Physical Sciences and Mathematics Commons^™

Advanced Computational Methodologies To Study Binding Free Energies Of Biomolecular Complexes, Rajat Kumar Pal

Dissertations, Theses, and Capstone Projects

Molecular recognition is the basis of biological mechanisms and is a key element to consider while formulating effective and safe drugs. Pharmaceutical drugs are designed so as to bind a target protein even at very low concentrations to alter the diseased conditions without interfering with normal biological processes. In a rational drug design process, this is achieved by acquiring information about the chemical structure and the physical and chemical properties of the target protein receptor to gain insights on how changing the chemical composition of the substrate drug could affect the protein-drug interaction and binding affinities. Computational models are used …

Robust Neural Machine Translation, Abdul Rafae Khan

Dissertations, Theses, and Capstone Projects

This thesis aims for general robust Neural Machine Translation (NMT) that is agnostic to the test domain. NMT has achieved high quality on benchmarks with closed datasets such as WMT and NIST but can fail when the translation input contains noise due to, for example, mismatched domains or spelling errors. The standard solution is to apply domain adaptation or data augmentation to build a domain-dependent system. However, in real life, the input noise varies in a wide range of domains and types, which is unknown in the training phase. This thesis introduces five general approaches to improve NMT accuracy and …

Study Of Reaction Dynamics Of Protonated/Deprotonated And Radical Cations Of Guanine In Nucleobases And Nucleosides: Singlet Oxygen Oxidation, C8-Water Addition, Cross-Linking With Lysine And Base-Pair Dissociation, Yan Sun

Dissertations, Theses, and Capstone Projects

Among the four DNA nucleobases, guanine (G) has the lowest oxidation potential and represents a preferential target for oxidation and ionization. This leads to the formation of guanine radical cation (G^•+) in various oxidative environments. Of the biologically relevant oxidants, electronically excited singlet oxygen (¹O₂) exclusively damages the guanine bases and gives rise to mutagenesis, DNA-protein cross-linking and cellular death. Combining our home-made electrospray ionization (ESI) guided-ion-beam tandem mass spectrometer, with reaction potential surface calculations and kinetics modeling, five projects have been accomplished as described below.

In project 1, the reactions of deuterated water …

Provenance Of Tin In The Late Bronze Age Balkans: Preparation Of Cassiterite For Sn Isotope Analysis And The Probabilistic And Spatial Analysis Of Sn Isotopes, Andrea H. Mason

Dissertations, Theses, and Capstone Projects

The sources of tin for the European Bronze Age (2200-1050 B.C.E.) have remained undetermined. Isotopic analysis has shown promise as a means of providing “fingerprints” of bronze artifacts that can be matched to their parental ore sources. This project has accomplished the following: (1) further tested and defined a method for the preparation of cassiterite for isotopic analysis, and (2), determined the provenance of tin used for metallurgy in the central Balkans during the later Bronze Age based on Sn isotopic compositions of bronze artifacts and local tin ores.

Two distinct methods have been applied in recent isotopic studies of …

Leveraging Antibodies For Positron Emission Tomography And Near-Infrared Fluorescence Imaging Of Cancer, Kimberly C. Fung

Dissertations, Theses, and Capstone Projects

The high specificity and affinity of antibodies make them attractive for developing drugs to diagnose and treat cancer. The overarching goal of this work is to explore the synthesis and use of antibody-based imaging agents in preclinical models of cancer. This work can be described as two-fold. In the first part, we investigated how the use of a glycans-specific bioconjugation strategy affects Fc gamma RI binding and why it results in improved in vivo performance of immunoconjugates. To do so, we used the clinically relevant positron emission tomography (PET) imaging agent, ⁸⁹Zr-DFO-pertuzumab, in mouse models of human breast cancer. …

Density Functional Theory Study Of Two-Dimensional Boron Nitride Films, Pradip R. Niraula

Dissertations, Theses, and Capstone Projects

Since graphene was isolated in 2004, the number of two-dimensional (2D) materials and their scientific relevance have grown exponentially. Besides graphene, one of the most important and technolocially promizing 2D materials that has emerged in recent years is hexagonal boron nitride, in its monolayer or multilayer form. In my thesis work, I used density functional theory (DFT) calculations to investigate the properties of boron nitride films. In particular, I first studied the properties (i.e. formation energy, defect states, and structure) of point charged defects in monolayer and bilayer hexagonal boron nitride, and subsequently, I focused on the linear and nonlinear …

