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Articles 1 - 11 of 11
Full-Text Articles in Entire DC Network
Prediction Of Fluid Viscosity Through Transient Molecular Dynamic Simulations, Jason Christopher Thomas
Prediction Of Fluid Viscosity Through Transient Molecular Dynamic Simulations, Jason Christopher Thomas
Theses and Dissertations
A novel method of calculating viscosity from molecular dynamics simulations is developed, benchmarked, and tested. The technique is a transient method which has the potential to reduce CPU requirements for many conditions. An initial sinusoidal velocity profile is overlaid upon the peculiar velocities of the individual molecules in an equilibrated simulation. The transient relaxation of this initial velocity profile is then compared to the corresponding analytical solution of the momentum equation by adjusting the viscosity-related parameters in the constitutive equation that relate the shear rate to the stress tensor. The newly developed Transient Molecular Dynamics (TMD) method was tested for …
Self-Consistent Multiscale Modeling In The Presence Of Inhomogeneous Fields, Ruichang Xiong, Rebecca L. Empting, Ian C. Morris, David J. Keffer
Self-Consistent Multiscale Modeling In The Presence Of Inhomogeneous Fields, Ruichang Xiong, Rebecca L. Empting, Ian C. Morris, David J. Keffer
Faculty Publications and Other Works -- Chemical and Biomolecular Engineering
Molecular dynamics (MD) simulations of a Lennard–Jones fluid in an inhomogeneous external field generate steady-state profiles of density and pressure with nanoscopic heterogeneities. The continuum level of mass, momentum, and energy transport balances is capable of reproducing the MD profiles only when the equation of state for pressure as a function of density is extracted directly from the molecular level of description. We show that the density profile resulting from simulation is consistent with both a molecular-level theoretical prediction from statistical mechanics as well as the solution of the continuum-level set of differential equations describing the conservation of mass and …
Theory And Simulation Of Metal-Organic Materials And Biomolecules, Jonathan L. Belof
Theory And Simulation Of Metal-Organic Materials And Biomolecules, Jonathan L. Belof
USF Tampa Graduate Theses and Dissertations
The emerging field of nanomaterials has raised a number of fascinating scientific questions that remain unanswered. Molecular theory and computer simulation are key tools to unlocking future discoveries in materials science, and various computational techniques and results toward this goal are elucidated here. High-performance computing methods (utilizing the latest supercomputers and codes) have been developed to explore and predict the chemistry and physical properties of systems as diverse as Metal-Organic Frameworks, discrete nanocubes, photoswitch molecules, porphyrins and several interesting enzymes. In addition, highlights of fundamental statistical physics, such as the Feynman-Hibbs effective partition function and generalized ensemble theory, are expounded …
Experimental And Theoretical Investigation Of Molecular Field Effects By Polarization-Resolved Resonant Inelastic X-Ray Scattering, Stephane Carniato, Renaud Guillemin, Wayne C. Stolte, Loic Journel, Richard Taieb, Dennis W. Lindle, Marc Simon
Experimental And Theoretical Investigation Of Molecular Field Effects By Polarization-Resolved Resonant Inelastic X-Ray Scattering, Stephane Carniato, Renaud Guillemin, Wayne C. Stolte, Loic Journel, Richard Taieb, Dennis W. Lindle, Marc Simon
Chemistry and Biochemistry Faculty Research
We present a combined theoretical and experimental study of molecular field effects on molecular core levels. Polarization-dependent resonant inelastic x-ray scattering is observed experimentally after resonant K-shell excitation of CF3Cl and HCl. We explain the linear dichroism observed in spin-orbit level intensities as due to molecular field effects, including singlet-triplet exchange, and interpret this behavior in terms of population differences in the 2px,y,z inner-shell orbitals. We investigate theoretically the different factors that can affect the electronic populations and the dynamical R dependence of the spin-orbit ratio. Finally, the results obtained are used to interpret the L-shell …
First-Principles Studies Of Shock-Induced Phenomena In Energetic Materials, Aaron Christopher Landerville
First-Principles Studies Of Shock-Induced Phenomena In Energetic Materials, Aaron Christopher Landerville
USF Tampa Graduate Theses and Dissertations
An understanding of the atomic-scale features of chemical and physical processes taking place behind the shockwave front will help in addressing some of the major challenges in energetic materials research. The high pressure shockwave environment can be simulated using computational techniques to predict mechanical and chemical properties of a shocked material. Density functional theory calculations were performed to investigate uniaxial compressions of diamond and both hydrostatic and uniaxial compressions of TATB and NEST-1. For diamond, we calculated shear stresses for uniaxial compressions in the , , and directions and discovered the anomalous elastic regime which is responsible for the significant …
