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Most asteroids originated in larger parent bodies that underwent accretion and heating during the first few million years of the solar system. We investigated the parent body of S-type asteroid 25143 Itokawa by developing a computational model which can approximate the thermal evolution of an early solar system body. We

Most asteroids originated in larger parent bodies that underwent accretion and heating during the first few million years of the solar system. We investigated the parent body of S-type asteroid 25143 Itokawa by developing a computational model which can approximate the thermal evolution of an early solar system body. We compared known constraints on Itokawa’s thermal history to simulations of its parent body and constrained its time of formation to between 1.6 and 2.5 million years after the beginning of the solar system, though certain details could allow for even earlier or later formation. These results stress the importance of precise data required of the material properties of asteroids and meteorites to place better constraints on the histories of their parent bodies. Additional mathematical and computational details are discussed, and the full code and data is made available online.

ContributorsHallstrom, Jonas (Author) / Bose, Maitrayee (Thesis director) / Beckstein, Oliver (Committee member) / Barrett, The Honors College (Contributor) / Department of Physics (Contributor) / Materials Science and Engineering Program (Contributor)
Created2023-05
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We implemented the well-known Ising model in one dimension as a computer program and simulated its behavior with four algorithms: (i) the seminal Metropolis algorithm; (ii) the microcanonical algorithm described by Creutz in 1983; (iii) a variation on Creutz’s time-reversible algorithm allowing for bonds between spins to change dynamically; and

We implemented the well-known Ising model in one dimension as a computer program and simulated its behavior with four algorithms: (i) the seminal Metropolis algorithm; (ii) the microcanonical algorithm described by Creutz in 1983; (iii) a variation on Creutz’s time-reversible algorithm allowing for bonds between spins to change dynamically; and (iv) a combination of the latter two algorithms in a manner reflecting the different timescales on which these two processes occur (“freezing” the bonds in place for part of the simulation). All variations on Creutz’s algorithm were symmetrical in time, and thus reversible. The first three algorithms all favored low-energy states of the spin lattice and generated the Boltzmann energy distribution after reaching thermal equilibrium, as expected, while the last algorithm broke from the Boltzmann distribution while the bonds were “frozen.” The interpretation of this result as a net increase to the system’s total entropy is consistent with the second law of thermodynamics, which leads to the relationship between maximum entropy and the Boltzmann distribution.

ContributorsLewis, Aiden (Author) / Chamberlin, Ralph (Thesis director) / Beckstein, Oliver (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Physics (Contributor)
Created2023-05
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Na+/H+ antiporters are vital membrane proteins for cell homeostasis, transporting Na+ ions in exchange for H+ across the lipid bilayer. In humans, dysfunction of these transporters are implicated in hypertension, heart failure, epilepsy, and autism, making them well-established drug targets. Although experimental structures for bacterial homologs of the human Na+/H+

Na+/H+ antiporters are vital membrane proteins for cell homeostasis, transporting Na+ ions in exchange for H+ across the lipid bilayer. In humans, dysfunction of these transporters are implicated in hypertension, heart failure, epilepsy, and autism, making them well-established drug targets. Although experimental structures for bacterial homologs of the human Na+/H+ have been obtained, the detailed mechanism for ion transport is still not well-understood. The most well-studied of these transporters, Escherichia coli NhaA, known to transport 2 H+ for every Na+ extruded, was recently shown to bind H+ and Na+ at the same binding site, for which the two ion species compete. Using molecular dynamics simulations, the work presented in this dissertation shows that Na+ binding disrupts a previously-unidentified salt bridge between two conserved residues, suggesting that one of these residues, Lys300, may participate directly in transport of H+. This work also demonstrates that the conformational change required for ion translocation in a homolog of NhaA, Thermus thermophilus NapA, thought by some to involve only small helical movements at the ion binding site, is a large-scale, rigid-body movement of the core domain relative to the dimerization domain. This elevator-like transport mechanism translates a bound Na+ up to 10 Å across the membrane. These findings constitute a major shift in the prevailing thought on the mechanism of these transporters, and serve as an exciting launchpad for new developments toward understanding that mechanism in detail.
ContributorsDotson, David L (Author) / Beckstein, Oliver (Thesis advisor) / Ozkan, Sefika B (Committee member) / Ros, Robert (Committee member) / Van Horn, Wade (Committee member) / Arizona State University (Publisher)
Created2016
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Description
I describe the first continuous space nuclear path integral quantum Monte Carlo method, and calculate the ground state properties of light nuclei including Deuteron, Triton, Helium-3 and Helium-4, using both local chiral interaction up to next-to-next-to-leading-order and the Argonne $v_6'$ interaction. Compared with diffusion based quantum Monte Carlo methods such

I describe the first continuous space nuclear path integral quantum Monte Carlo method, and calculate the ground state properties of light nuclei including Deuteron, Triton, Helium-3 and Helium-4, using both local chiral interaction up to next-to-next-to-leading-order and the Argonne $v_6'$ interaction. Compared with diffusion based quantum Monte Carlo methods such as Green's function Monte Carlo and auxiliary field diffusion Monte Carlo, path integral quantum Monte Carlo has the advantage that it can directly calculate the expectation value of operators without tradeoff, whether they commute with the Hamiltonian or not. For operators that commute with the Hamiltonian, e.g., the Hamiltonian itself, the path integral quantum Monte Carlo light-nuclei results agree with Green's function Monte Carlo and auxiliary field diffusion Monte Carlo results. For other operator expectations which are important to understand nuclear measurements but do not commute with the Hamiltonian and therefore cannot be accurately calculated by diffusion based quantum Monte Carlo methods without tradeoff, the path integral quantum Monte Carlo method gives reliable results. I show root-mean-square radii, one-particle number density distributions, and Euclidean response functions for single-nucleon couplings. I also systematically describe all the sampling algorithms used in this work, the strategies to make the computation efficient, the error estimations, and the details of the implementation of the code to perform calculations. This work can serve as a benchmark test for future calculations of larger nuclei or finite temperature nuclear matter using path integral quantum Monte Carlo.
ContributorsChen, Rong (Author) / Schmidt, Kevin E (Thesis advisor) / Alarcon, Ricardo O (Committee member) / Beckstein, Oliver (Committee member) / Comfort, Joseph R. (Committee member) / Shovkovy, Igor A. (Committee member) / Arizona State University (Publisher)
Created2020