Statistical, Nonlinear, and Soft Matter Physics Commons^™

Fwer Controlling Procedures In Simultaneous And Selective Inference, Li Yu

Dissertations

With increasing complexity of research objectives in clinical trials, a variety of relatively complex and less intuitive multiple testing procedures (MTPs) have been developed and applied in clinical data analysis. In order to make testing strategies more explicit and intuitive to communicate with non-statisticians, several flexible and powerful graphical approaches have recently been introduced in the literature for developing and visualizing newer MTPs. Nevertheless, some theoretical as well as methodological issues still remain to be fully addressed. This dissertation addresses several important issues arising in graphical approaches and related selective inference problems. It consists of three parts.

In the first …

Application Of Graphical Models In Protein-Protein Interactions And Dynamics, Amir Vajdi Hoojghan

Graduate Doctoral Dissertations

Every organism contains a few hundred to thousands of proteins. A protein is made of a sequence of molecular building blocks named amino acids. Amino acids will be referred to as residues. Every protein performs one or more functions in the cell. In order for a protein to do its job, it requires to bind properly to other partner proteins. Many genetic diseases such as cancer are caused by mutations (changes) of specific residues which cause disturbances in the functions of those proteins.

The problem of prediction of protein binding site is a crucial topic in computational biology. A protein …

Fatigue Performance And Shear Demand Distributions Of Clustered Shear Connectors In Composite Bridge Girders, Brian David Hillhouse

Graduate Theses and Dissertations

The current American Association of State Highway and Transportation Officials (AASHTO) Bridge Specifications assumes uniform shear flow demands at the steel-concrete interface of composite bridge girders. As stud pitch increases to beyond 24 in or as studs become clustered to account for pre-cast concrete decks, this assumed shear demand distribution may be unrepresentative. Understanding shear transfer and resulting demands on headed studs in composite beams are important for ensuring adequate composite design. This study investigates stud demands in composite bridge girders using large-scale fatigue testing and direct pressure measurements for stud force calculations. In this study, two large-scale composite beam …

Conforming Nanoparticle Sheets To Surfaces With Gaussian Curvature, Noah P. Mitchell, Remington L. Carey, Jelani Hannah, Yifan Wang, Sean P. Mcbride, Xiao-Min Lin, Heinrich M. Jaeger

Physics Faculty Research

Nanoparticle monolayer sheets are ultrathin inorganic-organic hybrid materials that combine highly controllable optical and electrical properties with mechanical exibility and remarkable strength. Like other thin sheets, their low bending rigidity allows them to easily roll into or conform to cylindrical geometries. Nanoparticle monolayers not only can bend, but also cope with strain through local particle rearrangement and plastic deformation. This means that, unlike thin sheets such as paper or graphene, nanoparticle sheets can much more easily conform to surfaces with com- plex topography characterized by non-zero Gaussian curvature, like spherical caps or saddles. Here, we investigate the limits of nanoparticle …

Magnetoelectric Memory Cells With Domain-Wall-Mediated Switching, Kirill Belashchenko, Oleg Tchernyshyov, Alexey Kovalev, Dmitri Nikonov

Kirill Belashchenko Publications

A magnetoelectric memory cell with domain - wall - mediated switching is implemented using a split gate architecture . The split gate architecture allows a domain wall to be trapped within a magnetoelectric antiferromagnetic ( MEAF ) active layer . An extension of this architecture applies to multiple gate linear arrays that can offer advantages in memory density , programmability , and logic functionality . Applying a small anisotropic in - plane shear strain to the MEAF can block domain wall precession to improve reliability and speed of switching

Reversible Motion In A Contact Line, Audrey Profeta, Esmeralda Orozco, Juan A. Ortiz Salazar, Dani Medina, Nathan C. Keim

STAR Program Research Presentations

When a body of liquid sits on a surface, an irregular border between the wet and dry regions of the surface exists, called the contact line. Driving this contact line back and forth repeatedly can change its shape.We use a syringe pump to cyclically infuse and withdraw a predetermined volume of water, and take photos of the contact line after each cycle. Comparing these images to each other determines if the contact line is returning to the same shape. We find that below a critical value of infused volume, after many cycles the contact line reaches a steady state in …

A Network Theoretical Approach To Real-World Problems: Application Of The K-Core Algorithm To Various Systems, Kate Burleson-Lesser

Dissertations, Theses, and Capstone Projects

The study of complex networks is, at its core, an exploration of the mechanisms that control the world in which we live at every scale, from particles no bigger than a grain of sand and amino acids that comprise proteins, to social networks, ecosystems, and even countries. Indeed, we find that, regardless of the physical size of the network's components, we may apply principles of complex network theory, thermodynamics, and statistical mechanics to not only better understand these specific networks, but to formulate theories which may be applied to problems on a more general level. This thesis explores several networks …

Interdisciplinary Studies Of Complex Network And Machine Learning And Its Applications, Shaojun Luo

Dissertations, Theses, and Capstone Projects

In this dissertation, we introduce the concept of network-based statistical inference methods of two types: network structure inference and variable inference. For network structure inference, we introduce correlation matrix, graphical Lasso, network clustering and identify the influencer in the network. For variable inference, we also introduce from Bayesian network, to Random Markov Field and Ising Model, Boltzmann and Restricted Boltzmann machine and the algorithm of Belief Propagation. Last but not the least, we introduce the most widely used neural network family and its two main types: Convolutional Neural Network and Recurrent Neural Network.

In Chapter 3 we provide an example …

Dynamics Of A Vertically Vibrated Doubly Tethered Granular Chain, Lorenzo P. Joquiño

The International Student Science Fair 2018

Polymer physics studies the structure and dynamics of polymers and polymeric systems. Results from polymer physics have been used in various fields such as biology, polymer processing, and electronics. Mechanical analogs like granular chain have been utilized in studying polymer dynamics as they are able to demonstrate coarsed-grained behavior of polymer motion while still being accurate about a polymer's properties at a larger length scale. In this study, vibrated granular chain of beads was used as an analog system to represent the polymer motion in a solution. The granular chain was confined to a circular container. Its both ends were …

Numerical And Analytical Bounds On Threshold Error Rates For Hypergraph-Product Codes, Alexey Kovalev, Sanjay Prabhakar, Ilya Dumer, Leonid P. Pryadko

Department of Physics and Astronomy: Faculty Publications

We study analytically and numerically decoding properties of finite-rate hypergraph-product quantum low density parity-check codes obtained from random (3,4)-regular Gallager codes, with a simple model of independent X and Z errors. Several nontrivial lower and upper bounds for the decodable region are constructed analytically by analyzing the properties of the homological difference, equal minus the logarithm of the maximum-likelihood decoding probability for a given syndrome. Numerical results include an upper bound for the decodable region from specific heat calculations in associated Ising models and a minimum-weight decoding threshold of approximately 7%.

Simulating The Electrical Properties Of Random Carbon Nanotube Networks Using A Simple Model Based On Percolation Theory, Roberto Abril Valenzuela

Physics

Carbon nanotubes (CNTs) have been subject to extensive research towards their possible applications in the world of nanoelectronics. The interest in carbon nanotubes originates from their unique variety of properties useful in nanoelectronic devices. One key feature of carbon nanotubes is that the chiral angle at which they are rolled determines whether the tube is metallic or semiconducting. Of main interest to this project are devices containing a thin film of randomly arranged carbon nanotubes, known as carbon nanotube networks. The presence of semiconducting tubes in a CNT network can lead to a switching effect when the film is electro-statically …

Pseudo Power Law Statistics In A Jammed, Amorphous Solid, Jacob Brian Hass

Physics

Simulations have shown that in many solid materials, rearrangements within the solid obey power-law statistics. A connection has been proposed between these statistics and the ability of a system to reach a limit cycle under cyclic driving. We study experimentally a 2D jammed solid that reaches such a limit cycle. Our solid consists of microscopic plastic beads adsorbed at an oil-water interface and cyclically sheared by a magnetically driven needle. We track each particles trajectory in the solid to identify rearrangements. By associating particles both spatially and temporally, we can measure the extent of each rearrangement. We study specifically the …

Inference And Control In Regulatory Genomics, Siddharth Sharma

Biology and Medicine Through Mathematics Conference

No abstract provided.

Vibrational Relaxation Theory For Systems Embedded In Microscopically Specified Reservoirs, Anastasia Aemilia Ierides

Physics & Astronomy ETDs

This dissertation is a study of the theoretical framework of the practical as well as fundamental problem of the process of relaxation to equilibrium of quantum mechanical systems. The fundamental aspect is concerned with the simultaneous occurrence of decoherence and population equilibration. The practical aspect deals with experimental observations of vibrational relaxation of molecules embedded in liquids or solids. The systems include, but are not limited to, the nondegenerate dimer and harmonic oscillator, in one case weak and in the other strong, interaction with a thermal bath. The time dependence of the energy and the temperature dependence of the relaxation …

Physical Applications Of The Geometric Minimum Action Method, George L. Poppe Jr.

Dissertations, Theses, and Capstone Projects

This thesis extends the landscape of rare events problems solved on stochastic systems by means of the \textit{geometric minimum action method} (gMAM). These include partial differential equations (PDEs) such as the real Ginzburg-Landau equation (RGLE), the linear Schroedinger equation, along with various forms of the nonlinear Schroedinger equation (NLSE) including an application towards an ultra-short pulse mode-locked laser system (MLL).

Additionally we develop analytical tools that can be used alongside numerics to validate those solutions. This includes the use of instanton methods in deriving state transitions for the linear Schroedinger equation and the cubic diffusive NLSE.

These analytical solutions are …

Standard And Anomalous Wave Transport Inside Random Media, Xujun Ma

Dissertations, Theses, and Capstone Projects

This thesis is a study of wave transport inside random media using random matrix theory. Anderson localization plays a central role in wave transport in random media. As a consequence of destructive interference in multiple scattering, the wave function decays exponentially inside random systems. Anderson localization is a wave effect that applies to both classical waves and quantum waves. Random matrix theory has been successfully applied to study the statistical properties of transport and localization of waves. Particularly, the solution of the Dorokhov-Mello-Pereyra-Kumar (DMPK) equation gives the distribution of transmission.

For wave transport in standard one dimensional random systems in …

Atmospheric Radiation And Tgfs: Unexplained Radiation In Our Skies, Adrian Gallegos

Honors College Research

There is a significant correlation between atmospheric electrification via thunderstorms and the occurrence of large emissions of x-ray and gamma ray radiation known as Terrestrial Gamma Ray Flashes (TGFs). Some physical phenomenon may be explained by either the RREA or Thermal Runaway models, but the scientific community as a whole is still largely at work on the theoretical frameworks.

Subsystem Eigenstate Thermalization Hypothesis, Anatoly Dymarsky, Nima Lashkari, Hong Liu

Physics and Astronomy Faculty Publications

Motivated by the qualitative picture of canonical typicality, we propose a refined formulation of the eigenstate thermalization hypothesis (ETH) for chaotic quantum systems. This formulation, which we refer to as subsystem ETH, is in terms of the reduced density matrix of subsystems. This strong form of ETH outlines the set of observables defined within the subsystem for which it guarantees eigenstate thermalization. We discuss the limits when the size of the subsystem is small or comparable to its complement. In the latter case we outline the way to calculate the leading volume-proportional contribution to the von Neumann and Renyi entanglment …

The Inferential Design Of Entropy And Its Application To Quantum Measurements, Kevin Vanslette

Legacy Theses & Dissertations (2009 - 2024)

This thesis synthesizes probability and entropic inference with Quantum Mechanics and quantum measurement [1-6]. It is shown that the standard and quantum relative entropies are tools \emph{designed} for the purpose of updating probability distributions and density matrices, respectively [1]. The derivation of the standard and quantum relative entropy are completed in tandem following the same inferential principles and design criteria. This provides the first design derivation of the quantum relative entropy while also reducing the number of required design criteria to two.

Developing A 3d In Vitro Model By Microfluidics, Hung-Ta Chien

Dissertations and Theses

In vitro tissue models play an important role in providing a platform that mimics the realistic tissue microenvironment for stimulating and characterizing the cellular behavior. In particular, the hydrogel-based 3D in vitro models allow the cells to grow and interact with their surroundings in all directions, thus better mimicking in vivo than their 2D counterparts. The objective of this thesis is to establish a 3D in vitro model that mimics the anatomical and functional complexity of the realistic cancer microenvironment for conveniently studying the transport coupling in porous tissue structures. We pack uniform-sized PEGDA-GelMA microgels in a microfluidic chip to …

Band Filling And Temperature Effects On Electrical Conductivity In Strongly Correlated Hybridized Electron Systems, Dylan T. Meyer

All Graduate Theses, Dissertations, and Other Capstone Projects

We investigate the effects of band filling as well as temperature change on the electrical conductivity of materials with strong interelectron interaction as well as band hybridization. This is done by use of the irreducible two-particle Green function method applied to strongly correlated electron systems described by the Periodic Anderson Model. It was found that there is a definite peak in electrical conductivity at low band occupancy when the d-energy sub-band is half filled. Conductivity was found to have a sharp drop with an increase in temperature as a result of thermal dispersion as well as a change in the …