to study the role of preparation of input states for open quantum experiments. We work out a theory for the general preparation procedure, and study two preparation procedures in detail. In specific, we study the stochastic preparation procedure and the projective preparation procedure and apply them to quantum process tomography. The two preparation procedures describe the ways to uncorrelate the state of the system and the environment. However the specifics of how this is implemented plays a role on the outcomes of the experiment. When the stochastic preparation procedure is applied properly, quantum process tomography yields a linear process maps. We point out what it means to apply the stochastic preparation procedure properly by constructing several simple examples where inconsistencies in preparations leads to errors. When the projective preparation procedure is applied, quantum process tomography leads to a non-linear process map. We show that these processes can only be consistently described by a general dynamical map, which we call M-map. The M-map contains all of the dynamical information for the state of the system without the affects of a preparation procedure. By carefully extracting some of this dynamical information, we construct a quantitative measure for the memory effect due to the initial correlations with the environment. / text
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EXCITED STATE PROTOTROPIC EQUILIBRIASchulman, Stephen G. (Stephen Gregory), 1940- January 1967 (has links)
No description available.
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Nuclear magnetic relaxation in polytetrafluorethylene, tetrafluorethylene-hexafluoropropylene copolymer, and polychlorotrifluoroethyleneWatras, Ronald Edward January 1972 (has links)
No description available.
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