Matching Items (16)
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- All Subjects: Physics
- Creators: Beckstein, Oliver
- Member of: Theses and Dissertations
- Member of: Barrett, The Honors College Thesis/Creative Project Collection
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
Sample delivery is an essential component in biological imaging using serial diffraction from X-ray Free Electron Lasers (XFEL) and synchrotrons. Recent developments have made possible the near-atomic resolution structure determination of several important proteins, including one G protein-coupled receptor (GPCR) drug target, whose structure could not easily have been determined otherwise (Appendix A). In this thesis I describe new sample delivery developments that are paramount to advancing this field beyond what has been accomplished to date. Soft Lithography was used to implement sample conservation in the Gas Dynamic Virtual Nozzle (GDVN). A PDMS/glass composite microfluidic injector was created and given the capability of millisecond fluidic switching of a GDVN liquid jet within the divergent section of a 2D Laval-like GDVN nozzle, providing a means of collecting sample between the pulses of current XFELs. An oil/water droplet immersion jet was prototyped that suspends small sample droplets within an oil jet such that the sample droplet frequency may match the XFEL pulse repetition rate. A similar device was designed to use gas bubbles for synchronized “on/off” jet behavior and for active micromixing. 3D printing based on 2-Photon Polymerization (2PP) was used to directly fabricate reproducible GDVN injectors at high resolution, introducing the possibility of systematic nozzle research and highly complex GDVN injectors. Viscous sample delivery using the “LCP injector” was improved with a method for dealing with poorly extruding sample mediums when using full beam transmission from the Linac Coherent Light Source (LCLS), and a new viscous crystal-carrying medium was characterized for use in both vacuum and atmospheric environments: high molecular weight Polyethylene Glycol.
ContributorsNelson, Garrett Charles (Author) / Spence, John C (Thesis advisor) / Weierstall, Uwe J (Thesis advisor) / Schmidt, Kevin E (Committee member) / Beckstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2015
Description
In this dissertation two kinds of strongly interacting fermionic systems were studied: cold atomic gases and nucleon systems. In the first part I report T=0 diffusion Monte Carlo results for the ground-state and vortex excitation of unpolarized spin-1/2 fermions in a two-dimensional disk. I investigate how vortex core structure properties behave over the BEC-BCS crossover. The vortex excitation energy, density profiles, and vortex core properties related to the current are calculated. A density suppression at the vortex core on the BCS side of the crossover and a depleted core on the BEC limit is found. Size-effect dependencies in the disk geometry were carefully studied. In the second part of this dissertation I turn my attention to a very interesting problem in nuclear physics. In most simulations of nonrelativistic nuclear systems, the wave functions are found by solving the many-body Schrödinger equations, and they describe the quantum-mechanical amplitudes of the nucleonic degrees of freedom. In those simulations the pionic contributions are encoded in nuclear potentials and electroweak currents, and they determine the low-momentum behavior. By contrast, in this work I present a novel quantum Monte Carlo formalism in which both relativistic pions and nonrelativistic nucleons are explicitly included in the quantum-mechanical states of the system. I report the renormalization of the nucleon mass as a function of the momentum cutoff, an Euclidean time density correlation function that deals with the short-time nucleon diffusion, and the pion cloud density and momentum distributions. In the two nucleon sector the interaction of two static nucleons at large distances reduces to the one-pion exchange potential, and I fit the low-energy constants of the contact interactions to reproduce the binding energy of the deuteron and two neutrons in finite volumes. I conclude by showing that the method can be readily applied to light-nuclei.
