# Physical Sciences and Mathematics Commons™

Articles 1 - 30 of 1482

## Full-Text Articles in Physical Sciences and Mathematics

Liboblivious: A C++ Library For Oblivious Data Structures And Algorithms, Scott D. Constable, Steve Chapin Oct 2018

#### Liboblivious: A C++ Library For Oblivious Data Structures And Algorithms, Scott D. Constable, Steve Chapin

##### Electrical Engineering and Computer Science - Technical Reports

Infrastructure as a service (IaaS) is an enormously beneficial model for centralized data computation and storage. Yet, existing network-layer and hardware-layer security protections do not address a broad category of vulnerabilities known as side-channel attacks. Over the past several years, numerous techniques have been proposed at all layers of the software/hardware stack to prevent the inadvertent leakage of sensitive data. This report discusses a new technique which integrates seamlessly with C++ programs. We introduce a library, libOblivious, which provides thin wrappers around existing C++ standard template library classes, endowing them with the property of memory-trace obliviousness.

Aug 2018

#### Fabrication And Characterization Of Superconducting Metamaterial Resonators, Haozhi Wang

##### Dissertations - ALL

Superconducting circuits operated at low temperatures have led to rapid advances in quantum information processing as well as quantum optics in the microwave regime. Engineered quantum systems with a dense spectrum of modes coupled to artificial atoms, or qubits, formed from superconducting circuits offer an opportunity to explore large-scale entanglement or perform quantum simulations of many-body phenomena. Recent research efforts into artificial metamaterials have yielded microwave and optical systems with numerous counterintuitive properties, including left-handed transmission, where the group velocity and phase velocity for a wave point in opposite directions. Metamaterial resonators implemented with superconducting thin-film circuits provide a route ...

Motility-Induced Phases: Out-Of-Equilibrium Droplets, Surfaces, And Survival, Adam Edward Patch Aug 2018

#### Motility-Induced Phases: Out-Of-Equilibrium Droplets, Surfaces, And Survival, Adam Edward Patch

##### Dissertations - ALL

Active matter represents a unique kind of out-of-equilibrium matter that is endowed with motility, the ability of each individual unit to move according to its own self-propulsion force. Objects of study in active matter include entities like birds and cells, which become particularly interesting at scales larger than the individuals, where we find emergent collective behavior like flocking and morphogenetic self-organization, respectively. One can study both microscopic and macroscopic behaviors of these particles using theory, simulation, and experiment, but largescale simulations are critically important to understanding some of the underlying statistical mechanical properties of active matter.

Motility-induced phase separation (MIPS ...

Statistical Mechanics Of Thermalized Ribbons And Sheets, Sourav Sanjukta Bhabesh Aug 2018

#### Statistical Mechanics Of Thermalized Ribbons And Sheets, Sourav Sanjukta Bhabesh

##### Dissertations - ALL

In this dissertation, we study the thermal behavior of two-dimensional sheets and ribbons. We study the effects of thermal fluctuations on the crumpling transition of elastic sheets. Existing two-dimensional sheets have a crumpling temperature which is very high and the crumpling transition has not been observed experimentally. We propose a mechanism using which one can tune this crumpling transition by changing the shape and geometry of >the sheet. We perform extensive molecular dynamics simulations by perforating the sheet with a dense array of holes and find that the critical temperature is a function of the removed area. Lastly, we look ...

#### Redefining The Scope Of Prenylation: Discovery Of “Forbidden” Substrate Recognition And Development Of Methods Utilizing Prenylated Proteins, Melanie Jane Blanden

##### Dissertations - ALL

Post-translational modifications play a central role in controlling biological function and cell behavior through changes in protein structure, activity, and localization. Prenylation is one such modification wherein a 15- or 20-carbon isoprenoid group is attached to a cysteine residue near the C-terminus of a substrate protein by one of three enzymes: protein farnesyltransferase (FTase), protein geranylgeranyltransferase type I (GGTase-I) or protein geranylgeranyltransferase type II (GGTase-II, also known as Rab GGTase). These covalent modifications can aid in protein association with cellular membranes, with this localization necessary for function of many prenylated proteins. FTase and GGTase-I have been proposed to recognize a ...

Aug 2018

#### Ghrelin Processing And Maturation: Developing A Molecular-Level Framework For Hormone Activation And Biological Function, Elizabeth Rose Cleverdon

##### Dissertations - ALL

Ghrelin is a 28 amino acid hormone involved in appetite stimulation, maintenance of energy balance, and a range of other neuroendocrine functions. Over the course of its expression and maturation, proghrelin (the prohormone of ghrelin) undergoes a unique posttranslational modification whereby a serine side chain is esterified with octanoic acid. Proghrelin then undergoes subsequent proteolysis to yield ghrelin. This octanoylation modification has been demonstrated to be required for ghrelin to activate its cognate receptor. Since acylated ghrelin has been linked with a variety of disease states, ghrelin signaling is a prime target for inhibition and inhibitor development. Biochemical and structural ...

Aug 2018

#### Assessing Dissolved Methane And Halogen Patterns In Groundwater Of New York State, Shannon Garvin

##### Theses - ALL

Due to the ban on hydraulic fracturing for natural gas in New York State (NYS), it serves as an ideal location to study the natural processes that control the migration of dissolved methane and high salinity fluids found at depth. The hydrogeologic setting of NYS is analogous to that of Northern Pennsylvania where unconventional exploration has not been restricted. Halogens geochemically behave conservatively and can be found in unique proportions. Therefore, they serve as useful tracers for the natural movement of groundwater. The focus of our study is to: 1) establish a more cohesive baseline for groundwater quality data for ...

Seasonally Resolved Δ18o From Pennsylvanian Mollusk Aragonite, Marie Yerill Jimenez Aug 2018

#### Seasonally Resolved Δ18o From Pennsylvanian Mollusk Aragonite, Marie Yerill Jimenez

##### Theses - ALL

Use of the δ18O thermometer in deep time investigations is complicated by uncertainty in the oxygen isotopic composition of seawater and an increasing potential for diagenetic alteration with age. These concerns are particularly important when considering that δ18O values from Paleozoic marine carbonates are generally low and show a depletion trend with increasing age. Competing explanations for this trend include increasing alteration with age, evolution of seawater δ18O through time, and increasing ocean temperatures with age. Demonstrating the preservation of original mineralogy, thus eliminating diagenesis as a factor, is a primary hurdle in deconvolving potential causes. Here, we report data ...

Aug 2018

#### Dispersive Transport And Drift Mobilities In Methylammonium Lead Iodide Perovskites, Brian Maynard

##### Dissertations - ALL

Perovskite solar cells (PSCs) have impacted the photovoltaic industry over the past decade with unprecedented boosts in photo-conversion efficiencies. Perovskites’ dramatic rise has been due to borrowed ideas and research from other types of solar cell geometries. The initial surge in perovskite research started in 2009 with the discovery of unusually long photocharge carrier lifetimes and ambipolar diffusion. These discoveries changed the geometry of the solar cell from a dye-sensitized structure to n-i-p. The work done in this dissertation focuses on thin film methyl-ammonium lead iodide perovskites in n-i-p structures made by the National Renewable Energy Laboratory and Iowa State ...

Formal Verification Of A Modern Boot Loader, Scott D. Constable, Rob Sutton, Arash Sahebolamri, Steve Chapin Aug 2018

#### Formal Verification Of A Modern Boot Loader, Scott D. Constable, Rob Sutton, Arash Sahebolamri, Steve Chapin

##### Electrical Engineering and Computer Science - Technical Reports

We introduce the Syracuse Assured Boot Loader Executive (SABLE), a trustworthy secure loader. A trusted boot loader performs a cryptographic measurement (hash) of program code and executes it unconditionally, allowing later-stage software to verify the integrity of the system through local or remote attestation. A secure loader differs from a trusted loader in that it executes subsequent code only if measurements of that code match known-good values. We have applied a rigorous formal verification technique recently demonstrated in practice by NICTA in their verification of the seL4 microkernel. We summarize our design philosophy from a high level and present our ...

Cosmological Perturbations In The Early Universe, Gizem Sengor Jun 2018

#### Cosmological Perturbations In The Early Universe, Gizem Sengor

##### Dissertations - ALL

One essence in capturing the history of primordial fluctuations that arise during inflation and eventually lead to formation of large scale structures in the universe, relies on quantizing general relativity coupled to a scalar field. This is a system that respects diffeomorphism invariance, the freedom of choosing the coordinate system to work with without changing the physics. Hence the way to handle its quantization requires an understanding of how to quantize diffeomorphisms. Deciding on suitable coordinate choices and making sure that this gauge fixing, which is unavoidable in any calculation, does not effect the end result, is tricky. In this ...

#### Surface Water And Groundwater In A Changing Climate: Applications Of Hydrogeophysics And Trend Analysis To Understand Hydrologic Systems, Robin Glas

##### Dissertations - ALL

Water resources are being impacted by anthropogenic climate change worldwide, the nature and severity of that impact is determined by geographic position, local topography, underlying geology, and human influences such as land use, water availability, and water regulation. As global temperatures continue to rise due to greenhouse gas emissions, it is imperative that we better understand how water availability fluctuates with changes in air temperature, rainfall, snowpack, and glacial ice. This dissertation provides an analysis of the hydrologic response to both short-term and long-term climatic changes in both humid-temperate and semi-arid tropical regions. Within the tropical alpine zone, shifts in ...

#### Implicit Fixed-Point Proximity Framework For Optimization Problems And Its Applications, Xiaoxia Liu

##### Dissertations - ALL

A variety of optimization problems especially in the field of image processing are not differentiable in nature. The non-differentiability of the objective functions together with the large dimension of the underlying images makes minimizing the objective function theoretically challenging and numerically difficult. The fixed-point proximity framework that we will systematically study in this dissertation provides a direct and unified methodology for finding solutions to those optimization problems. The framework approaches the models arising from applications straightforwardly by using various fixed point techniques as well as convex analysis tools such as the subdifferential and proximity operator.

With the notion of proximity ...

Stormwater Inputs In Urban Streams: Impact And Persistence Of Effects On Stream Temperature, Samuel Harrison Caldwell Jun 2018

#### Stormwater Inputs In Urban Streams: Impact And Persistence Of Effects On Stream Temperature, Samuel Harrison Caldwell

##### Theses - ALL

Stream temperature is an important metric for determining the health of a stream system, and derived from complex interactions between climate, weather, and local landscape characteristics. In urban areas, stream temperature is additionally influenced by impervious surfaces as well as stormwater infrastructure that translates water quickly to stream channels. Disentangling the impacts of spatial and temporal drivers of the stream temperature regime is therefore a complex task. To improve understanding of spatial and temporal variability in stream temperatures, we combined in situ stream temperature loggers with thermal infrared (TIR) imagery collected via unmanned aerial vehicles (UAV) along a 2.25 ...

Jun 2018

#### A Solid-State Theoretical And Experimental Analysis Of Nitroguanidine And Gunshot Residues, Rebecca Prendergast

##### Theses - ALL

Low-frequency spectroscopic techniques, including terahertz time-domain spectroscopy and THz-Raman spectroscopy, are used in conjunction with solid-state density functional theory simulations to investigate the vibrational modes of the explosive propellant nitroguanidine and three gunshot residues. Terahertz spectroscopy and low-frequency Raman spectroscopy are used to probe these small organic crystalline systems because the low-frequency (sub-200 cm-1) spectra for these systems are either, in the case of terahertz, not yet published in the spectral range obtained in this work, or in the case of Raman, not focused on in the literature. Low-frequency spectra and the corresponding solid-state density functional theory simulations can provide ...

May 2018

#### Evaluating The Effects Of Hydrogeologic Processes On The Fate Of Salinity And Halogens In Headwater Catchments, Kristina M. Gutchess

##### Dissertations - ALL

The transport of solutes from their source to natural water systems is a critical control on the chemistry and potability of drinking water supplies. Therefore, developing a thorough understanding not only of contaminant sources, but also of the controls on the movement of solutes through catchments, is essential to providing accurate assessments of how future environmental stressors (e.g. land cover, population growth, and climate change) may affect water resources.

Halogens (specifically, chloride (Cl), bromide (Br), and iodine (I)) occur naturally at low levels in terrestrial aquatic ecosystems, and may also originate from a suite of anthropogenic sources. Due to ...

May 2018

#### Auslander-Reiten Sequences Over Gorenstein Rings Of Dimension One, Robert Roy

##### Dissertations - ALL

Let R be a complete local Gorenstein ring of dimension one, with maximal ideal m. We show that if M is a maximal Cohen-Macaulay R-module which begins an Auslander-Reiten sequence, then this sequence is produced by an endomorphism of m, which we call a Frobenius element. We observe that Frobenius elements can be easier to identify when R is a graded ring, instead of complete local. We give an example application, determining the shape of some components of Auslander-Reiten quivers. We also adapt results due to Zacharia and others, from the setting of Artin algebras. This allows us to list ...

#### Discriminant Analysis As A Decision-Making Tool For Geochemically Fingerprinting Sources Of Groundwater Salinity And Other Work, Nathaniel Chien

##### Theses - ALL

The thesis presented herein is a compilation of two different research projects I have been fortunate enough to work on during my graduate career at Syracuse University. The first and most complete project is a data analysis study using linear discriminant analysis to differentiate between sources of groundwater salinity in water samples from shallow groundwater wells. It is a model validation study that builds on previous work spearheaded by the Earth Sciences Department at Syracuse University. It represents some of my best work performed at Syracuse and should be considered the bulk of my thesis submission. Due to successful publication ...

