Matching Items (4)
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- All Subjects: 2D materials
- All Subjects: Theoretical Physics
- Creators: Beckstein, Oliver
- Status: Published
Description
The structure of glass has been the subject of many studies, however some
details remained to be resolved. With the advancement of microscopic
imaging techniques and the successful synthesis of two-dimensional materials,
images of two-dimensional glasses (bilayers of silica) are now available,
confirming that this glass structure closely follows the continuous random
network model. These images provide complete in-plane structural information
such as ring correlations, and intermediate range order and with computer
refinement contain indirect information such as angular distributions, and
tilting.
This dissertation reports the first work that integrates the actual atomic
coordinates obtained from such images with structural refinement to enhance
the extracted information from the experimental data.
The correlations in the ring structure of silica bilayers are studied
and it is shown that short-range and intermediate-range order exist in such networks.
Special boundary conditions for finite experimental samples are designed so atoms
in the bulk sense they are part of an infinite network.
It is shown that bilayers consist of two identical layers separated by a
symmetry plane and the tilted tetrahedra, two examples of
added value through the structural refinement.
Finally, the low-temperature properties of glasses in two dimensions
are studied. This dissertation presents a new approach to find possible
two-level systems in silica bilayers employing the tools of rigidity theory
in isostatic systems.
details remained to be resolved. With the advancement of microscopic
imaging techniques and the successful synthesis of two-dimensional materials,
images of two-dimensional glasses (bilayers of silica) are now available,
confirming that this glass structure closely follows the continuous random
network model. These images provide complete in-plane structural information
such as ring correlations, and intermediate range order and with computer
refinement contain indirect information such as angular distributions, and
tilting.
This dissertation reports the first work that integrates the actual atomic
coordinates obtained from such images with structural refinement to enhance
the extracted information from the experimental data.
The correlations in the ring structure of silica bilayers are studied
and it is shown that short-range and intermediate-range order exist in such networks.
Special boundary conditions for finite experimental samples are designed so atoms
in the bulk sense they are part of an infinite network.
It is shown that bilayers consist of two identical layers separated by a
symmetry plane and the tilted tetrahedra, two examples of
added value through the structural refinement.
Finally, the low-temperature properties of glasses in two dimensions
are studied. This dissertation presents a new approach to find possible
two-level systems in silica bilayers employing the tools of rigidity theory
in isostatic systems.
ContributorsSadjadi, Seyed Mahdi (Author) / Thorpe, Michael F (Thesis advisor) / Beckstein, Oliver (Committee member) / Schmidt, Kevin E (Committee member) / Treacy, Michael Mj (Committee member) / Arizona State University (Publisher)
Created2018
Description
The continuous random network (CRN) model of network glasses is widely accepted as a model for materials such as vitreous silica and amorphous silicon. Although it
has been more than eighty years since the proposal of the CRN, there has not been conclusive experimental evidence of the structure of glasses and amorphous
materials. This has now changed with the advent of two-dimensional amorphous materials. Now, not only the distribution of rings but the actual atomic ring
structure can be imaged in real space, allowing for greater charicterization of these types of networks. This dissertation reports the first work done
on the modelling of amorphous graphene and vitreous silica bilayers. Models of amorphous graphene have been created using a Monte Carlo bond-switching method
and MD method. Vitreous silica bilayers have been constructed using models of amorphous graphene and the ring statistics of silica bilayers has been studied.
has been more than eighty years since the proposal of the CRN, there has not been conclusive experimental evidence of the structure of glasses and amorphous
materials. This has now changed with the advent of two-dimensional amorphous materials. Now, not only the distribution of rings but the actual atomic ring
structure can be imaged in real space, allowing for greater charicterization of these types of networks. This dissertation reports the first work done
on the modelling of amorphous graphene and vitreous silica bilayers. Models of amorphous graphene have been created using a Monte Carlo bond-switching method
and MD method. Vitreous silica bilayers have been constructed using models of amorphous graphene and the ring statistics of silica bilayers has been studied.
ContributorsKumar, Avishek (Author) / Thorpe, Michael F (Thesis advisor) / Ozkan, Sefika B (Committee member) / Beckstein, Oliver (Committee member) / Treacy, Michael Mj (Committee member) / Arizona State University (Publisher)
Created2014
Description
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
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 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