Hydrophobic Fluoropolymer Nano-Coatings: Study Of Anti-Reflective And Anti-Soiling Properties And Applications, Illya Nayshevsky

Dissertations, Theses, and Capstone Projects

Anti-reflective, anti-soiling and self-cleaning coatings are currently of interest for photovoltaic (PV) cover glass applications due to their potential to increase the amount of light transmitted through the glass and improve efficiency by reducing the number of contaminants bound to the surface of the glass (soiling). Naturally occurring dew is known to exacerbate soiling via cementation of dust on the glass surface. To address these challenges, fluorinated ethylene-propylene (FEP) polymer coatings were formed on solar cover glass using a lamination-peeling technique. This process forms a thin (thick) polymer coating on the glass with a nano-texture that can be controlled by …

Perspectives Of Global Warming, Diomaris Padilla Dr.

Open Educational Resources

This course is designed to foster an interest in global environmental issues by informing the student of both the anthropogenic and natural causes for climate change. While focusing on the scientific aspects of climate change, a broader study will include issues pertaining to global policy and economics in order to engage the student in public policy debates.

Math 220p Foundations Of Mathematics, Nicholas Vlamis

Open Educational Resources

No abstract provided.

Esd Ideas: Why Are Glaciations Slower Than Deglaciations?, Christine J. Ramadhin, Chuixiang Yi

Publications and Research

The Earth’s climate during the Quaternary is dominated by short warm interglacials and longer cold glaciations paced by external forcings such as changes in insolation. Although not observed in the solar radiation changes, the time series of the cycles display asymmetry since transitions to full glacial conditions are slower than the termination of glaciations. Here an idea is proposed for the slower transition by identifying and describing two negative sea ice feedbacks dominant during the glaciation process that could serve as a control on the intermediate stage and decrease the pace of the process.

Effect Of Direct-Current Magnetic Field On The Specific Absorption Rate Of Metamagnetic Comnsi: A Potential Approach To Switchable Hyperthermia Therapy, K C. Ugochukwu, M M. Sadiq, E S. Biegel, L Meagher, M R. Hill, Karl G. Sandeman, A Haydon, K Suzuki

Publications and Research

Materials with 1st order antiferromagnetic (AFM) to high-magnetization (MM) phase transition known for their inverse magnetocaloric effect, abrupt rise in magnetization and magnetoelastic coupling, are promising for application in combined simultaneous diagnosis and targeted cancer therapy. A therapy that combines alternating-current (ac) and direct-current (dc) magnetic fields for simultaneous magnetic hyperthermia therapy (MHT) and magnetic resonance imaging (MRI), using same magnetic particles for heating and as con- trast agents. We report a proof-of-concept study on the induction heating ability of 1st order metamagnetic material with moderate specific absorption rates (SAR) and no tendency for agglomeration, for potential MHT and MRI …

Projected Impacts Of Climate Change On Risk Of Spring Frost And Fire Blight For Malus Domestica, Paul J. Racco

Theses and Dissertations

The impact of climate change is projected for apple phenology, frost attrition, and fire blight risk under the highest emissions scenario through the 21st century.

Coding For The Public Good: Front-End Website Design And Development, Devorah Kletenik

Open Educational Resources

This activity helps student design and develop a front-end of a website, from wireframes through HTML/CSS/Javascript. It includes design questions for students, including the invocation of Ben Schneiderman's eight golden rules for interface design.

Note: this activity assumes prior knowledge of web development. Since this activity is designed for an HCI course, with a focus on interface design, students are not expected to create a back-end for it. This activity can obviously be modified for a full-stack experience.

Needfinding, Devorah Kletenik

Open Educational Resources

This activity guides students through the process needfinding to identify areas of need for their creation of a technology for the "public good." Students will conduct contextual inquiry to identify the needs of their target audience.

Personas, Scenarios And Storyboards, Devorah Kletenik

Open Educational Resources

This activity guides students towards the creation of personas, scenarios and storyboards for a product/website that they are creating.

Public Interest Technology: Coding For The Public Good, Devorah Kletenik

Open Educational Resources

These slides are used to guide a discussion with students introducing them to the notion of public interest technology and coding for the public good. The lesson is intended to spark a discussion with students about different sorts of technology and their societal ramifications.

Accessibility: The Whys And The Hows, Devorah Kletenik

Open Educational Resources

This presentation introduces Computer Science students to the notion of accessibility: developing software for people with disabilities. This lesson provides a discussion of why accessibility is important (including the legal, societal and ethical benefits) as well as an overview of different types of impairments (visual, auditory, motor, neurological/cognitive) and how developers can make their software accessible to users with those disabilities. This lesson includes videos and links to readings and tutorials for students.

Accessibility Evaluation, Devorah Kletenik

Open Educational Resources

This activity guides students through the evaluation of a website that they have created to see if it is accessible for users with disabilities. Students will simulate a number of different disabilities (e.g. visual impairments, color blindness, auditory impairments, motor impairments) to see if their website is accessible; they will also use automated W3 and WAVE tools to evaluate their sites. Students will consider the needs of users with disabilities by creating a persona and scenario of a user with disabilities interacting with their site. Finally, students will write up recommendations to change their site and implement the changes.

Research Paper Development Assignment: Guidelines, Cerr Worksheets, Global Learning Worksheet, And Powerpoint Presentation Prompts And Rubric, Angela Padilla

Open Educational Resources

❏ This Research Paper Assignment is designed for NSF & LMF courses (STEM majors). The assignment is to have students research a global scientific issue. Possible topics that work well for this assignment contain solar panel use, the increase in health issues (like respiratory or mental health conditions) due to global warming/climate change, animal (and other living organism) extinction (or increase) due to global warming, sea level rise, coastal flooding, how the increase in ocean plastics affects the ocean and its species (which affect the environment/climate), etc. However, any global scientific topic will do.

❏ The assignment’s main objectives are …

Universal Gravitation And Circular Motion, Xin Gao

Open Educational Resources

This is designed to serve as a pre-lab. Students will be asked to watch videos linked to in the instructions before the lecture and complete a worksheet with thought- provoking questions guiding them to relating circular motion with the motion of a satellite or planet, and then think about what force is serving as the centripetal force for planets when they move around the sun. Students will also be prompted to think about whether or not there is really no gravity in space, so as to realize how misleading those terms, such as “weightless” or “zero gravity in space” are.

An Invitation To Linear Algebra (2nd Edition), David N. Pham, Jonathon Funk, Wenjian Liu

Open Educational Resources

This is an OER textbook on linear algebra.

Trigonometry: A Brief Conversation, Carolyn D. King Phd, Tam Evelyn, Fei Ye Phd, Beata Ewa Carvajal

Open Educational Resources

These five units are specifically tailored to foster the mastery of a few selected trigonometry topics that comprise the one credit MA-121 Elementary Trigonometry course. Each unit introduces the topic, provides space for practice, but more importantly, provides opportunities for students to reflect on the work in order to deepen their conceptual understanding.

These units have also been assigned to students of other courses such as pre-calculus and calculus as a review of trigonometric basics essential to those courses. This is the second edition of the materials. Units 4 and 5 have been edited to reflect suggestions from instructors who …

A Brief Introduction To The Applications Of Small Organic Molecules As Food Additives, Zhou Zhou

Open Educational Resources

A new chapter in Introductory Organic Chemistry course. Lecture PowerPoint file and laboratory document are also included in this work.

• The goal of this chapter is to cover the basic ground of the food additives from the perspective of organic chemistry. This chapter has three parts.
  • Part one: Introduction of the food additive industry including the history, definition and the purposes of food additives.
  • Part two: The terminology in food additives and in organic chemistry, how to locate trustworthy data sheets for chemicals, and how to interpret the toxicity data.
  • Part three: Different families of organic compounds used as food …

Ecosystem Health In Guánica Bay And La Parguera, Puerto Rico: Remote Sensing Of Ocean Color And Metal Analysis Of Coral Tissue And Surficial Sediments, Jahnelle Howe

Dissertations and Theses

Guánica Bay is an estuary located in southwest Puerto Rico, with a coral reef ecosystem at its periphery. This ecosystem is affected by sediments, nutrients, and contaminants from the watershed through the Bay and into the offshore water. This project evaluates Guánica Bay and La Parguera coastal areas through remote sensing and chemical analysis to assess coastal ecosystem health. The concentration of metals in two coral species and their associated surface sediments was were analyzed by X-ray fluorescence (XRF) and Direct Mercury Analyzer (DMA- 80). Ocean color remote sensing was used to estimate nutrient inputs and phytoplankton biomass through chlorophyll- …

