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Modeling The Self-Assembly Of Ordered Nanoporous Materials, Szu-Chia Chien

Doctoral Dissertations

Porous materials are of great importance in many fields due to their wide applications. An ongoing theme in this area is the tailoring of materials for specific applications. With a better understanding of the formation mechanisms, tailoring and controlling the pore structure may be achieved. The objective of this research is acquiring further understanding of the fundamental physics that govern the formation of these materials using molecular simulations. We are aiming to unravel the assembly process of silica porous materials using a semi-rigid silica tetrahedral model. This model together with reaction ensemble Monte Carlo simulations allows us to study the …

Computational Insights Into Nitrogen-Related Biocatalysis, Bogdan Florin Ion

Electronic Theses and Dissertations

Nitrogen-dependent reactions are prevalent and essential in many biochemical systems. These chemical reactions are ensured to occur at physiological rates via the catalytic power of enzymes. Important to some reactions, their catalysis is also dependent on cofactors such as NAD+, metal ions, and active site water molecules. In this dissertation, several nitrogen-related biochemical systems are investigated using complementary computational methods such as docking, molecular dynamics simulations, quantum chemical clusters, and quantum mechanics/molecular mechanics. The use of this multi-scale computational approach has been successfully applied to investigate the catalytic mechanisms, substrate binding, and roles of key active site residues of both …

With Vibrationally Excited Thiophosgene Molecule And Double-Well Ion Traps, Dmytro Shyshlov

Dissertations (1934 -)

For practical realization of quantum information processing we need a quantum system that provides reliable preparation of the initial state, high-fidelity quantum gate operations, error tolerance, readout of the result of quantum computation and scalability of the system to increase the number of qubits. In this dissertation we show how these requirements can be addressed for molecular quantum computer. For computational study of quantum information processing with molecules we employ thiophosgene (SCCl2) molecule that has been used as a test system for quantum control experiments [Mol. Phys. 105, 1999 (2007)]. We investigate the gateway scheme of control in which transitions …

Molexpl: A Tool For Ab Initio Data Exploration And Visualization, Xueying Wang, Nicolas Onofrio, Alejandro Strachan

The Summer Undergraduate Research Fellowship (SURF) Symposium

Density functional theory (DFT) based on ab initio theory, is a powerful method to resolve the electronic structure of atoms, molecules and solids. However, in practical, DFT is limited to few hundreds of atoms. To overcome this limitation, researchers have developed empirical interatomic potentials implemented in molecular dynamics (MD) simulations. MD ignores the movements of electrons and describes bonding and non-bonding interaction as a function of the distance between atoms called force fields (FF) or interatomic potentials. These empirical potentials are optimized against large datasets of DFT calculations relevant to describe the interactions between the atoms included in the training …

Using Dissipative Particle Dynamics For Modeling Surfactants, Yuchen Zhang, Arezoo M. Ardekani

The Summer Undergraduate Research Fellowship (SURF) Symposium

Oil recovery is an industrial process that injects aqueous solutions into an oil reservoir to pump out crude oil and promote the oil production. The aqueous solution contains surfactants for reducing the interfacial tension (IFT) between aqueous phase and oil. The critical micelle concentration (CMC) is the concentration of surfactant above which micelles form and the interfacial tension reaches a plateau. Our research seeks to measure IFT and CMC for surfactants using dissipative particle dynamics (DPD) technique, which is a coarse-grained method based on the molecular dynamics. We first study how IFT is influenced by the surfactant concentration. Furthermore, another …

Computational Modeling Of Rna-Small Molecule And Rna-Protein Interactions, Lu Chen

Dissertations & Theses (Open Access)

The past decade has witnessed an era of RNA biology; despite the considerable discoveries nowadays, challenges still remain when one aims to screen RNA-interacting small molecule or RNA-interacting protein. These challenges imply an immediate need for cost-efficient while predictive computational tools capable of generating insightful hypotheses to discover novel RNA-interacting small molecule or RNA-interacting protein. Thus, we implemented novel computational models in this dissertation to predict RNA-ligand interactions (Chapter 1) and RNA-protein interactions (Chapter 2).

