Physical Sciences and Mathematics Commons^™

Designing Computational Biology Workflows With Perl - Part 1 & 2, Esma Yildirim

Open Educational Resources

This manual guides the instructor to combine the partial files of the virtual machine image and construct sequencer.ova file. It is accompanied by the partial files of the virtual machine image.

Titanium Dioxide Sensitized With Porphyrin Dye As A Photocatalyst For The Degradation Of Water Pollutants, Kevin Reyes, Ivana Jovanovic

Publications and Research

TiO2 was sensitized with a porphyrin, Tetra(4-carboxyphenyl) porphyrin(TCPP) and used as photocatalyst under visible light for degradation of aqueous solutions of methylene blue (MB) dye. The quantification of the degradation of MB was assessed by UV-Vis spectroscopy. The results of this procedure showed the decrease in concentration of MB over time when reaction is exposed to visible light. The TiO2-TCPP complex was tested as well for the recovery of metals from the AgNO3 aqueous solution. The reduction of silver cations to silver metal was observed through formation of black precipitate.

The Dionysus Project: Classifying & Monitoring Vineyards With Satellite Remote Sensing & Image Analysis, Evelin Perez-Flores, Nicole Flores, Rachel Zinberg, Dionne Huston, Aaron Davitt, Kyle Mcdonald

Publications and Research

Climate change is expected to impact the wine industry by shifting suitable growing regions away from established regions and increasing the demand for freshwater supplies to maintain vineyard health. This creates challenges for maintaining vineyards since the grapevines need to be appropriately stressed to produce quality grapes for quality wine. This requires precision management of freshwater application and canopy management to produce a grape that has the appropriate concentration of flavors and sugars. Vineyards in the U.S. are typically monitored by vineyard managers at the large scale, lacking the resolution needed to identify grapevine growth at the subfield level. Vineyard …

Understanding The Impact Of Peer-Led Workshops On Student Learning, Afolabi Ibitoye, Nadia Kennedy, Armando Cosme

Publications and Research

As students we often wonder why some subjects are easy to understand and requires not much effort in terms of re-reading the material, for us to grasp what it entails. One subject seems to remain elusive and uneasy for a vast majority of learners at all levels of education; that subject is Mathematics, it is one subject that most learners finds difficult even after doubling the amount of time spent on studying the material. My intention is to explore ways to make Mathematics easier for other students using feedback from students enrolled in NSF mathematics peer leading workshops, and use …

A Comparative Study Of Incidence Of Domestic Violence Between Immigrant And Non-Immigrant Women In The United States Of America, Nadia A. Gordon, Urmi Ghosh-Dastidar, Janet Liou-Mark, Shamita Dasgupta

Publications and Research

Immigrant women in the USA come from various socio-economic, cultural, and religious backgrounds. Some of these women suffer from domestic violence; however, due to their strict cultural or social structure, they often stay quiet and rarely report these incidents to the authorities. Additionally, since these immigrant women face more challenges than their non-immigrant peers, they are more reluctant or unlikely to leave their abusive partners. An analysis was completed using published data as an attempt to establish if any statistically significant differences exist between reported incidences among immigrant women and non-immigrant women. A chi-square analysis (χ² = 14.53; p-value …

Simulation As A Predictor In Probability, Xiaona Zhou

Publications and Research

In this study, we simulate bivariate normal data. We gain intuition about the bivariate normal distribution by comparing the generated data to the associated bivariate normal density surface. We also get results about covariance and correlation. We will use tools from linear algebra to discuss transformations of random normal vectors, and the use of contours.

A Pretargeted Spect Imaging Strategy Employing Technetium-99m Based On Bioorthogonal Diels-Alder Click Chemistry, Justin H. Walsh

Dissertations, Theses, and Capstone Projects

A series of related N₃S ^99mTc-peptide complexes were synthesized and tested for use in pretargeting SPECT imaging that utilizes the bioorthogonal Diels-Alder click reaction between tetrazine (Tz) and transcyclooctene (TCO). The objective was to optimize the excretory pathways of the ^99mTc-peptide complexes for maximum tumor targeting with the in vivo “click” and minimum non-target uptake. The ^99mTc–tetrazine constructs were prepared by reaction of ^99mTc-peptide complexes (^99mTc-FKC, ^99mTc-FKCR, ^99mTc-DKC, and ^99mTc-SKC) with Tz-NHS or Tz-PEG₅-NHS to form ^99mTc FK(Tz)C, ^99mTc-FK(PEG₅-Tz)CR, ^99mTc-DK(PEG₅-Tz)C, …

Online Learning And Planning For Crowd-Aware Service Robot Navigation, Anoop Aroor