Mechanisms Of Value-Biased Prioritization In Fast Sensorimotor Decision Making, Kivilcim Afacan-Seref

Dissertations and Theses

In dynamic environments, split-second sensorimotor decisions must be prioritized according to potential payoffs to maximize overall rewards. The impact of relative value on deliberative perceptual judgments has been examined extensively, but relatively little is known about value-biasing mechanisms in the common situation where physical evidence is strong but the time to act is severely limited. This research examines the behavioral and electrophysiological indices of how value biases split-second perceptual decisions and the possible mechanisms underlying the process. In prominent decision models, a noisy but statistically stationary representation of sensory evidence is integrated over time to an action-triggering bound, and value-biases …

Lake Volume Data Analyses: A Deep Look Into The Shrinking And Expansion Patterns Of Lakes Azuei And Enriquillo, Hispaniola, Mahrokh Moknatian, Michael Piasecki

Publications and Research

This paper presents the development of an evenly spaced volume time series for Lakes Azuei and Enriquillo both located on the Caribbean island of Hispaniola. The time series is derived from an unevenly spaced Landsat imagery data set which is then exposed to several imputation methods to construct the gap filled uniformly‐spaced time series so it can be subjected to statistical analyses methods. The volume time series features both gradual and sudden changes the latter of which is attributed to North Atlantic cyclone activity. Relevant cyclone activity is defined as an event passing within 80 km and having regional monthly …

Double Inclusive Small-X Gluon Production And Their Azimuthal Correlations In A Biased Ensemble, Gary Kapilevich

Publications and Research

We consider double gg → g production in the presence of a bias on the unintegrated gluon distribution of the colliding hadrons or nuclei. Such bias could be due to the selection of configurations with a greater number of gluons or higher mean transverse momentum squared or, more generally, due to a modified spectral shape of the gluon distribution in the hadrons. Hence, we consider reweighted functional averages over the stochastic ensemble of small-x gluons. We evaluate explicitly the double inclusive gluon transverse momentum spectrum in high-energy collisions, and their azimuthal correlations, for a few simple examples of biases.

Optical Potts Machine Through Networks Of Three-Photon Down-Conversion Oscillators, Mostafa Honari-Latifpour, Mohammad-Ali Miri

Publications and Research

In recent years there has been a growing interest in optical simulation of lattice spin models for applications in classical computing. Here, we propose optical implementation of a three-state Potts spin model by using networks of coupled parametric oscillators with phase tristability. We first show that the cubic nonlinear process of spontaneous three-photon down-conversion is accompanied by a tristability in the phase of the subharmonic signal between three states with 2��/3 phase contrast. The phase of such a parametric oscillator behaves like a three-state spin system. Next, we show that a network of dissipatively coupled three-photon down-conversion oscillators emulates the …

Just A Bit Of Physics Can Tell So Much: A Unique Story Of The Start Of The Earth-Moon System, Fred J. Cadieu

Publications and Research

The start of the Earth-Moon system has been studied to show that this was an exceptionally violent event. One result was that Earth became the terrestrial planet with the highest average density. Another result was that Earth acquired enough mass and radioactive elements that it is expected to maintain a molten core region and magnetic field for the expected life of the Earth. Earth alone of the terrestrial planets was then able to develop plate tectonics as a long term energy release mechanism. The dipole magnetic field of the Sun reverses periodically, currently at the rate of about every 11 …

V-Slam And Sensor Fusion For Ground Robots, Ejup Hoxha

Dissertations and Theses

In underground, underwater and indoor environments, a robot has to rely solely on its on-board sensors to sense and understand its surroundings. This is the main reason why SLAM gained the popularity it has today. In recent years, we have seen excellent improvement on accuracy of localization using cameras and combinations of different sensors, especially camera-IMU (VIO) fusion. Incorporating more sensors leads to improvement of accuracy,but also robustness of SLAM. However, while testing SLAM in our ground robots, we have seen a decrease in performance quality when using the same algorithms on flying vehicles.We have an additional sensor for ground …