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Transient Molecular Dynamics Simulations Of Viscosity For Simple Fluids, Richard L. Rowley, Jason C. Thomas
Transient Molecular Dynamics Simulations Of Viscosity For Simple Fluids, Richard L. Rowley, Jason C. Thomas
Faculty Publications
A transient molecular dynamics (TMD) method has been developed for simulation of fluid viscosity. In this method a sinusoidal velocity profile is instantaneously overlaid onto equilibrated molecular velocities, and the subsequent decay of that velocity profile is observed. The viscosity is obtained by matching in a least-squares sense the analytical solution of the corresponding momentum transport boundary-value problem to the simulated decay of the initial velocity profile. The method was benchmarked by comparing results obtained from the TMD method for a Lennard-Jones fluid with those previously obtained using equilibrium molecular dynamics (EMD) simulations. Two different constitutive models were used in …
Simulation Of Plasticity In Nanocrystalline Silicon, M. J. Demkowicz, A. S. Argon, D. Farkas, Megan Frary
Simulation Of Plasticity In Nanocrystalline Silicon, M. J. Demkowicz, A. S. Argon, D. Farkas, Megan Frary
Materials Science and Engineering Faculty Publications and Presentations
Molecular dynamics investigation of plasticity in a model nanocrystalline silicon system demonstrates that inelastic deformation localizes in intergranular regions. The carriers of plasticity in these regions are atomic environments that can be described as high-density liquid-like amorphous silicon. During fully developed flow, plasticity is confined to system-spanning intergranular zones of easy flow. As an active flow zone rotates out of the plane of maximum resolved shear stress during deformation to large strain, new zones of easy flow are formed. Compatibility of the microstructure is accommodated by processes such as grain rotation and formation of new grains. Nano-scale voids or cracks …
Parallel Fast Multipole Method For Molecular Dynamics, Reid G. Ormseth
Parallel Fast Multipole Method For Molecular Dynamics, Reid G. Ormseth
Theses and Dissertations
We report on a parallel version of the Fast Multipole Method (FMM) implemented in the classical molecular dynamics code, NAMD (Not Another Molecular Dynamics program). This novel implementation of FMM aims to minimize interprocessor communication through the modification of the FMM grid to match the hybrid force and spatial decomposition scheme already present in NAMD. This new implementation has the benefit of replacing all-to-all communications broadcasts with direct communications between nearest neighbors. This results in a significant reduction in the amount of communication compared to earlier attempts to integrate FMM into common molecular dynamics programs. The early performance of FMM …
Construction And Application Of Computationally Tractable Theories On Nonlinear Spectroscopy, Christine L. Neipert
Construction And Application Of Computationally Tractable Theories On Nonlinear Spectroscopy, Christine L. Neipert
USF Tampa Graduate Theses and Dissertations
Nonlinear optical processes probe systems in unique manners. The signals obtained from nonlinear spectroscopic experiments are often significantly different than more standard linear techniques, and their intricate nature can make it difficult to interpret the experimental results. Given the complexity of many nonlinear lineshapes, it is to the benefit of both the theoretical and experimental communities to have molecularly detailed computationally amenable theories of nonlinear spectroscopy. Development of such theories, bench marked by careful experimental investigations, have the ability to understand the origins of a given spectroscopic lineshape with atomistic resolution. With this goal in mind, this manuscript details the …
Design Of Surface Acoustic Wave Sensors With Nanomaterial Sensing Layers: Application To Chemical And Biosensing, Subramanian K.R.S Sankaranarayanan
Design Of Surface Acoustic Wave Sensors With Nanomaterial Sensing Layers: Application To Chemical And Biosensing, Subramanian K.R.S Sankaranarayanan
USF Tampa Graduate Theses and Dissertations
Surface acoustic wave (SAW) sensors detect chemical and biological species by monitoring the shifts in frequency of surface acoustic waves generated on piezoelectric substrates. Incorporation of nanomaterials having increased surface area as sensing layer have been effective in improving the sensitivity as well as miniaturization of SAW sensors. Selectivity, sensitivity and speed of response are the three primary aspects for any type of sensor. This dissertation focuses on design and development of SAW devices with novel transducer configurations employing nanomaterial sensing layers for enhanced sensing, improved selectivity, and speed of response. The sensing mechanism in these SAW sensors is a …
Adaptive Treatment Of Van Der Waals Interactions In Empirical Bond-Order Potentials With Application To Junction Formation In Carbon Nanotubes, Aibing Liu
All Dissertations
Molecular dynamics (MD) simulation of reactive condensed-phase hydrocarbon systems is a challenging research area. The AIREBO potential is particularly useful in this area because it can simulate bond breaking and bond forming during chemical reactions. It also includes non-bonded interactions for systems with significant intermolecular interactions.
The first part of this dissertation describes a method to adaptively incorporate van der Waals interaction of carbon atoms into the AIREBO force field. In bond-order potentials, the covalent bonding interactions adapt to the local chemical environment, allowing bonded interactions to change in response to local chemical changes.
Non-bonded interactions should adjust to their …
Modeling Acoustic Effects On Shear Coaxial Jet Flow Utilizing Molecular Dynamic Simulation, Jermaine S. Sailsman
Modeling Acoustic Effects On Shear Coaxial Jet Flow Utilizing Molecular Dynamic Simulation, Jermaine S. Sailsman
Theses and Dissertations
The purpose of this research is to determine if acoustical effects on a coaxial shear injection jet flow can be modeled through the use of molecular dynamic simulation. Molecular dynamic simulations model flows as a group of interacting particles. The flow in this research was simulated using nitrogen molecules. The initial task involved achieving effective geometry for a simulated coaxial jet. The coaxial jet geometry was driven by the desire for simulations to operate in the continuum regime, which requires very low Knudsen numbers. Three outer to inner jet ratios of 0.0, 1.0, and 6.0 were examined with the inner …
Molecular Dynamics Simulation Studies Of Dna And Proteins: Force Field Parameter Development Of Small Ligands And Convergence Analysis For Simulations Of Biomolecules, Anne Loccisano
Electronic Theses and Dissertations
In the first part of this dissertation, CHARMM force field parameters for DNA minor groove-binding polyamides were developed. The parameterization involved the subdivision of the polyamides into model compounds, which were calibrated against MP2/6-31G(d) data. To test the new parameters, fourteen 10 ns molecular dynamics crystal simulations have been carried out on a DNA/polyamide complex at low (113K) and high (300K) temperatures. Of the 18 helical parameters examined, only one (stagger) is found to be statistically significant from the crystal structure with a t-test at the 95% confidence level. For the high temperature, stagger is non-significant at the 97% confidence …