Dissertations, Theses, and Capstone Projects

Mobile service robots are increasingly used in indoor environments (e.g., shopping malls or museums) among large crowds of people. To efficiently navigate in these environments, such a robot should be able to exhibit a variety of behaviors. It should avoid crowded areas, and not oppose the flow of the crowd. It should be able to identify and avoid specific crowds that result in additional delays (e.g., children in a particular area might slow down the robot). and to seek out a crowd if its task requires it to interact with as many people as possible. These behaviors require the ability …

A Differential Algebra Approach To Commuting Polynomial Vector Fields And To Parameter Identifiability In Ode Models, Peter Thompson

Dissertations, Theses, and Capstone Projects

In the first part, we study the problem of characterizing polynomial vector fields that commute with a given polynomial vector field. One motivating factor is that we can write down solution formulas for an ODE that corresponds to a planar vector field that possesses a linearly independent commuting vector field. This problem is also central to the question of linearizability of vector fields. We first show that a linear vector field admits a full complement of commuting vector fields. Then we study a type of planar vector field for which there exists an upper bound on the degree of a …

The Forensic Analysis Of Skin-Safe Stamp Pad Inks, Swetha Rajagopal

Student Theses

Skin-safe stamp pad inks are currently being used at locations such as clubs, zoos and other events with the purpose of stamping individuals that visit the location. This is done in an attempt to monitor the number and activity of visitors. Ink manufacturing companies generally tend to experiment with a number of different combinations of the different components of ink, in order to obtain desirable properties. The combinations are usually proprietary and that very nature of the inks ends up making them, possibly unique and individual. The analysis, identification and possible individualization of the chemical composition of these inks could …

Novel Heterocyclic Methodology For The Construction Of Natural Products, Robert C. Lapo

Dissertations, Theses, and Capstone Projects

The synthesis of heterocyclic compounds and their incorporation into total synthesis strategies are described. Three synthetic methodologies toward substituted indoles, isochromans, and fused multi-ring oxazolidinones have been examined. With the progress that has been made, further investigations will hopefully carry the concept to completion.

Chapter I is an introductory examination of the varied types and systematic nomenclature of heterocyclic structures, including common names. This continues on to their commercial and industrial usage, and their great importance in biological systems and natural product chemistry. Finally, examples of heterocycles in fused-ring natural products and examples of historical and/or commercial value are examined …

Topological Insulating States In Photonics And Acoustics, Xiang Ni

Dissertations, Theses, and Capstone Projects

Recent surge of interest in topological insulators, insulating in their interior but conducting at the surfaces or interfaces of different domains, has led to the discovery of a variety of new topological states, and their topological invariants are characterized by numerous approaches in the category of topological band theory. The common features shared by topological insulators include, the topological phase transition occurs if the bulk bandgap is formed due to the symmetries reduction, the topological invariants exist characterizing the global properties of the material and inherently robust to disorder and continuous perturbations irrespective of the local details. Most importantly, these …

Preparation Of Enantioenriched Alkyltin Species And Their Application In Stereospecific Transformations, Glenn O. Ralph

Dissertations, Theses, and Capstone Projects

Organometallic reagents containing the tin-carbon bond are used extensively in modern synthetic chemistry for the formation of new bonds to carbon. Over recent decades, transition metal catalyzed cross coupling reactions between two C(sp²) centers have been widely developed. However, the introduction of a C(sp³) center complicates the catalytic cycle, and opens unproductive chemical pathways which lead to isomerization, elimination, and racemization. Our lab has developed a modified-Stille reaction to combat the deleterious effects of β-hydride elimination. Our protocol enables unactivated 2° alkyl organotin nucleophiles to undergo efficient cross coupling reactions with C(sp²) electrophiles, avoiding …

An Investigation Of Alkylboron Transmetallation In Palladium-Catalyzed Suzuki Reactions, Benjamin Murray

Dissertations, Theses, and Capstone Projects

Through the past 40 years, carbon-carbon cross-coupling reactions have greatly enhanced the ability of chemists to synthesize C(sp²)-C(sp²) bonds and more recently C(sp²)-C(sp³) bonds. In particular, the Suzuki reaction has proven to be invaluable with its high yields, good functional group tolerance, and low toxicity of reagents. One of the component steps of the catalytic cycle of this reaction is transmetallation, in which the nucleophilic species transfers its organic component to the metal center (generally palladium). The mechanism of transfer from primary alkylboron nucleophiles was studied in the 1990's via use of …

A Mobile Cyber-Physical System Framework For Aiding People With Visual Impairment, Martin Goldberg

Dissertations, Theses, and Capstone Projects

It is a challenging problem for researchers and engineers in the assistive technology (AT) community to provide suitable solutions for visually impaired people (VIPs) through AT to meet orientation, navigation and mobility (ONM) needs. Given the spectrum of assistive technologies currently available for the purposes of aiding VIPs with ONM, our literature review and survey have shown that there is a reluctance to adopt these technological solutions in the VIP community.

