Physical Sciences and Mathematics Commons^™

Electrochemical Resistive-Pulse Sensing In Biological Systems, Rui Jia

Dissertations, Theses, and Capstone Projects

Electrochemical resistive-pulse (ERP) sensing with conductive carbon nanopipettes (CNPs) is a powerful technique for detecting single nanoscopic entities, such as single liposomes and biological vesicles, enabling qualitative and quantitative analysis of the redox molecules contained in such entities. ERP experiments were first carried out in biological system by inserting a conductive carbon nanopipette into a macrophage cell to sample single vesicles and measuring reactive oxygen and nitrogen species (ROS/RNS) contained inside them.

Besides sensing intracellular vesicles in macrophage cells, we applied this technique to direct detect single extracellular vesicles (EVs) released from a specific cell, and analysis of reactive oxygen …

Dynamics Of Spin And Charge Of Color Centers In Diamond Under Cryogenic Conditions, Richard G. Monge

Dissertations, Theses, and Capstone Projects

Individual quantum systems in semiconductors are currently the most sought-after platform for applications in quantum science. Most notably, the nitrogen-vacancy (NV) center in diamond features a defect deep within the electronic bandgap, making it amenable for precise manipulation to help pave the way to perform fundamental quantum physics experimentation. The NV center also offers long coherence times and versatile spin-dependent fluorescent properties, making it an ideal candidate for a nanoscale magnetometer. Furthermore, multi-color excitation offers deterministic charge state manipulation. While ambient operation has been key to their appeal, bringing NVs to cryogenic conditions opens new opportunities for alternate forms of …

Thermodynamics Of Learning With Parametric Probabilistic Models, Shervin Sadat Parsi

Dissertations, Theses, and Capstone Projects

This study delves into the learning process within the Probabilistic Parametric Models (PPMs) framework from a unique thermodynamic perspective. By exploring the core concepts of thermodynamics and its innate connection with information theory, we showcase how this interdisciplinary approach can effectively contribute to the domain of machine learning. In the initial chapter, we establish the link between the learning problem in PPMs and a thermodynamic process by reframing various elements of the learning process within the context of thermodynamics. We introduce novel information-theoretic measurements that provide insights into the information learned in both the parameter space and the overall performance …

Out-Of-Distribution Generalization Of Deep Learning To Illuminate Dark Protein Functional Space, Tian Cai

Dissertations, Theses, and Capstone Projects

Dark protein illumination is a fundamental challenge in drug discovery where majority human proteins are understudied, i.e. with only known protein sequence but no known small molecule binder. It's a major road block to enable drug discovery paradigm shift from single-targeted which looks to identify a single target and design drug to regulate the single target to multi-targeted in a Systems Pharmacology perspective. Diseases such as Alzheimer's and Opioid-Use-Disorder plaguing millions of patients call for effective multi-targeted approach involving dark proteins. Using limited protein data to predict dark protein property requires deep learning systems with OOD generalization capacity. Out-of-Distribution (OOD) …

The Role Of Nuclear Quantum Effects In Supercooled Water And Amorphous Ice, Ali H. Eltareb

Dissertations, Theses, and Capstone Projects

Water is one of the most important substances on Earth and plays a fundamental role in numerous scientific and engineering applications. Interestingly, water behaves much differently than other liquids. For example, water shows an anomalous density maximum at 277 K, the solid phase (ice) is less denser than the liquid, and its thermodynamic response functions, such as the specific heat C_P and isothermal compressibility κ_T, also increase anomalously upon cooling. In the glassy state, water can exist in two different forms, low-density and high-density amorphous ice (LDA and HDA). While water has been scrutinized for many centuries, …

Construction And Performance Optimization Of Bioconjugated Nanosensors For Early Detection Of Breast Cancer And Pro-Inflammatory Diseases, Pooja Gaikwad