Targeting RNA has not garnered comparable interest as protein, and is restricted by lack of computational tools for structure-based drug design. To test the potential …

Traction-Separation Relationships For Hydrogen-Induced Grain Boundary Embrittlement In Nickel Via Molecular Dynamics Simulations, Wesley Allen Barrows

Graduate Theses and Dissertations

The deleterious effects of atomic and molecular hydrogen on the mechanical properties of metals have long been observed. Although several theories exist describing the mechanisms by which hydrogen negatively influences the failure of materials, a consensus has yet to be reached regarding the exact mechanism or combination of mechanisms. Two mechanisms have gained support in explaining hydrogen’s degradative role in non-hydride forming metals: hydrogen-enhanced localized plasticity and hydrogen-enhanced decohesion. Yet, the interplay between these mechanisms and microstructure in metallic materials has not been explained. Accordingly, for this thesis, the three main objectives are: (i) to develop a numerical methodology to …

Molecular Dynamics Simulations Of A Suspended Particle In A Fluid Near A Wall, Jianwei Ju

Mechanical Engineering ETDs

The behavior of the suspended particles in a fluid is an important subject in fluid flow studies. Earlier research works mostly were performed using a continuum treatment on a macro scale level. Recent developments in the field of micro- and nanofluids have led to a renewed interest in molecular hydrodynamics phenomena. The micro hydrodynamic interactions between particles and solid surfaces have been shown to play important roles in the ordering of particles in vibrated fluids, self-organization of biological cells, and collective dynamics of swimming particles[Voth2002, Riedel2005, Hernandez2005], micro-electronic fluid behaviors and also have great prospects in industry applications. Though a …

Activating The Msh2/Msh6 Apoptotic Pathway In Cancer Cells Using Non-Reserpine Compounds, Jacob M. Mauceri

Honors College Theses

DNA mismatch repair (MMR) is a system that is highly conserved in both prokaryotes and eukaryotes. The heterodimeric protein MutSα and a suite of associated proteins are essential in the recognition and repair of DNA afflicted with mispaired bases and short insertion/deletion loops, but are also implicated in funneling damaged cells towards apoptosis via a key conformational change in a subunit of the MutSα complex. This conformation can be bound specifically by the small molecule reserpine. Molecular dynamics modeling and virtual screening were used to identify additional small molecule novel ligands with the predicted ability to selectively bind this “death” …

A Computational Study Of Anisotropically Curved Nanoparticles Binding To Lipid Membranes, Alexander David Olinger

Electronic Theses and Dissertations

Many cellular processes require drastic change in the cells morphology. Proteins help stimulate these morphological changes by binding to the membranes surface and imposing their curvature on the structure. The dynamics behind the collective generation of curvature in a membrane by a group of proteins is still illusive. Using coarse grained molecular dynamics with a langevin thermostat, we plan to shed light on these dynamics by modeling a nanoparticle after one member of the BAR domain family of proteins (F-BAR domains). This particular member of the family is gently curved compared to others and binds to the membrane only through …

Dnag As An Antibacterial Target, Zorik Chilingaryan

University of Wollongong Thesis Collection 1954-2016

The rise of “superbugs” – antibiotic resistant infection-causing bacteria - poses a catastrophic threat to public health, and prompts the investigation of new drug targets. In this work, the inhibition of specific proteins in bacterial DNA replication machinery – a rich source of new targets - was investigated.

The single stranded DNA-binding protein, SSB, is an interaction hub that engages in vital interactions with several partner proteins through a flexible C-terminal peptide motif (DDDIPF; SSB-Ct). Based on available crystal structures of SSB-Ct with partner proteins, molecular dynamics simulations were used to identify mobile elements of SSB-Ct and important interactions in …

Molecular Dynamics Simulation Of Fracture Behaviour In Nanocrystalline Fcc Structures, Linqing Pei

University of Wollongong Thesis Collection 1954-2016

The study of material failure has always been very important for human beings. Previous studies were mostly conducted at the macroscopic and microscopic scale based on continuum mechanics. However, the effect of nanostructural features on fracture has not been fully understood. Therefore, it is necessary to investigate the fracture mechanics at the atomic scale. Computational modelling, particularly atomistic (or molecular) simulation is becoming an increasingly important technology with which to analyse fracture. In this thesis, molecular dynamics (MD) simulations were carried out to investigate the fracture behaviours in Face Centred Cubic (fcc) nanocrystals.