Motivated by these findings, we think it critical to re-examine and rethink the approaches that have been taken. It is our belief that we need to take a different …

Mild Synthesis Of Perylene Tetracarboxylic Monoanhydrides With Potential Applications In Organic Optoelectronics, Xizhe Zhao

Dissertations, Theses, and Capstone Projects

Perylene tetracarboxylic derivatives are considered good n-type semi-conductors. In past decades, there has been extensive study on their synthesis and electronic properties. Because of the high electron affinity, the ability to form π-π stacks, they have been widely utilized in organic photovoltaic solar cells, field-effect transistors and light-emitting diodes. Many of those applications prefer unsymmetrically substituted perylene tetracarboxylic derivatives. Perylene monoanhydrides are the most versatile intermediates for the preparation of unsymmetrically substituted perylene tetracarboxylic derivatives. In this thesis, I focused on introducing new synthesis methods for perylene monoanhydrides with labile functional group and their potential applications in organic optoelectronics.

In …

Understanding Water Consumption And Energy Trends In New York City, Wen Yong Huang, Johann Thiel

Publications and Research

In this study, we will be using the NYC Open Data website to examine publicly available data sets on water and energy consumption in New York City. In particular, we will use various scientific programming and machine learning modules in Python to analyze and visualize trends in water and energy usage within the five boroughs.

On The Complexity Of Computing Galois Groups Of Differential Equations, Mengxiao Sun

Dissertations, Theses, and Capstone Projects

The differential Galois group is an analogue for a linear differential equation of the classical Galois group for a polynomial equation. An important application of the differential Galois group is that a linear differential equation can be solved by integrals, exponentials and algebraic functions if and only if the connected component of its differential Galois group is solvable. Computing the differential Galois groups would help us determine the existence of the solutions expressed in terms of elementary functions (integrals, exponentials and algebraic functions) and understand the algebraic relations among the solutions.

Hrushovski first proposed an algorithm for computing the differential …

Analysis Of A Group Of Automorphisms Of A Free Group As A Platform For Conjugacy-Based Group Cryptography, Pavel Shostak

Dissertations, Theses, and Capstone Projects

Let F be a finitely generated free group and Aut(F) its group of automorphisms.

In this monograph we discuss potential uses of Aut(F) in group-based cryptography.

Our main focus is on using Aut(F) as a platform group for the Anshel-Anshel-Goldfeld protocol, Ko-Lee protocol, and other protocols based on different versions of the conjugacy search problem or decomposition problem, such as Shpilrain-Ushakov protocol.

We attack the Anshel-Anshel-Goldfeld and Ko-Lee protocols by adapting the existing types of the length-based attack to the specifics of Aut(F). We also present our own version of the length-based attack that significantly increases the attack' success …

Peptide Mediated Co-Assembly Of Porphyrin: Towards Sustainable Biomaterials For Light Harvesting And Catalysis, Wsm Nadeesha K. Wijerathne

Dissertations, Theses, and Capstone Projects

The diverse molecular functions of naturally occurring biomaterials designed from proteins are fundamentally based on a set of conserved building blocks, namely the 20 gene coded amino acids. The supramolecular structures and functions of proteins dictates by the self-assembly, where the complexity of proteins arise from a large number of amino acids. Generation of biomimetic systems that resemble the structures and functions of proteins is of great interest yet challenging due to the tremendous complexity of the natural systems. It is important to investigate alternative strategies to design much simpler systems that exhibit the same or similar function as proteins. …

Raman And Surface Enhanced Raman Spectroscopy For Forensic Analysis: Case Studies On The Identification Of Illicit Substances And Artist Pigments, Abed Haddad

Dissertations, Theses, and Capstone Projects

Raman spectroscopy is an effective tool for detecting trace amounts of material by fingerprint-like vibrational spectra. At times, the weak intensity of Raman scattering can make it difficult to distinguish trace materials. This shortcoming is addressed by surface‐enhanced Raman spectroscopy (SERS), which produces strong signal enhancements when target compounds are near metal nanoparticles. For the first part of this thesis, the identification of fentanyl and carfentanil, main culprits in the opioid epidemic, was done using normal Raman and the SERS spectroscopy. As an aid in the assignment of the spectral lines, a computational model was built using Density Functional Theory …

Ligand Selectivity In The Recognition Of Protoberberine Alkaloids By Hybrid-2 Human Telomeric G-Quadruplex: Binding Free Energy Calculation, Fluorescence Binding, And Nmr Experiments, Nanjie Deng, Junchao Xia, Lauren Wickstrom, Clement Lin, Kaibo Wang, Peng He, Yunting Yin, Danzhou Yang

