Doctor of Philosophy, The Ohio State University, 2022, Chemical Engineering

In molecular dynamics (MD) simulations, coarse grained force fields significantly reduce the computational burden when predicting the structural properties of materials, but negatively impact the resulting transport property predictions, typically accelerating the dynamic evolution of the system. Using the methods of equilibrium and non-equilibrium MD simulations, the nanoscale structure of neat polymer grafted-nanoparticle (PGN) assemblies deposited on a smooth surface, and the transport properties of simple linear ethers are explored. Specifically, generic coarse grained bead-spring models are used to reach the time and length scales associated with entanglements, and to isolate the effect of architecture on the nanoscale structure and chain conformations of entangled and hexagonally packed PGN monolayers, which consist solely of nanoparticles (NPs) protected by grafted polymer chains. At increased graft densities brushes are dryer and more aligned, with decreased interpenetration between chains on neighboring canopies. This leads to fewer interparticle entanglements per chain, which are increasingly localized to interstitial regions. Chains also have increased alignment normal to the NP surface at high graft density, and increased intraparticle entanglement density near the surface. The inverse relationship between graft density and the degree of interparticle entanglement of the brush suggests that higher graft density monolayers will have reduced toughness and robustness under strain. Understanding these relationships, and generally connecting experimentally tunable parameters to molecular-scale structure and overall material properties, will provide insight into optimal design of future materials. In the second part of the thesis, finer transferable atomistic and united atom force fields are used to better capture trends in diffusivity and apparent viscosity across a range of temperatures and shear rates for a series of linear ethers. Specifically, tren (open full item for complete abstract)

Committee: Isamu Kusaka (Advisor); Kurt Koelling (Committee Member); Lisa Hall (Advisor) Subjects: Chemical Engineering

Doctor of Philosophy, The Ohio State University, 2022, Chemistry

Biological organisms need to respond to changes in their surrounding environments to maintain homeostasis. On a cellular level, responding generally involves activating or repressing gene expression by forming feedback circuits that sense changes of physiochemical cues or physical factors. The interactions between environmental changes and cellular responses are often “allosteric”, by which the sensed signals propagate to a remote responding element. Understanding the corresponding allosteric pathways and quantifying the relevant biological information flows are the foundation to reveal the secrets of life. Homo-oligomeric ligand-activated proteins are ubiquitous in biology. My research aims to understand the allosteric response mechanism of the model ring-shaped, homo-oligomeric TRAP (trp RNA-binding attenuation protein). TRAP serves as an orthogonal gene-regulatory switch to control Trp (tryptophan) production in Bacilli via Trp-dependent mRNA binding. This cyclic 12mer (or 11mer) protein sensor is activated by binding up to an equivalent number of Trp molecules to subsequently bind to specific sequences in the 5'UTR of the trp operon. When activated by Trp, binding of TRAP to this trp leader results in attenuated transcription and translation of enzymes responsible for Trp biosynthesis. To understand how TRAP senses and responds to Trp concentration, we first examined its homotropic binding to multiple Trp ligands, and how these Trp binding events influence heterotropic binding to RNA. As described in chapter 2, to probe the allosteric coupling between ligand binding sites, we developed the nearest-neighbor (NN) statistical thermodynamic binding model, comprising microscopic free energies for ligand binding to isolated sites ΔGN0, and for coupling between one or both adjacent sites, ΔGN1 and ΔGN2, respectively. The resulting partition function (PF) could be used to simulate the effects of these parameters on population distributions for 2N possible ligand (open full item for complete abstract)

Committee: Mark Foster (Advisor); Steffen Lindert (Committee Member); Rafael Brüschweiler (Committee Member); Vicki Wysocki (Committee Member) Subjects: Biochemistry; Biophysics; Molecular Physics

Doctor of Philosophy, The Ohio State University, 2021, Physics

Here I develop computationally efficient quantitative models to describe the behavior of DNA-based systems. DNA is of fundamental biological importance, and its physical properties have been harnessed for technological applications. My work involves each of these aspects of DNA function, and thus provides broad insight into this important biomolecule. First, I examine how DNA mismaches are repaired in the cell. Protein complexes involved in DNA mismatch repair appear to diffuse along dsDNA in order to locate a hemimethylated incision site via a dissociative mechanism. I study the probability that these complexes locate a given target site via a semi-analytic, Monte Carlo calculation that tracks the association and dissociation of the complexes. I compare such probabilities to those obtained using a non-dissociative diffusive scan, and determine that for experimentally observed diffusion constants, search distances, and search durations in vitro, both search mechanisms are highly efficient for a majority of hemimethylated site distances. I then examine the space of physically realistic diffusion constants, hemimethylated site distances, and association lifetimes and determine the regions in which dissociative searching is more or less efficient than non-dissociative searching. I conclude that the dissociative search mechanism is advantageous in the majority of the physically realistic parameter space, suggesting that the dissociative search mechanism confers an evolutionary advantage. I then turn to synthetic DNA structures, initially focusing on a composite DNA nano-device. In particular, manipulation of temperature can be used to actuate DNA origami nano-hinges containing gold nanoparticles. I develop a physical model of this system that uses partition function analysis of the interaction between the nano-hinge and nanoparticle to predict the probability that the nano-hinge is open at a given temperature. The model agrees well with experimental data and pre (open full item for complete abstract)

Committee: Ralf Bundschuh PhD (Advisor); Carlos Castro PhD (Committee Member); Michael Poirier PhD (Committee Member); Hirata Christopher PhD (Committee Member) Subjects: Biophysics; Nanotechnology; Physics; Polymers; Theoretical Physics

Doctor of Philosophy, Case Western Reserve University, 1994, Physics

Extensive experimental studies of fluid hydrocarbons in the lubricating range of molar mass have been undertaken sometime ago by American Petroleum Institute Project 42, located in the Departments of Chemistry and Physics at Pennsylvania State University. In these studies systematic structural changes were introduced, so that the equation of state (e.o.s.) as well as the viscosities of linear paraffins, branched hydrocarbons, and various rings attached to n-alkanes tails are known. Hence this material became the basis for various semi-empirical or empirical structural correlations. We proceed here with the hole theory of Simha-Somcynsky (SS) which has proven quantitatively successful for low as well as high molar mass system and examine e.o.s. data. We demonstrate the success of the theory and obtain the characteristic volume (ν*), energy (varepsilon*) and flexibility (c) parameters as functions of chain length for the different structures. For the short chains in question these represent averages over the terminal and internal units. By suitable generalization of the SS theory developed for physical mixtures we decompose these averages into the individual group contributions. The accuracy of the numerical procedures employed is tested by back computations. Sometime ago A. Bondi developed structural rules for the computation of Van der Waals excluded group volumes. Interesting correlations between these and the above ν* values, defined for a 6-12 potential, are obtained. In the same way we examine correlations between D. W. Van Krevelen's and P. J. Hoftyzer's cohesive group energies and varepsilon* values.

Committee: Robert Simha (Advisor) Subjects: