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Comparative Analysis Of Conformational Transition Pathways In Homologous Proteins, Dylan Sebastien Ogden

Graduate Theses and Dissertations

Molecular dynamics (MD) simulations are routinely used to study the dynamics of proteins. However, conventional MD limited to the sampling of local conformational changes as the functionally important conformational transitions of proteins often extend beyond the timescales of the simulations employed, for example, membrane transport proteins. We have determined the combination of multiple MD based techniques that allows for a rigorous characterization of energetics and kinetics of large-scale conformational changes in membrane proteins. The methodology is based on biased, nonequilibrium collective variable based simulations including nonequilibrium pulling, string method with swarms of trajectories, bias-exchange umbrella sampling, and rate estimation techniques. …

Static And Dynamical Properties Of Multiferroics, Sayed Omid Sayedaghaee

Graduate Theses and Dissertations

Since the silicon industrial revolution in the 1950s, a lot of effort was dedicated to the research and development activities focused on material and solid-state sciences. As a result, several cutting-edge technologies are emerging including the applications of functional materials in the design and enhancement of novel devices such as sensors, highly capable data storage media, actuators, transducers, and several other types of electronic tools. In the last two decades, a class of functional materials known as multiferroics has captured significant attention because of providing a huge potential for new designs due to possessing multiple ferroic order parameters at the …

Predicting The Mechanical Properties Of Nanocomposites Reinforced With 1-D, 2-D And 3-D Nanomaterials, Scott Edward Muller

Graduate Theses and Dissertations

Materials with features at the nanoscale can provide unique mechanical properties and increased functionality when included as part of a nanocomposite. This dissertation utilizes computational methods at multiple scales, including molecular dynamics (MD) and density functional theory (DFT), and the coupled atomistic and discrete dislocation multiscale method (CADD), to predict the mechanical properties of nanocomposites possessing nanomaterials that are either 1-D (carbyne chains), 2-D (graphene sheets), or 3-D (Al/amorphous-Si core-shell nanorod).

The MD method is used to model Ni-graphene nanocomposites. The strength of a Ni-graphene nanocomposite is found to improve by increasing the gap between the graphene sheet and a …

Molecular Dynamics Simulations Of Dna-Functionalized Nanoparticle Building Blocks On Gpus, Tyler Landon Fochtman

Graduate Theses and Dissertations

This thesis discusses massively parallel molecular dynamics simulations of nBLOCKs using graphical processing units. nBLOCKs are nanoscale building blocks composed of gold nanoparticles functionalized with single-stranded DNA molecules. To explore greater simulation time scales we implement our nBLOCK computational model as an extension to the coarse grain molecular simulator oxDNA. oxDNA is parameterized to match the thermodynamics of DNA strand hybridization as well as the mechanics of single stranded DNA and double stranded DNA. In addition to an in-depth review of our implementation details we also provide results of the model validation and performance tests. These validation and performance tests …

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 …

Dynamical Properties Of Ferroelectric Perovskites (Ba,Sr)Tio3 And Pb(Zr,Ti)O3 Systems From First Principles, Jeevaka Weerasinghe

Graduate Theses and Dissertations

A first-principles-based effective Hamiltonian scheme which incorporates coupling between ferroelectric (FE) and antiferrodistortive (AFD) motions is applied to Pb(Zr,Ti)O₃ alloys. It validates the existence of two modes of E symmetry (rather than the single E(1TO) soft mode) in the 50-75 cm^-1 range for temperatures smaller than 200 K and for compositions falling within the Rhombohedral R3c phase. Coupling between long-range-ordered FE and AFD motions is shown to be the cause of the additional mode and more insight into its nature is provided. This scheme is further used to reveal a field-induced anticrossing involving FE and AFD degrees of …

Molecular Dynamics Study Of Diffusion Of O2 Penetrates In Uncrosslinked Polydimethysiloxane (Pdms), Crosslinked Pdms, And Pdms-Based Nanocomposites, Varun Ullal

Graduate Theses and Dissertations

Molecular dynamics simulations are used to study diffusion of O₂ molecules in pure polydimethysiloxane (PDMS), crosslinked PDMS, and PDMS-based nanocomposites. The PDMS chains and penetrates are modeled using a hybrid interatomic potential which treats the Si-O atoms along the chain backbone explicitly while coarse-graining the methyl side groups and penetrates. By tracking the diffusion of penetrates in the system and subsequently computing their mean-squared displacement, diffusion coefficients are obtained. In pure PDMS models of varying molecular weight, diffusivity of the O₂2 penetrates is found to have an inverse relationship with chain length. Simulation models with longer chains …