Nanotwinned Copper (Cu) has an unusual combination …

The Kinetics Of Ni/Al Reactive Intermetallic Composites, Mathew Joseph Cherukara

Open Access Dissertations

Molecular dynamics (MD) simulations have been used to study the underlying physics and atomistic mechanisms of the reaction progression in Ni/Al reactive intermetallic composites. Preparation of these composites, either through deposition techniques or through the process of mechanical ball milling, gives rise to a periodic ordered, nanolaminated structure and in the first part of this thesis, the effects of this laminate period, ignition temperature and volumetric defects are studied. The presence of defects not only speeds up the reaction by as much as 5 times, but changes the nature of mass transport from diffusive to partly ballistic. Subsequently, the feasibility …

Picosecond To Terahertz Perturbation Of Interfacial Water And Electropermeabilization Of Biological Membranes, P. Thomas Vernier, Zachary A. Levine, Ming-Chak Ho, Shu Xiao, Iurii Semenov, Andrei G. Pakhomov

Bioelectrics Publications

Non-thermal probing and stimulation with subnanosecond electric pulses and terahertz electromagnetic radiation may lead to new, minimally invasive diagnostic and therapeutic procedures and to methods for remote monitoring and analysis of biological systems, including plants, animals, and humans. To effectively engineer these still-emerging tools, we need an understanding of the biophysical mechanisms underlying the responses that have been reported to these novel stimuli. We show here that subnanosecond (≤500 ps) electric pulses induce action potentials in neurons and cause calcium transients in neuroblastoma-glioma hybrid cells, and we report complementary molecular dynamics simulations of phospholipid bilayers in electric fields in which …

Changing Cpu Frequency In Comd Proxy Application Offloaded To Intel Xeon Phi Co-Processors, Gary Lawson, Masha Sosonkina, Yuzhong Shen

Computational Modeling & Simulation Engineering Faculty Publications

Obtaining exascale performance is a challenge. Although the technology of today features hardware with very high levels of concurrency, exascale performance is primarily limited by energy consumption. This limitation has lead to the use of GPUs and specialized hardware such as many integrated core (MIC) co-processors and FPGAs for computation acceleration. The Intel Xeon Phi co-processor, built upon the MIC architecture, features many low frequency, energy efficient cores. Applications, even those which do not saturate the large vector processing unit in each core, may benefit from the energy-efficient hardware and software of the Xeon Phi. This work explores the energy …

Novel Phosphotidylinositol 4,5-Bisphosphate Binding Sites On Focal Adhesion Kinase, Jun Feng, Blake Mertz

Faculty & Staff Scholarship

Focal adhesion kinase (FAK) is a protein tyrosine kinase that is ubiquitously expressed, recruited to focal adhesions, and engages in a variety of cellular signaling pathways. Diverse cellular responses, such as cell migration, proliferation, and survival, are regulated by FAK. Prior to activation, FAK adopts an autoinhibited conformation in which the FERM domain binds the kinase domain, blocking access to the activation loop and substrate binding site. Activation of FAK occurs through conformational change, and acidic phospholipids such as phosphatidylinositol 4,5-bisphosphate (PIP2) are known to facilitate this process. PIP2 binding alters the autoinhibited conformation of the FERM and kinase domains …

Atomistic Simulation Of Plasticity Mediated By Grain Boundary And Stacking Fault Tetrahedron In Fcc Metals, Liang Zhang

University of Wollongong Thesis Collection 1954-2016

Nanocrystalline material has been the subject of widespread research over the past couple of decades. When the grain sizes of crystals are down to nanoscale, the so-called nanocrystalline material can exhibit distinct physical properties, unlike their conventional counterparts. The strength and plastic deformation of nanocrystalline material were among the most broadly investigated properties from the mechanical and material perspective. But since the rapid increases in computational power, atomistic simulation has been used extensively to study the mechanical properties of nanocrystalline material from which enormous progress has been made in computational simulation to understand the deformation mechanisms at an atomic scale. …

Deformation Mechanisms In Nanotwinned Materials By Molecular Dynamics Simulations, Xing Zhao

University of Wollongong Thesis Collection 1954-2016

Molecular dynamics simulations are performed to investigate the deformation mechanisms of nanotwinned materials. The simulations oftextured polycrystalline Cu under tensile loading parallel to the twin boundary (TB) reveal that the transmissions of dislocations dominate the plastic deformation. The majority of the TBs retain their initial coherency even after a considerable deformation. The tensile strength monotonically increases as the twin spacing decreases. The main strengthening effect in nanotwinned Cu results from TB restricting the dislocation transmission across TB. Dislocation processes involved in the slip-twin interactions are identified at atomic level, including the direct and indirect transmissions. The direct transmission involves either …