Publications and Research

The human telomeric G-quadruplex (G4) is an attractive target for developing anticancer drugs. Natural products protoberberine alkaloids are known to bind human telomeric G4 and inhibit telomerase. Among several structurally similar protoberberine alkaloids, epiberberine (EPI) shows the greatest specificity in recognizing the human telomeric G4 over duplex DNA and other G4s. Recently, NMR study revealed that EPI recognizes specifically the hybrid-2 form human telomeric G4 by inducing large rearrangements in the 50-flanking segment and loop regions to form a highly extensive four-layered binding pocket. Using the NMR structure of the EPI-human telomeric G4 complex, here we perform molecular dynamics free …

Squarefree Totients P-1 And Primitive Roots, Nelson A. Carella

Publications and Research

This note determines an effective asymptotic formula for the number of squarefree totients $p-1$ with a fixed primitive root t u 6= ±1, v2

Densities For The Repeating Decimals Problems, Nelson A. Carella

Publications and Research

Let \(p\geq 2\) be a prime, and let $1/p=0.\overline{x_{w-1} \ldots x_1x_0}$, $x_i \in \{0,1, 2, \ldots , 9\}$. The period $w\geq 1$ of the repeating decimal $1/p$ is a divisor of $p-1$. This note shows that the counting function for the number of primes with maximal period $w=p-1$ has an effective lower bound $\pi_{10}(x)=\# \{ p\leq x:\ord_p(10)=p-1 \}\gg x/ \log x$. This is a lower bound for the number of primes \(p\leq x\) with a fixed primitive root \(10 \bmod p\) for all large

numbers \(x\geq 1\). An extension to repeating decimal $1/p$ with near maximal period $w=(p-1)/r$, where $r …

Validation Of A Lottery, Xiaona Zhou

Publications and Research

The NY Pick 4 lottery consists of four "randomly" chosen digits from 0 to 9. For this to be fair, each digit should be equally likely to occur. To determine whether this is the case, a Chi-squared goodness of fit test will be applied to historical data. This provides a quantitative way of measuring how well the observed frequency of digits matches our expectations of a fair lottery. We also explore the "Lucky Sum", which is also a part of the Pick 4. We determine which sum is most likely to occur, and what the odds of winning are if …

Deep Learning Enables Robust Assessment And Selection Of Human Blastocysts After In Vitro Fertilization, Pegah Khosravi, Ehsan Kazemi, Qiansheng Zhan, Jonas E. Malmsten, Marco Toschi, Pantelis Zisimopoulos, Alexandros Sigaras, Stuart Lavery, Lee A. D. Cooper, Cristina Hickman, Marcos Meseguer, Zev Rosenwaks, Olivier Elemento, Nikica Zaninovic, Iman Hajirasouliha

Publications and Research

Visual morphology assessment is routinely used for evaluating of embryo quality and selecting human blastocysts for transfer after in vitro fertilization (IVF). However, the assessment produces different results between embryologists and as a result, the success rate of IVF remains low. To overcome uncertainties in embryo quality, multiple embryos are often implanted resulting in undesired multiple pregnancies and complications. Unlike in other imaging fields, human embryology and IVF have not yet leveraged artificial intelligence (AI) for unbiased, automated embryo assessment. We postulated that an AI approach trained on thousands of embryos can reliably predict embryo quality without human intervention. We …

Lecture 6: Mobile Application And Product Development, Nyc Tech-In-Residence Corps

Open Educational Resources

Lecture for the course "CSCI 380 - Mobile Application and Product Development" delivered at John Jay College in Spring 2019 by Bhargava Chinthirla and Eric Spector as part of the Tech-in-Residence Corps program.

Lecture 3: Mobile Application And Product Development, Nyc Tech-In-Residence Corps

Open Educational Resources

Lecture for the course "CSCI 380 - Mobile Application and Product Development" delivered at John Jay College in Spring 2019 by Bhargava Chinthirla and Eric Spector as part of the Tech-in-Residence Corps program.

Csci 380-04 Selected Topics In Computer Science: Mobile Application And Product Development, Bhargava Chinthirla, Eric Spector, Nyc Tech-In-Residence Corps

Open Educational Resources

No abstract provided.

Lecture 5: Mobile Application And Product Development, Nyc Tech-In-Residence Corps

Open Educational Resources

Lecture for the course "CSCI 380 - Mobile Application and Product Development" delivered at John Jay College in Spring 2019 by Bhargava Chinthirla and Eric Spector as part of the Tech-in-Residence Corps program.