ContributorsMadeira, Lucas (Author) / Schmidt, Kevin E (Thesis advisor) / Alarcon, Ricardo (Committee member) / Beckstein, Oliver (Committee member) / Erten, Onur (Committee member) / Arizona State University (Publisher)
Created2018
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
Fluctuations with a power spectral density depending on frequency as $1/f^\alpha$ ($0<\alpha<2$) are found in a wide class of systems. The number of systems exhibiting $1/f$ noise means it has far-reaching practical implications; it also suggests a possibly universal explanation, or at least a set of shared properties. Given this diversity, there are numerous models of $1/f$ noise. In this dissertation, I summarize my research into models based on linking the characteristic times of fluctuations of a quantity to its multiplicity of states. With this condition satisfied, I show that a quantity will undergo $1/f$ fluctuations and exhibit associated properties, such as slow dynamics, divergence of time scales, and ergodicity breaking. I propose that multiplicity-dependent characteristic times come about when a system shares a constant, maximized amount of entropy with a finite bath. This may be the case when systems are imperfectly coupled to their thermal environment and the exchange of conserved quantities is mediated through their local environment. To demonstrate the effects of multiplicity-dependent characteristic times, I present numerical simulations of two models. The first consists of non-interacting spins in $0$-field coupled to an explicit finite bath. This model has the advantage of being degenerate, so that its multiplicity alone determines the dynamics. Fluctuations of the alignment of this model will be compared to voltage fluctuations across a mesoscopic metal-insulator-metal junction. The second model consists of classical, interacting Heisenberg spins with a dynamic constraint that slows fluctuations according to the multiplicity of the system's alignment. Fluctuations in one component of the alignment will be compared to the flux noise in superconducting quantum interference devices (SQUIDs). Finally, I will compare both of these models to each other and some of the most popular models of $1/f$ noise, including those based on a superposition of exponential relaxation processes and those based on power law renewal processes.
ContributorsDavis, Bryce F (Author) / Chamberlin, Ralph V (Thesis advisor) / Mauskopf, Philip (Committee member) / Wolf, George (Committee member) / Beckstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2018
Description
STEM education stands for science, technology, engineering and mathematics, and is necessary for students to keep up with global competition in the changing job market, technological advancements and challenges of the future. However, American students are lacking STEM achievement at the state, national and global levels. To combat this lack of achievement I propose that STEM instruction should begin in preschool, be integrated into the curriculum and be inquiry based. To support this proposal I created a month-long physics unit for preschoolers in a Head Start classroom. Students investigated the affect of incline, friction and weight on the distance of a rolling object, while developing their pre-math, pre-literacy and social emotional skills.
ContributorsGarrison, Victoria Leigh (Author) / Kelley, Michael (Thesis director) / Dahlstrom, Margo (Committee member) / Barrett, The Honors College (Contributor) / Division of Teacher Preparation (Contributor)
Created2015-05
Description
Over the past few years, the issue of childhood trauma in the United States has become significant. A growing number of children are experiencing abuse, neglect, or some other form of maltreatment each year. Considering the stressful home lives of maltreated children, the one sure sanctuary is school. However, this idea requires teachers to be actively involved in identifying and caring for the children who need it most. Traumatic childhood experiences leave lasting scars on its victims, so it is helpful if teachers learn how to identify and support children who have lived through them. It is unfortunate that teachers will most likely encounter children throughout their career who have experienced horrendous things, but it is a reality. With this being said, teachers need to develop an understanding of what traumatized children live with, and learn how to address these issues with skilled sensitivity. Schools are not just a place where children learn how to read and write; they build the foundation for a successful life. This project was designed to provide teachers with a necessary resource for helping children who have suffered traumatic experiences. The methodology of this project began with interviews with organizations specializing in working with traumatized children such as Arizonans for Children, Free Arts for Abused Children, The Sojourner Center, and UMOM. The next step was a review of the current literature on the subject of childhood trauma. The findings have all been compiled into one, convenient document for teacher use and distribution. Upon completion of this document, an interactive video presentation will be made available through an online education website, so that distribution will be made simpler. Hopefully, teachers will share the information with people in their networks and create a chain reaction. The goal is to make it available to as many teachers as possible, so that more children will receive the support they need.