Multiscale Friction Using A Nested Internal State Variable Model For Particulate Materials, Tonya Williams Stone
Multiscale Friction Using A Nested Internal State Variable Model For Particulate Materials, Tonya Williams Stone
Theses and Dissertations
In the current study we use a multiscale computational methodology to develop an internal state variable model that captures frictional effects during the compaction of particulate materials. Molecular dynamics simulations using EAM potentials were performed to model the contact behavior of spherical nickel nanoparticles. Simulation results for models consisting of various particle sizes and contact angles were compared to quantify the length scale effects of friction. The influence of friction on the microstructure was shown from the nucleation of dislocations near the interface region during sliding. By using an internal state variable theory to couple the microstructural changes due to …
Molecular Dynamics Study Of Crystal Plasticity During Nanoindentation In Ni Nanowires, V. Dupont, F. Sansoz
Molecular Dynamics Study Of Crystal Plasticity During Nanoindentation In Ni Nanowires, V. Dupont, F. Sansoz
Aerospace Engineering - Daytona Beach
Molecular dynamics simulations were performed to gain fundamental insight into crystal plasticity, and its size effects in nanowires deformed by spherical indentation. This work focused on-oriented single-crystal, defect-free Ni nanowires of cylindrical shape with diameters of 12 and 30 nm. The indentation of thin films was also comparatively studied to characterize the influence of free surfaces in the emission and absorption of lattice dislocations in single-crystal Ni. All of the simulations were conducted at 300 K by using a virtual spherical indenter of 18 nm in diameter with a displacement rate of1 ms1. No significant effect of sample size was …
Self-Consistent Multiscale Modeling In The Presence Of Inhomogeneous Fields, David Keffer
Self-Consistent Multiscale Modeling In The Presence Of Inhomogeneous Fields, David Keffer
David Keffer
Molecular dynamics (MD) simulations of a Lennard–Jones fluid in an inhomogeneous external field generate steady-state profiles of density and pressure with nanoscopic heterogeneities. The continuum level of mass, momentum, and energy transport balances is capable of reproducing the MD profiles only when the equation of state for pressure as a function of density is extracted directly from the molecular level of description. We show that the density profile resulting from simulation is consistent with both a molecular-level theoretical prediction from statistical mechanics as well as the solution of the continuum-level set of differential equations describing the conservation of mass and …
Nano-Mechanics Of Cartilage Glycosaminoglycans Using Molecular Dynamics Methods, Kevin Neil Hendrickson
Nano-Mechanics Of Cartilage Glycosaminoglycans Using Molecular Dynamics Methods, Kevin Neil Hendrickson
Master's Theses
Articular Cartilage (AC) is the main load carrying material in synovial joints {Hamerman, 1962} and degeneration of AC can cause pain in the form of arthritis. Current work is centered on the method of replacing damaged cartilage inside the body (in vivo) with tissue engineered outside the body (ex vivo) {Temenoff, 2000}. In order to engineer tissue ex vivo similar to the native tissue in structure and function there must be a comprehensive understanding of the mechanical properties of AC. This work focuses on the study of glycosaminoglycans (GAGs), a molecule known to be primarily responsible for the compressive stiffness …
Computational Studies On Fatty Acid Synthesis: From Mechanisms To Drug Design, Matthew Edward Mckenzie
Computational Studies On Fatty Acid Synthesis: From Mechanisms To Drug Design, Matthew Edward Mckenzie
LSU Doctoral Dissertations
The first committed steps of the Fatty Acid synthesis pathway involves the de/carboxylation reactions of biotin. By understanding this step, potential novel antimicrobial agents could be discovered. The current tools of drug discovery can only help the research in finding and modifying potential hits. Finding a lead candidate from these programs are often equated to finding a needle in a haystack, which is due to the many assumptions used in molecular docking. The fundamental reaction kinetics can not be described by these techniques and a detailed study of the decarboxylation reaction is investigated using ab initio molecular dynamics. In this …
Oxidation Modeling By Means Of Molecular Dynamics, Chaiyod Soontrapa
Oxidation Modeling By Means Of Molecular Dynamics, Chaiyod Soontrapa
UNLV Theses, Dissertations, Professional Papers, and Capstones
Oxidation modeling is normally engineered to study systems at macroscopic scales, mostly in analytical forms based on diffusion theories. The associated time scale is usually in months, days, or minutes, and the length scale is in the order of microns. In this dissertation, oxidation modeling is performed at atomistic scale with the time and length scales in picoseconds and angstroms, respectively, using molecular dynamics. Molecular dynamics simulations generate trajectories of each atom or particle in a system according to the laws of physics. Studying oxidations under the atomistic point of view can offer new insights on atomic behaviors and influencing …