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Articles 1 - 11 of 11
Full-Text Articles in Physical Sciences and Mathematics
Computer Simulations Of Diffusional Isotope Effects And Dynamical Properties Of Silicate Melts, Haiyang Luo
Computer Simulations Of Diffusional Isotope Effects And Dynamical Properties Of Silicate Melts, Haiyang Luo
LSU Doctoral Dissertations
Silicate melts have served as transport agents in the chemical and thermal evolution of Earth. Diffusional isotope effect in silicate melts is the key to interpret isotope variations in lots of geological samples. Isotopic mass dependence of diffusion is commonly expressed as (Di/Dj)=(mj/mi)^β, where Di and Dj are diffusion coefficients of two isotopes whose masses are mi and mj. However, how the dimensionless empirical parameter β depends on temperature, pressure, and composition remains poorly constrained. Viscosity and electrical conductivity are two fundamental dynamical properties of silicate melts needed to constrain melt distribution in Earth's interior but remain unclear for most …
Solvation Structures And Dynamics Of Small Molecules: Experimental And Computational Studies Using Carbonyl Vibrational Modes As Probe, Xiaoliu Zhang
Solvation Structures And Dynamics Of Small Molecules: Experimental And Computational Studies Using Carbonyl Vibrational Modes As Probe, Xiaoliu Zhang
LSU Doctoral Dissertations
Solutions are ubiquitous in both the global environment and the human body, and play a significant role in scientific research and industrial production. The structures and dynamics of solutions have been studied for centuries. However, conventional experimental methods, whose intrinsic measuring time is on the order of nanoseconds to microseconds, could not detect the fast dynamics taking place in the solution on the timescale of femto- and pico-second. In this dissertation, the ultrafast two-dimensional infrared (2DIR) spectroscopy was applied to characterize the structure and dynamics in three different types of solutions on the sub-picosecond timescale. Linear Fourier transform infrared spectroscopy …
Pattern Mining And Events Discovery In Molecular Dynamics Simulations Data, Shobhit Sandesh Shakya
Pattern Mining And Events Discovery In Molecular Dynamics Simulations Data, Shobhit Sandesh Shakya
LSU Doctoral Dissertations
Molecular dynamics simulation method is widely used to calculate and understand a wide range of properties of materials. A lot of research efforts have been focused on simulation techniques but relatively fewer works are done on methods for analyzing the simulation results. Large-scale simulations usually generate massive amounts of data, which make manual analysis infeasible, particularly when it is necessary to look into the details of the simulation results. In this dissertation, we propose a system that uses computational method to automatically perform analysis of simulation data, which represent atomic position-time series. The system identifies, in an automated fashion, the …
A Hybrid Framework Of Iterative Mapreduce And Mpi For Molecular Dynamics Applications, Shuju Bai
A Hybrid Framework Of Iterative Mapreduce And Mpi For Molecular Dynamics Applications, Shuju Bai
LSU Doctoral Dissertations
Developing platforms for large scale data processing has been a great interest to scientists. Hadoop is a widely used computational platform which is a fault-tolerant distributed system for data storage due to HDFS (Hadoop Distributed File System) and performs fault-tolerant distributed data processing in parallel due to MapReduce framework. It is quite often that actual computations require multiple MapReduce cycles, which needs chained MapReduce jobs. However, Design by Hadoop is poor in addressing problems with iterative structures. In many iterative problems, some invariant data is required by every MapReduce cycle. The same data is uploaded to Hadoop file system in …
Visualization Of Time-Varying Data From Atomistic Simulations And Computational Fluid Dynamics, Bidur Bohara
Visualization Of Time-Varying Data From Atomistic Simulations And Computational Fluid Dynamics, Bidur Bohara
LSU Doctoral Dissertations
Time-varying data from simulations of dynamical systems are rich in spatio-temporal information. A key challenge is how to analyze such data for extracting useful information from the data and displaying spatially evolving features in the space-time domain of interest. We develop/implement multiple approaches toward visualization-based analysis of time-varying data obtained from two common types of dynamical simulations: molecular dynamics (MD) and computational fluid dynamics (CFD). We also make application case studies. Parallel first-principles molecular dynamics simulations produce massive amounts of time-varying three-dimensional scattered data representing atomic (molecular) configurations for material system being simulated. Rendering the atomic position-time series along with …
A Study Of The Elongation Of Fibrils Of The Alzheimer's Amyloid Beta Protein With A Coarse-Grained Force Field, Ana Rojas
LSU Doctoral Dissertations
Alzheimer’s disease (AD) is a brain disorder named after the German psychiatrist Alois Alzheimer, who first described the disease in 1906. AD is a form of dementia, characterized by impairment of memory and other intellectual abilities, caused by the loss of neurons and synapses (the structures that permit communication between neurons) in certain regions of the brain. Although the mechanism by which neurons are affected is not yet well understood, research points to a small protein, the beta-amyloid peptide (Abeta), as the first suspect. Ab chains are present in the brains of healthy individuals, but in AD patients, they associate …
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 …
Space-Time Multiresolution Approach To Atomistic Visualization, Dipesh Bhattarai
Space-Time Multiresolution Approach To Atomistic Visualization, Dipesh Bhattarai
LSU Doctoral Dissertations
Time-varying three-dimensional positional atomistic data are rich in spatial and temporal information. The problem is to understand them. This work offers multiple approaches that enable such understanding. An interactive atomistic visualization system is developed integrating complex analyses with visualization to present the data on space-time multiresolution basis facilitating the information extraction and generate understanding. This work also shows the usefulness of such an integrated approach. The information obtained from the analyses represents the system at multiple length and time scales. Radial distribution function (RDF) provides a complete average spatial map of the distribution of the atoms in the system which …
Molecular-Dynamics Simulations Of Self-Assembled Monolayers (Sam) On Parallel Computers, Satyavani Vemparala
Molecular-Dynamics Simulations Of Self-Assembled Monolayers (Sam) On Parallel Computers, Satyavani Vemparala
LSU Doctoral Dissertations
The purpose of this dissertation is to investigate the properties of self-assembled monolayers, particularly alkanethiols and Poly (ethylene glycol) terminated alkanethiols. These simulations are based on realistic interatomic potentials and require scalable and portable multiresolution algorithms implemented on parallel computers. Large-scale molecular dynamics simulations of self-assembled alkanethiol monolayer systems have been carried out using an all-atom model involving a million atoms to investigate their structural properties as a function of temperature, lattice spacing and molecular chain-length. Results show that the alkanethiol chains tilt from the surface normal by a collective angle of 25o along next-nearest neighbor direction at 300K. At …
Massively Parallel Molecular Dynamics Simulations Of Crack-Front Dynamics And Morphology In Amorphous Nanostructured Silica, Cindy Lynn Rountree
Massively Parallel Molecular Dynamics Simulations Of Crack-Front Dynamics And Morphology In Amorphous Nanostructured Silica, Cindy Lynn Rountree
LSU Doctoral Dissertations
Atomistic aspects of dynamic fracture in amorphous and nanostructured silica are herein studied via Molecular dynamics (MD) simulations, ranging from a million to 113 million atom system. The MD simulations were performed on massivelly parallel computers using highly efficient multi-resolution algorithms. Crack propagation in these systems is accompanied by nucleation and growth of nanometer scale cavities up to 20 nm ahead of the crack front. Cavities coalesce and merge with the advancing crack to cause mechanical failure. Recent AFM studies in silica glasses confirm this scenario of fracture [1]. The morphology of the fracture surfaces is studied by calculating the …
Molecular Dynamics Simulations Of Adhesion And Nanoidentation Of Gallium Arsenide, Francis Brent Neal, Jr.
Molecular Dynamics Simulations Of Adhesion And Nanoidentation Of Gallium Arsenide, Francis Brent Neal, Jr.
LSU Doctoral Dissertations
The purpose of this dissertation is to investigate the nanoscale hardness of gallium arsenide thin films and the elastic-plastic behavior of gallium arsenide under an indenter. These investigations were carried out using molecular dynamics (MD) simulations. The simulations are based on interatomic potentials that accurately reproduce many properties of bulk GaAs. The MD simulations performed required scalable and efficient algorithms for implementation on large parallel computers. Nanoindentation simulations were performed using an ideal indenter that was held rigid during the simulation. To reduce the transient effects due to loading, the traversal of the indenter was interrupted periodically to allow the …