#### Late-Quaternary Seismic Stratigraphic Framework And Paleolimnology Of Walker Lake, Nevada, Mattie Friday

##### Theses - ALL

The western USA has experienced heightened sensitivity to drought in recent years, and these conditions are compounded by a rapidly expanding population. Lake deposits are sensitive archives useful for reconstructing past hydroclimate, and such paleorecords can provide constraints for future planning. Walker Lake, Nevada is a terminal basin in the westernmost Basin and Range province. It contains a long sediment record extending at least to the late Pleistocene. Ten sediment cores, and ~300 km of CHIRP seismic reflection data were acquired from the lake in 2013 to develop a detailed environmental history from the lake’s stratigraphic record. Seven sequences ...

#### Muon/Pion Separation Using Convolutional Neural Networks For The Microboone Charged Current Inclusive Cross Section Measurement., Jessica Nicole Esquivel

##### Dissertations - ALL

The purpose of this thesis was to use Convolutional Neural Networks (CNN) to separate muons and pions for use in increasing the acceptance rate of muons below the implemented 75cm track length cut in the Charged Current Inclusive (CC-Inclusive) event selection for the CC-Inclusive Cross-Section Measurement. In doing this, we increase acceptance rate for CC-Inclusive events below a specific momentum range.

#### Exploration Of Transition Metal Catalyzed C−C And C−N Bond Formation To Access Synthetically Elusive Small Molecules, Alexandre Dixon

##### Dissertations - ALL

Herein is disclosed accounts of fundamentally different projects. The focus of this research enveloped the development of synthetic methods to access structurally complex small molecules, especially in the realm of C–C and C–N bond formations. The scope of reactions discussed revolve especially around ruthenium and palladium catalysis, accessing underexplored heterocyclic motifs. The utility of these techniques toward the synthesis of small molecules in drug discovery cannot be understated, as there are few ways to access these elusive moieties. The content is divided into the following four chapters:

The development of methods for the stereoselective synthesis of polysubstituted 1 ...

The Structure Of 4-Clusters In Fullerenes, Jennifer Edmond May 2018

#### The Structure Of 4-Clusters In Fullerenes, Jennifer Edmond

##### Dissertations - ALL

Fullerenes can be considered to be either molecules of pure carbon or the trivalent plane graphs with all hexagonal and (exactly 12) pentagonal faces that models these molecules. Since carbon atoms have valence 4 and our models have valence 3, the edges of a perfect matching are doubled to bring the valence up to 4 at each vertex. The edges in this perfect matching are called a Kekule structure and the hexagonal faces bounded by three Kekule edges are called benzene rings. A maximal independent (disjoint) set of benzene rings for a given Kekule structure is called a Clar set ...

#### Lelong Numbers And Geometric Properties Of Upper Level Sets Of Currents On Projective Space, James Heffers

##### Dissertations - ALL

Let $T$ be a positive closed bidegree $(p,p)$ current in $\mathbb{P}^n$. In this thesis, our goal is to understand more about the geometric properties of the sets of highly singular points of the current $T$. Lelong numbers will be the main tool used for determining how singular a point of a current is. For the first main result of this thesis, we let $T$ be a positive closed current of bidimension $(1,1)$ with unit mass on the complex projective space $\mathbb P^2$. For $\alpha > 2/5$ and $\beta = (2-2\alpha)/3$ we show that if ...

A Formally Veriﬁed Heap Allocator, Arash Sahebolamri, Scott D. Constable, Steve J. Chapin Jan 2018

#### A Formally Veriﬁed Heap Allocator, Arash Sahebolamri, Scott D. Constable, Steve J. Chapin

##### Electrical Engineering and Computer Science - Technical Reports

We present the formal verification of a heap allocator written in C. We use the Isabelle/HOL proof assistant to formally verify the correctness of the heap allocator at the source code level. The C source code of the heap allocator is imported into Isabelle/HOL using CParser and AutoCorres. In addition to providing the guarantee that the heap allocator is free of bugs and therefore is suitable for use in security critical projects, our work facilitates verification of other projects written in C that utilize Isabelle and AutoCorres.