Dissertations, Theses, and Capstone Projects

In recent years, nanosensors have emerged as a tool with strong potential in medical diagnostics. Single-walled carbon nanotube (SWCNT) based optical nanosensors have notably garnered interest due to the unique characteristics of their near-infrared fluorescence emission, including tissue transparency, photostability, and various chiralities with discrete absorption and fluorescence emission bands. Additionally, the optoelectronic properties of SWCNT are sensitive to the surrounding environment, which makes them suitable for in vitro and in vivo biosensing. Single-stranded (ss) DNA-wrapped SWCNTs have been reported as optical nanosensors for cancers and metabolic diseases. Breast cancer and cardiovascular diseases are the most common causes of death …

Phase Transitions And Thermal Stability Of The Magnetic Dual Chiral Density Wave Phase In Cold, Dense Qcd, William G. Gyory

Dissertations, Theses, and Capstone Projects

The correct description of strongly interacting matter at extreme densities and low temperatures remains poorly understood. We analyze the magnetic dual chiral density wave (MDCDW) phase, an inhomogeneous chiral condensate that arises in cold, dense quark matter in a magnetic field. We first review the background theory and derive the free energy of the condensate. Then we show how the phase transitions can be studied using a generalized Ginzburg-Landau expansion, and we derive a convenient all-orders formula for the coefficients. Using these tools, we compute the order parameters, critical temperature, and threshold temperature over a range of chemical potentials and …

The Development Of Novel Radioscandium And Hydroxypyridinonate Based Radiopharmaceuticals, Michael Phipps

Dissertations, Theses, and Capstone Projects

The use of radiometals in radiopharmaceutical development has drastically increased over the last decade, owed in part to the diverse chemistry and emission characteristics of the radiometals, which allow chemists to create a toolbox of agents to better tailor patient care. Challenges with the use of radiometals include the selection of the metal and the development of optimized chelators to cover the diverse chemistry of the metals which make up the majority of the periodic table. Scandium is the first transition metal and has multiple radioisotopes whose emission characteristics have potential application in medicine. 3,4,3-LI(1,2-HOPO) is a chelator whose denticity, …

Evaluation Of Symmetric Functions And Boolean Functions Over Stochastic Input, Naifeng Liu

Dissertations, Theses, and Capstone Projects

In our daily life, we often face situations where we need to make precise judgments based on initially unknown information, while gathering all the evidence to make informed conclusions can be very costly. In this dissertation, we explore the problem of optimizing the decision-making process under uncertainty, and we focus on problems that can be found in both theoretical computer science and discrete mathematics. The primary goal is to develop approximation algorithms with guaranteed worst-case performance. These algorithms aim to minimize the expected cost of acquiring information necessary for evaluating fundamental functions, such as Boolean and symmetric functions. Furthermore, we …

Quantifying Temperature-, Pressure-, And Nuclear Quantum Effects On Hydrophobic And Hydrophilic Water-Mediated Interactions, Justin T. Engstler

Dissertations, Theses, and Capstone Projects

Water-mediated interactions (WMIs) are responsible for diverse processes in aqueous solutions, including protein folding and nanoparticle aggregation. WMI may be affected by changes in temperature and pressure, and hence, they can alter chemical/physical processes that occur in aqueous environments. Traditionally, attention has been focused on hydrophobic interactions while, in comparison, the role of hydrophilic and hybrid (hydrophobic–hydrophilic) interactions have been mostly overlooked. Here, we study the role of T and P on the WMI between nanoscale (i) hydrophobic–hydrophobic, (ii) hydrophilic–hydrophilic, and (iii) hydrophilic–hydrophobic pairs of (hydroxylated/non-hydroxylated) graphene-based surfaces. We find that hydrophobic, hydrophilic, and hybrid interactions are all sensitive to …

Nonlinear Processes In Room Temperature Exciton-Polaritons, Prathmesh Deshmukh

Dissertations, Theses, and Capstone Projects

Strong light-matter coupling in solid state systems is an intriguing process that allows one to exploit the advantages of both light and matter. In this context, microcavities have become essential platforms for studying the strong coupling regime, where hybrid light-matter states known as exciton-polaritons form, leading to enhanced light matter interaction, modified material properties, and novel quantum phenomena. In this thesis, we explore the phenomenology of exciton-polaritons in strained TMD microcavities, 2D perovskites, fluorescent proteins and organic dyes encompassing thermalization, polariton lasing, and the observation of nonlinear effects.

