PhD, University of Cincinnati, 2024, Arts and Sciences: Chemistry

The cytoskeleton, a key feature of the cell, acts as scaffolding that is responsible for maintaining the cell shape as well as forming a highway system for intra-cellular transportation. Thus, the cell must maintain strict regulation of its cytoskeleton to undergo deliberate change. Microtubules, an essential biopolymer of the cytoskeleton, are routinely severed by specific AAA (ATPases Associated with cellular Activities) nanomachines. Severing is required for a variety of significant cellular functions including, but not limited to, cellular division and neurogenesis. Changes to microtubules themselves, their various regulatory processes, and these proteins would have far reaching, serious implications on the viability and health of the cell and its organism. The microtubule severing enzymes are katanin, spastin, and fidgetin. Recent structural studies have solved hexameric structures for katanin and spastin in the presence of cofactors indicating they operate via a global conformational change induced by ATP hydrolysis. Simulations were previously used to study the functional states of both severing enzymes where it was identified that in long time-scales, at least one conformation will disassemble in the absence of cofactors. To further understand this observed disassembly process and the influence of the cofactors, a similar study of the resulting lower order oligomers was designed in part one. Through machine learning and in-house developed analyses, we recognized significant allosteric shifts due to the presence of ligands and neighboring protomers. During this study we also identified a particular region of katanin that is highly correlated with ligand binding from the helical bundle domain (HBD). We developed StELa, an in-house clustering algorithm, to characterize observed structural changes from simulation which identified a specific local conformational change due to ligand binding. In part two, this method was compared with other available algor (open full item for complete abstract)

Committee: Ruxandra Dima Ph.D. (Committee Chair); Ryan White Ph.D. (Committee Member); Anna Gudmundsdottir Ph.D. (Committee Member) Subjects: Chemistry

Doctor of Philosophy, The Ohio State University, 2019, Materials Science and Engineering

Titanium (Ti) and its alloys have a wide range of applications in biomedical, automotive and aerospace industries due to their excellent strength to weight ratio and corrosion resistance. Alpha phase Ti has hexagonal closed packed (hcp) structure that shows anisotropic plastic deformation; 〈 a 〉 type slip on prism planes is the easiest to activate but cannot accommodate deformation along the 〈 c 〉 axis. The low temperature ductility of Ti is linked to twinning. Therefore, understanding the mechanisms behind the twin nucleation and growth in Ti alloys is important from both theoretical and industrial application points of view. To that end, the present study seeks a better understanding of the atomic scale processes involved in twin nucleation mechanisms and the effect of alpha-stabilizing solutes such as interstitial oxygen, substitutional aluminum and rare earth elements on twinning. Systematic molecular dynamics (MD) simulations are used to identify the underlying mechanism of twin nucleation from dislocation/grain boundary interactions. Density functional theory (DFT) simulations are employed to examine the effect of oxygen interstitials on the twinning behavior of Ti. A systematic framework has been developed to predict the diffusion of interstitial elements near the twin boundaries in hcp alloys. Next, uncertainty that arises from first-principles calculations in predicting diffusion coefficients are quantified. Finally, solute segregation to the twin boundaries as a new mechanism for dynamic strain aging (DSA) is investigated in Ti and other hcp alloys.

Committee: Maryam Ghazisaeidi (Advisor); Michael Mills (Committee Member); Wolfgang Windl (Committee Member) Subjects: Computer Science; Materials Science

MS, University of Cincinnati, 2006, Engineering : Mechanical Engineering

Even with the ever-increasing and affordable computational power, detailed atomistic analysis of large domains using molecular dynamics remains prohibitively expensive. This motivates the use of continuum type of simulation methods such as the finite element method in order to reduce the computational expense. However, the accuracy in FEM simulation is often unsatisfactory. As a result, efforts are being made to combine the advantages of the simulation methods at different scales into a multiscale framework. The main goal for this thesis is to develop a coupled atomistic-continuum formulation for a nanoscale system. The main challenge is in attaining a reflectionless boundary at the interface of the molecular dynamics and finite element simulation. The finite element mesh is generally much coarser than the atomic spacing. Thus it can't represent the fine scale portion of the displacement, resulting in incorrect information being supplied to the atomistic simulation which subsequently leads to reflection of phonons at the interface. Most of the research effort so far has been towards attaining a reflectionless boundary at the interface of the two simulations by using variety of methods. In all these approaches, the focus has been to achieve accurate description of the system in the region where we have molecular dynamics. The regions where the finite elements are used don't give very accurate results. In this thesis a space-time description for a 1D atomistic system is developed. We have considered a system having harmonic interatomic potential with nearest neighbor interaction only. The objectives for the space-time formulation development are two folds: first, we aim at overcoming the time scale limit by constructing approximation in the time domain. Secondly with the introduction of fine scale variables, we provide a multiscale description of the field variable. This is the key in achieving a truly reflectionless boundary condition. More specifically we have devel (open full item for complete abstract)

Committee: Dr. Dong Qian (Advisor) Subjects: Engineering, Mechanical

Doctor of Philosophy, The Ohio State University, 2003, Physics

Under pressure, titanium transforms from the hexagonal-closed-packed (hcp) structure to the high pressure omega phase. This phase transition from hcp (alpha) to omega (omega) is martensitic: there is a macroscopic cell change, described by a strain tensor, coupled with microscopic internal relaxations of the unit cell, described by shuffle vectors. In addition, the transformation occurs directly and without diffusion. Despite this, the atomistic transformation was not known. Trace amounts (1 at.%) of oxygen impurities shut down the shock-induced transformation. Ab initio, tight-binding, and classical potential calculations model the hcp to omega transformation, and the effects of impurities on the transformation. A new pathway generation and sorting algorithm systematically searches through all possible pathways to find the most probable homogeneous mechanism. A new mechanism is found with a barrier 4 times lower than any other homogeneous mechanisms, even when nucleation effects are considered. Using molecular dynamics, the transformation from hcp to omega moves across the interphase boundary under pressure at a finite temperature. The interstitial impurities oxygen, nitrogen, carbon, and substitutional impurities aluminum and vanadium shift both the energy barrier between and the relative energies of alpha and omega; these changes explain the shutdown of the alpha to omega transformation by oxygen and aluminum. The final result is an atomistic understanding of the Ti alpha to omega transformation: moving from the homogeneous energy barrier to nucleation effects to finite temperature to the effect of impurities. This serves as a template for future studies of the atomistic mechanisms of other martensitic transformations.

Committee: John Wilkins (Advisor) Subjects: Physics, Condensed Matter