#### Effects Of Sodium Chloride On Anthracene Photolysis Kinetics In Aqueous-Organic Solutions, Kyle Blaha

##### Theses - ALL

Polycyclic aromatic hydrocarbons (PAHs) are dangerous pollutants. The photolysis kinetics of PAHs are of interest because they are carcinogenic and can increase in toxicity through photodegradation into secondary products. They are often associated with particulate matter. The composition and physical properties of the particulate matter can affect PAH photolysis kinetics. We investigated the effects of sodium chloride on the photolysis kinetics of the PAH anthracene in water and octanol as well as mixed-phase solutions (water-octanol), which were used as models for aqueous-organic aerosols. A non-linear dependence on sodium chloride concentrations was observed. Sodium chloride enhanced photolysis at concentrations up to ...

Continuum Models Of Collective Migration In Living Tissues, Kazage J. Christophe Utuje Aug 2017

#### Continuum Models Of Collective Migration In Living Tissues, Kazage J. Christophe Utuje

##### Dissertations - ALL

This dissertation investigates the physical mechanics of collective cell migration in monolayers of epithelial cells. Coordinated cell motion underlies a number of biological processes, including wound healing, morphogenesis and cancer metastasis, and is controlled by the interplay of single cell motility, cell-cell adhesions, cell-substrate interaction, and cell contractility modulated by the acto-myosin cytoskeleton. Here we examine the competing roles of these mechanisms via a continuum model of a tissue as an active elastic medium, where mechanical deformations are coupled to and feed back onto chemical signaling.

We begin in Chapter 1 with a brief review of cell migration at both ...

Pattern Formation In Active Nematics, Prashant Mishra Aug 2017

#### Pattern Formation In Active Nematics, Prashant Mishra

##### Dissertations - ALL

This thesis presents analytical and numerical studies of the nonequilibrium dynamics of active nematic liquid crystals. Active nematics are a new class of liquid crystals consisting of elongated rod-like units that convert energy into motion and spontaneously organize in large-scale structures with orientational order and self-sustained flows. Examples include suspensions of cytoskeletal filaments and associated motor proteins, monolayers of epithelial cells plated on a substrate, and bacteria swimming in a nematic liquid crystal. In these systems activity drives the continuous generation and annihilation of topological defects and streaming flows, resulting in spatio-temporal chaotic dynamics akin to fluid turbulence, but that ...

#### Qubit Coupled Mechanical Resonator In An Electromechanical System, Yu Hao

##### Dissertations - ALL

This thesis describes the development of a hybrid quantum electromechanical system. In this system the mechanical resonator is capacitively coupled to a superconducting transmon which is embedded in a superconducting coplanar waveguide (CPW) cavity. The difficulty of achieving high quality of superconducting qubit in a high-quality voltage-biased cavity is overcome by integrating a superconducting reflective T-filter to the cavity. Further spectroscopic and pulsed measurements of the hybrid system demonstrate interactions between the ultra-high frequency mechanical resonator and transmon qubit. The noise of mechanical resonator close to ground state is measured by looking at the spectroscopy of the transmon. At last ...

#### Stable Sparse Orthogonal Factorization Of Ill-Conditioned Banded Matrices For Parallel Computing, Qian Huang

##### Dissertations - ALL

Sequential and parallel algorithms based on the LU factorization or the QR factorization have been intensely studied and widely used in the problems of computation with large-scale ill-conditioned banded matrices. Great concerns on existing methods include ill-conditioning, sparsity of factor matrices, computational complexity, and scalability. In this dissertation, we study a sparse orthogonal factorization of a banded matrix motivated by parallel computing. Specifically, we develop a process to factorize a banded matrix as a product of a sparse orthogonal matrix and a sparse matrix which can be transformed to an upper triangular matrix by column permutations. We prove that the ...

Mappings Between Annuli Of Smallest P-Harmonic Energy, Daniel Cuneo Aug 2017

#### Mappings Between Annuli Of Smallest P-Harmonic Energy, Daniel Cuneo

##### Dissertations - ALL

An important topic in the calculus of variations is the study of traction-free problems, in which deformations between given domains in $\mathbb{R}^n$ are allowed to slip on the boundary, without prescribing boundary values. For annuli $\A = \A(r, R)$ and $\A^* = \A(r_*, R_*)$, we seek the traction-free minimizer of the $p$-harmonic energy among homeomorphisms in Sobolev class $W^{1, p}(\A, \A^*)$. For such a mapping, the $p$-harmonic energy is defined by \begin{equation*}

\mathcal{E}_p[h] = \int\limits_{\A} |Dh(x)|^p dx

\end{equation*}

Classical methods fail for traction-free problems. We will ...