Transition metal dichalcogenides (TMDs) have emerged as a remarkable class of two- …

Fuglede's Conjecture In Some Finite Abelian Groups, Thomas Fallon

Dissertations, Theses, and Capstone Projects

This dissertation thoroughly examines Fuglede's Conjecture within some discrete settings, shedding light on its intricate details. Fuglede's Conjecture establishes a profound connection between the geometric property of being a tiling set and the analytical attribute of being a spectral set. By exploring the conjecture on various discrete settings, this thesis delves into the implications and ramifications of the conjecture, unraveling its implications within the field.

Optimization And Application Of Graph Neural Networks, Shuo Zhang

Dissertations, Theses, and Capstone Projects

Graph Neural Networks (GNNs) are widely recognized for their potential in learning from graph-structured data and solving complex problems. However, optimal performance and applicability of GNNs have been an open-ended challenge. This dissertation presents a series of substantial advances addressing this problem. First, we investigate attention-based GNNs, revealing a critical shortcoming: their ignorance of cardinality information that impacts their discriminative power. To rectify this, we propose Cardinality Preserved Attention (CPA) models that can be applied to any attention-based GNNs, which exhibit a marked improvement in performance. Next, we introduce the Directional Node Pair (DNP) descriptor and the Robust Molecular Graph …

Centrality Effects On Heavy-Flavor Quark Production And Invariant Yield In Phenix Proton–Gold Collisions At Center-Of-Mass Energy 200 Gev, And Assembly, Testing, Calibration, And Installation Of The Sphenix Hadronic Calorimeters, Daniel Richford

Dissertations, Theses, and Capstone Projects

Hadrons created in heavy-ion collisions interact with the open color-charge of the quark-gluon plasma through their constituent quarks. The medium imparts substantial modifications to heavy-flavor hadrons' momentum spectra. For collisions of small systems, the centrality of those collisions affects both the production of heavy-quarks and the medium modifications that the heavy-quarks experience. This analysis uses the PHENIX detector at the Relativistic Heavy Ion Collider, which collected data from proton--gold collisions in 2015, with a trigger to preference the collection of the five-percent most-central collisions. This analysis uses the distance-of-closest-approach of electron tracks to study semileptonic decays from charm and bottom …

Rotation Period Distributions And Light Curve Morphologies Of Low Mass Stars And Young Associations, Mark Popinchalk

Dissertations, Theses, and Capstone Projects

This dissertation is centered around the rotation periods of low-mass stars and association of young stars. Rotation periods are a link to the age of the star, as they lose angular momentum over time. To understand how this angular momentum evolves requires understanding the rotation period distributions of a range of stellar types and ages. Traditionally, M dwarf stars and young stars were challenging to describe due to their intrinsic faintness and dispersed sky positions respectively. I approached this subject from several directions.

Synthesis Of Biologically Active Tropolones And Stereochemically Rich Compounds Via Cross-Coupling Reactions, Nana B. Agyemang

Dissertations, Theses, and Capstone Projects

Over the past years the Murelli lab has established research based on the synthesis and biological evaluations of alpha-hydroxytropolones (alpha-HTs). These seven-membered aromatic rings have three contiguous oxygen atoms that chelates to metals, thus, biologically having the ability to bind dinuclear metalloenzymes and promoting inhibition. Synthetic routes to alpha-HT’s are scarce and therefore has been the main driving force in developing efficient and general synthetic methods to obtain variations in alpha-HTs, enabling SAR studies. The Murelli lab have therefore developed an oxidopyrylium cycloaddition/ring-opening strategy that is able to generate polysubstituted alpha-HTs starting from kojic acid, a cheap and readily available …

Stereospecific Cross-Coupling Reactions With Enantioenriched Electrophiles, Iv Kraja

Dissertations, Theses, and Capstone Projects

We have developed a novel palladium-catalyzed stereospecific C(sp³)–C(sp³) Stille cross-coupling reaction between carbastannatrane nucleophiles and α-(trifluoromethyl) benzylic tosylates. This constitutes the first example of a stereospecific C(sp³)–C(sp³) cross-coupling reaction using an enantioenriched electrophile and an alkyltin nucleophile. This system has the potential to be extended to cross-coupling reactions using configurationally stable enantioenriched nucleophiles, thus enabling stereochemical control of two newly formed contiguous stereocenters. Generating enantioenriched α-(trifluoromethyl) benzylic compounds also has importance in pharmaceutical and agrochemical industries.