ContributorsHanrahan, Katelyn Ann (Author) / Dahlstrom, Margo (Thesis director) / Kelley, Michael (Committee member) / Division of Teacher Preparation (Contributor) / Sanford School of Social and Family Dynamics (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
The atomic force microscope (AFM) is capable of directly probing the mechanics of samples with length scales from single molecules to tissues and force scales from pico to micronewtons. In particular, AFM is widely used as a tool to measure the elastic modulus of soft biological samples by collecting force-indentation relationships and fitting these to classic elastic contact models. However, the analysis of raw force-indentation data may be complicated by mechanical heterogeneity present in biological systems. An analytical model of an elastic indentation on a bonded two-layer sample was solved. This may be used to account for substrate effects and more generally address experimental design for samples with varying elasticity. This model was applied to two mechanobiology systems of interest. First, AFM was combined with confocal laser scanning fluorescence microscopy and finite element analysis to examine stiffness changes during the initial stages of invasion of MDA-MB-231 metastatic breast cells into bovine collagen I matrices. It was determined that the cells stiffen significantly as they invade, the amount of stiffening is correlated with the elastic modulus of the collagen gel, and inhibition of Rho-associated protein kinase reduces the elastic modulus of the invading cells. Second, the elastic modulus of cancer cell nuclei was investigated ex situ and in situ. It was observed that inhibition of histone deacetylation to facilitate chromatin decondenstation result in significantly more morphological and stiffness changes in cancerous cells compared to normal cells. The methods and results presented here offer novel strategies for approaching biological systems with AFM and demonstrate its applicability and necessity in studying cellular function in physiologically relevant environments.
ContributorsDoss, Bryant Lee (Author) / Ros, Robert (Thesis advisor) / Lindsay, Stuart (Committee member) / Nikkhah, Mehdi (Committee member) / Beckstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2015
Description
Cell adhesion is an important aspect of many biological processes. The atomic force microscope (AFM) has made it possible to quantify the forces involved in cellular adhesion using a technique called single cell force spectroscopy (SCFS). AFM based SCFS offers versatile control over experimental conditions for probing directly the interaction between specific cell types and specific proteins, surfaces, or other cells. Transmembrane integrins are the primary proteins involved in cellular adhesion to the extra cellular matix (ECM). One of the chief integrins involved in the adhesion of leukocyte cells is αMβ2 (Mac-1). The experiments in this dissertation quantify the adhesion of Mac-1 expressing human embryonic kidney (HEK Mac-1), platelets, and neutrophils cells on substrates with different concentrations of fibrinogen and on fibrin gels and multi-layered fibrinogen coated fibrin gels. It was shown that multi-layered fibrinogen reduces the adhesion force of these cells considerably. A novel method was developed as part of this research combining total internal reflection microscopy (TIRFM) with SCFS allowing for optical microscopy of HEK Mac-1 cells interacting with bovine serum albumin (BSA) coated glass after interacting with multi-layered fibrinogen. HEK Mac-1 cells are able to remove fibrinogen molecules from the multi-layered fibrinogen matrix. An analysis methodology for quantifying the kinetic parameters of integrin-ligand interactions from SCFS experiments is proposed, and the kinetic parameters of the Mac-1 fibrinogen bond are quantified. Additional SCFS experiments quantify the adhesion of macrophages and HEK Mac-1 cells on functionalized glass surfaces and normal glass surfaces. Both cell types show highest adhesion on a novel functionalized glass surface that was prepared to induce macrophage fusion. These experiments demonstrate the versatility of AFM based SCFS, and how it can be applied to address many questions in cellular biology offering quantitative insights.
ContributorsChristenson, Wayne B (Author) / Ros, Robert (Thesis advisor) / Beckstein, Oliver (Committee member) / Lindsay, Stuart (Committee member) / Ugarova, Tatiana (Committee member) / Arizona State University (Publisher)
Created2016
Description
The relation between water and protein physics is a topic of much interest. Molecular dynamics (MD) simulations of biomolecules are a common computational technique to obtain atomistic insight into the physical behavior of biomolecules, including the nature of the interaction between water and the protein. In order to model biomolecules at the highest level of accuracy, an explicit, atomistic representation of the water is typically necessary. The number of water molecules that need to be simulated is normally on the order of thousands. The high dimensional MD dataset is then expanded with considerably more dimensions. We describe here a set of tools which can be used to extract general features of the water behavior, which can then be utilized to build simplified models of the water kinetics which make quantitative predictions, such as the flux rate through a pore.
ContributorsWelland, Ian (Author) / Beckstein, Oliver (Committee member) / Matyushov, Dmitry (Committee member) / Barrett, The Honors College (Contributor)
Created2015-12