Computational Studies On Alpha-Synuclein In Explicit Solvent: Implications In Parkinson’S Disease, Hongyi Yang

All ETDs from UAB

α-Synuclein (αS) is a cytosolic protein expressed at high levels in the human brain and concentrated in presynaptic nerve terminals. Although the precise nature of αS in vivo remains unclear, the aggregation of αS, from its soluble, functional forms into highly organized amyloid fibrils, has been substantially implicated in the pathology of a number of neurodegenerative diseases collectively known as synucleinopathies. The long-term goal of this project is to understand the molecular mechanisms that initiate αS oligomerization in aqueous solution. A novel computational methodology involving protein modeling and atomistic molecular dynamics (MD) simulations is used in this work. The objective …

The Interaction Mechanisms Of A Screw Dislocation With A Defective Coherent Twin Boundary In Copper, Qiongjiali Fang

Graduate College Dissertations and Theses

Σ3{111} coherent twin boundary (CTB) in face-centered-cubic (FCC) metals and alloys have been regarded as an efficient way to simultaneously increase strength and ductility at the nanoscale. Extensive study of dislocation-CTB interaction has been carried out by a combination of computer simulations, experiments and continuum theory. Most of them, however, are based on the perfect CTB assumption. A recent study [Wang YM, Sansoz F, LaGrange T, et al. Defective twin boundaries in nanotwinned metals. Nat Mater. 2013;12(8):697-702.] has revealed the existence of intrinsic kink-like defects in CTBs of nanotwinned copper through nanodiffraction mapping technique, and has confirmed the effect of …

The Structural Heterogeneity And Dynamics Of Base Stacking And Unstacking In Nucleic Acids, Ada Anna Sedova

Legacy Theses & Dissertations (2009 - 2024)

Base stacking provides stability to nucleic acid duplexes, and base unstacking is involved in numerous biological functions related to nucleic acids, including replication, repair, transcription, and translation. The patterns of base stacking and unstacking in available nucleic acid crystal structures were classified after separation into their individual single strand dinucleotide components and clustering using a k-means-based ensemble clustering method. The A- and B-form proximity of these dinucleotide structures were assessed to discover that RNA dinucleotides can approach B-form-like structures. Umbrella sampling molecular dynamics simulations were used to obtain the potential of mean force profiles for base unstacking at 5'-termini for …

Molecular Dynamics Simulations Of Small Systems To Improve Base Pairing Parameters Of The Amber-99 Force Field, Angelo Christopher Setaro

Legacy Theses & Dissertations (2009 - 2024)

Simulations of biochemical systems are being increasingly used to further our understanding of those systems. In broad strokes, chemical simulations can be broken into two categories, those that are rooted in a quantum mechanical approach and those that are classically rooted. Molecular dynamics is one such classical method, which propagates motion of a chemical system via repeatedly solving Newton’s Laws of motion. This approach is less computationally intensive than the quantum mechanical methods and allows for the simulation of systems of tens of thousands of atoms, if not more.

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 …

Modeling And Simulation Of Molecular Couette Flows And Related Flows, Wei Li

Mathematics & Statistics Theses & Dissertations

In this thesis, molecular Couette flow is clearly defined and the modeling and simulation of this kind of flow is systematically investigated. First, the integral equations for the velocity of gaseous Couette flow and related flows are derived from linearized Boltzmann BGK equation with Maxwell boundary condition and solved with high precision by using Chebyshev collocation and chunk-based collocation methods. The velocity profiles of gaseous Couette flows and related flows with a wide range of Knudsen number and the Maxwell boundary condition of various accommodation ratios are obtained. Moreover, the order of convergence of the numerical methods is also discussed …

Classical And Ab Initio Qm/Mm Simulations Of Bacterial Enzymes, Sajeewa Walimuni Dewage

Wayne State University Dissertations

This thesis describes analyses performed on three enzyme systems. Chapter 2, 3, and 4 involve studies carried out on the GatCAB enzyme of H. pylori and S. aureus. Since information at the electronic level was not required for these studies, sampling of the configuration space carried out at the molecular mechanics level was adequate. In Chapter 2, the snapshots sampled using MD were used as input for average correlation difference calculations and average RMSD difference calculations to ascertain the existence of a communication pathway between two subunits of GatCAB. Experimental and computational results obtained, suggest the existence of a communication …