Through the development of this reaction, our findings show that the addition …

Tunable Linear And Nonlinear Metasurfaces Based On Hybrid Gold-Graphene Plasmons, Matthew Feinstein

Dissertations, Theses, and Capstone Projects

Optical Metasurfaces are planar structures that are patterned with subwavelength structures and are very thin compared to the wavelength of light. Despite their thinness, these structured materials can strongly interact with incident light to effect the functionalities of conventional optical components, such as rotation of the polarization state, beam steering, lensing, spectral filtering, and holography, to name a few. Metasurfaces can also facilitate nonlinear optical effects, such as the mixing of beams at different frequencies to generate a beam at a new frequency.

The ability to alter the behavior of a metasurface during operation is highly desired for applications such …

On The Spectrum Of Quaquaversal Operators, Josiah Sugarman

Dissertations, Theses, and Capstone Projects

In 1998 Charles Radin and John Conway introduced the Quaquaversal Tiling. A three dimensional hierarchical tiling with the property that the orientations of its tiles approach a uniform distribution faster than what is possible for hierarchical tilings in two dimensions. The distribution of orientations is controlled by the spectrum of a certain Hecke operator, which we refer to as the Quaquaversal Operator. For example, by showing that the largest eigenvalue has multiplicity equal to one, Charles Radin and John Conway showed that the orientations of this tiling approach a uniform distribution. In 2008, Bourgain and Gamburd showed that this operator …

Singlet Oxygen-Mediated Conformational Flexibility, Antioxidant, And Isomerization Studies In Chemistry And Biochemistry, Oliver Turque

Dissertations, Theses, and Capstone Projects

Three chapters are included in this dissertation, each of which describes non-oxidative reactions, with peroxy intermediates formed between singlet oxygen (¹O₂) and substrate. (1) Novel discoveries related to the intermediate formed by ¹O₂ and dimethyl disulfane are explored. (2) A new mechanism is proposed, wherein the dihedral angle CS–SC (θ) determines the pro- or antioxidant activity of an organic disulfide. (3) A review of ¹O₂'s ability to facilitate the geometric isomerization of alkenes and polyenes is presented in Chapter 3.

Chapter 1 investigates the role of singlet oxygen potentially …

Separation Of Zr From Complex Matrices For Isotope Harvesting Applications, Jake A. Bence

Dissertations, Theses, and Capstone Projects

Zr isotopes have various applications in nuclear science, such as ⁸⁶Zr and ⁸⁹Zr in nuclear medicine, ⁸⁸Zr as a diagnostic isotope relevant to stockpile stewardship, and the fission product ⁹⁵Zr useful as an s-process branch nucleus for study in astrophysics. To access these isotopes of interest, dedicated production methods and subsequent processing chemistry are required. Direct production routes can be technically challenging and difficult to obtain enough activity to meet demand. The processing chemistry of Zr isotopes is tedious due to the tendency for Zr to hydrolyze in solution without highly acidic conditions or a strong …

Ai-Supported Academic Advising: Exploring Chatgpt’S Current State And Future Potential Toward Student Empowerment, Daisuke Akiba, Michelle C. Fraboni

Publications and Research

Artificial intelligence (AI), once a phenomenon primarily in the world of science fiction, has evolved rapidly in recent years, steadily infiltrating into our daily lives. ChatGPT, a freely accessible AI-powered large language model designed to generate human-like text responses to users, has been utilized in several areas, such as the healthcare industry, to facilitate interactive dissemination of information and decision-making. Academic advising has been essential in promoting success among university students, particularly those from disadvantaged backgrounds. Unfortunately, however, student advising has been marred with problems, with the availability and accessibility of adequate advising being among the hurdles. The current study …

Syllabus For Computational Physics (Phys 39907), Mark D. Shattuck

Open Educational Resources

Syllabus for City College of New York Computational Physics course.

Approaches To The Erdős–Straus Conjecture, Ivan V. Morozov

Publications and Research

The Erdős–Straus conjecture, initially proposed in 1948 by Paul Erdős and Ernst G. Straus, asks whether the equation 4/n = 1/x + 1/y + 1/z is solvable for all n ∈ N and some x, y, z ∈ N. This problem touches on properties of Egyptian fractions, which had been used in ancient Egyptian mathematics. There exist many partial solutions, mainly in the form of arithmetic progressions and therefore residue classes. In this work we explore partial solutions and aim to expand them.

Simultaneous Values Of The Totient Function, Nelson Carella

Publications and Research

A pair of integers $n$ and $n+k$ is a simultaneous solution of an arithmetic function $f:\mathbb{N}\longrightarrow \mathbb{R}$ if $f(n)=f(n+k)$, where $k\ne0$ is a fixed integer. This article shows that the totient function has infinitely many simultaneous solutions. In particular, $\varphi(n)=\varphi(n+2)$ infinitely often as $n\to\infty$.

Lecture Notes On Cloud Computing (Ver. Summer 2023), Jun Li

Open Educational Resources

No abstract provided.

Balanced Blended Space: Foundational Human–Ai Dialogues In A Symmetry-Based Mediation Framework, David Smith

Publications and Research

This working paper documents the early development of the Balanced Blended Space (BBS) framework through a series of iterative interactions between a cognitive agent (human researcher) and a computational agent (AI system) conducted in 2023. The work is motivated by the need for a universal theoretical model capable of describing the integration of physical, virtual, and conceptual spaces, particularly in response to increasing fragmentation across contemporary communication systems.

BBS is proposed as a symmetry-based mediation framework in which relationships between domains—such as physical and virtual space, cognition and computation, and multiple sensory modalities—are treated as structurally equivalent and mappable. Central …

Optical Response Of 3d Model Topological Nodal-Line Semimetal, Sita Kandel, Godfrey Gumbs, Oleg L. Berman

Publications and Research

Wepresent a semi-analytical expression for both longitudinal and transverse optical conductivities of a model TNLSM employing the Kubo formula with emphasis on the optical spectral weight redistribution, deduced from appropriate Green’s func tions. In this semimetal, the conduction and valence bands cross each other along a one- dimensional curve protected by certain symmetry group in the 3D Brillouin zone. Although the crossing cannot be removed by any perturbations, it can be adjusted by continuous tuning of the Hamiltonian with a parameter α. When α>0, the two bands cross each other near the Γ point in the (kx,ky) plane of …

A Review Of Theropithecus Oswaldi With The Proposal Of A New Subspecies, Dagmawit Abebe Getahun, Eric Delson, Chalachew Mesfin Seyoum

Publications and Research

Theropithecus oswaldi darti, as currently understood, is the oldest Theropithecus taxon in the fossil record and the earliest subspecies in the Theropithecus oswaldi lineage. Theropithecus oswaldi darti is typified at the site of Makapansgat in South Africa, and a similar form (T. o. cf. darti) is usually recognized at Hadar, Dikika, some Middle Awash localities, and Woranso-Mille in Ethiopia. This taxon is also tentatively believed to occur in Kenya at Kanam and Koobi Fora and in Member C of the Shungura Formation in Ethiopia. While there is a general consensus that the East African ‘darti’ specimens are …

Structural Anomaly Detection, Shoufu Luo

Dissertations, Theses, and Capstone Projects

As computer systems become more complex and powerful, the threat of sophisticated and persistent computer attacks increases dramatically. Traditional intrusion detection systems that rely on log analysis struggle to keep pace with these evolving threats, as the attacking trails are often buried in high-volume and high-velocity legitimate activities in the system. Despite tremendous progress in applying machine learning techniques to anomaly-based intrusion detection, such methods continue to suffer from a high false positive rate due to the diversity and variability of individual behavior.To address this problem, this thesis proposes a new framework for detecting structural anomalies in computer systems. The …