Physical Sciences and Mathematics Commons^™

On Communication For Distributed Babai Point Computation, Maiara F. Bollauf, Vinay A. Vaishampayan, Sueli I.R. Costa

Publications and Research

We present a communication-efficient distributed protocol for computing the Babai point, an approximate nearest point for a random vector X∈Rn in a given lattice. We show that the protocol is optimal in the sense that it minimizes the sum rate when the components of X are mutually independent. We then investigate the error probability, i.e. the probability that the Babai point does not coincide with the nearest lattice point, motivated by the fact that for some cases, a distributed algorithm for finding the Babai point is sufficient for finding the nearest lattice point itself. Two different probability models for X …

Graph-Theoretic Partitioning Of Rnas And Classification Of Pseudoknots-Ii, Louis Petingi

Publications and Research

Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called blocks and determine whether each block contains a pseudoknot or not. As pseudoknots can not be contained into two different blocks, this characterization allow us to efficiently isolate smaller RNA fragments and classify them as pseudoknotted or pseudoknot-free regions, while keeping these sub-structures intact. Moreover we have extended the partitioning algorithm by classifying a pseudoknot as either recursive or non-recursive in order to continue with our research …

Decoding Clinical Biomarker Space Of Covid-19: Exploring Matrix Factorization-Based Feature Selection Methods, Farshad Saberi-Movahed, Mahyar Mohammadifard, Adel Mehrpooya, Mohammad Rezaei-Ravari, Kamal Berahmand, Mehrdad Rostami, Saeed Karami, Mohammad Najafzadeh, Davood Hajinezhad, Mina Jamshidi, Farshid Abedi, Mahtab Mohammadifard, Elnaz Farbod, Farinaz Safavi, Mohammadreza Dorvash, Shahrzad Vahedi, Mahdi Eftekhari, Farid Saberi-Movahed, Iman Tavassoly

Publications and Research

One of the most critical challenges in managing complex diseases like COVID-19 is to establish an intelligent triage system that can optimize the clinical decision-making at the time of a global pandemic. The clinical presentation and patients’ characteristics are usually utilized to identify those patients who need more critical care. However, the clinical evidence shows an unmet need to determine more accurate and optimal clinical biomarkers to triage patients under a condition like the COVID-19 crisis. Here we have presented a machine learning approach to find a group of clinical indicators from the blood tests of a set of COVID-19 …

Pattern Of Use Of Electronic Health Record (Ehr) Among The Chronically Ill: A Health Information National Trend Survey (Hints) Analysis, Rose Calixte, Sumaiya Islam, Zainab Toteh Osakwe, Argelis Rivera, Marlene Camacho-Rivera

Publications and Research

Effective patient–provider communication is a cornerstone of patient-centered care. Patient portals provide an effective method for secure communication between patients or their proxies and their health care providers. With greater acceptability of patient portals in private practices, patients have a unique opportunity to manage their health care needs. However, studies have shown that less than 50% of patients reported accessing the electronic health record (EHR) in a 12-month period. We used HINTS 5 cycle 1 and cycle 2 to assess disparities among US residents 18 and older with any chronic condition regarding the use of EHR for secure direct messaging …

Geologist Syed Humayun Akhter Is Leading The Bangladesh Open University, Nazrul I. Khandaker

Publications and Research

No abstract provided.

Fingerprinting The Cretaceous-Paleogene Boundary Impact With Zn Isotopes, Ryan Mathur, Brandon Mahan, Marissa Spencer, Linda Godfrey, Neil Landman, Matthew Garb, D. Graham Pearson, Sheng-Ao Liu, Francisca E. Oboh-Ikuenobe

Publications and Research

Numerous geochemical anomalies exist at the K-Pg boundary that indicate the addition of extraterrestrial materials; however, none fingerprint volatilization, a key process that occurs during large bolide impacts. Stable Zn isotopes are an exceptional indicator of volatilityrelated processes, where partial vaporization of Zn leaves the residuum enriched in its heavy isotopes. Here, we present Zn isotope data for sedimentary rock layers of the K-Pg boundary, which display heavier Zn isotope compositions and lower Zn concentrations relative to surrounding sedimentary rocks, the carbonate platform at the impact site, and most carbonaceous chondrites. Neither volcanic events nor secondary alteration during weathering and …

Dynamic Parameter Estimation From Partial Observations Of The Lorenz System, Eunice Ng

Theses and Dissertations

Recent numerical work of Carlson-Hudson-Larios leverages a nudging-based algorithm for data assimilation to asymptotically recover viscosity in the 2D Navier-Stokes equations as partial observations on the velocity are received continuously-in-time. This "on-the-fly" algorithm is studied both analytically and numerically for the Lorenz equations in this thesis.

The Exact Factorization Equations For One- And Two-Level Systems, Bart Rosenzweig

Theses and Dissertations

Exact Factorization is a framework for studying quantum many-body problems. This decomposes the wavefunctions of such systems into conditional and marginal components. We derive corresponding evolution equations for molecular systems whose conditional electronic subsystems are described by one or two Born-Oppenheimer levels and develop a program for their mathematical study.

Lab Exercises For Statistics Using Excel, Julia Nebia, Steven Cosares, Milena Cuellar

Open Educational Resources

This document contains the text associated with a series of computer-based lab exercises to help students apply the concepts usually included in a first course in Statistics. A compressed file has been included that contains a separate folder for each lab. In each folder is an excel spreadsheet file and an editable word document providing the instructions for students to complete the exercise. The exercises are not numbered in the folders, so you can select any subset of these exercises to assign to your students. You are free to modify the instructions in any way you see fit, e.g., to …

Covid-19 Impact On Radiology Students’ Distance Learning (Summer 2021), Mary Lee, Jason Chan, Cheryann Jackson-Holmes, Renzo Marmolejo, Zoya Vinokur

Publications and Research

The Radiological Technology students have adjusted from the urgent distance learning that was enacted in the Spring of 2020, to the hybrid distance learning that is currently in place. This hybrid distance learning is the same way the incoming class of radiological technology students were taught. Both cohorts of students were tracked over the year by online anonymous surveys. We wanted to know how students were adapting to distance learning, if their focus and motivation varied over the course of the year due to changing pandemic conditions. For the students that were working, what impact did it have on their …

Smooth Global Approximation For Continuous Data Assimilation, Kenneth R. Brown

Theses and Dissertations

This thesis develops the finite element method, constructs local approximation operators, and bounds their error. Global approximation operators are then constructed with a partition of unity. Finally, an application of these operators to data assimilation of the two-dimensional Navier-Stokes equations is presented, showing convergence of an algorithm in all Sobolev topologies.

21st Century Ecopoetics And Ecotheory, Robert Balun

Open Educational Resources

Ecopoetics is the study of literature that is concerned with ecology and nature. However, beyond just literature about nature, this course will examine how ecology and nature have become complicated in the 21st century, the age of the Anthropocene, the age of the climate crisis and the 6th mass extinction (don’t worry, we will define these and other key terms).

In the 21st century, humans are now confronted with a growing awareness of their destructive impact on the earth, its environments, and its human and non-human inhabitants. In this class we will examine how ecology and nature have become complicated …

Direct Observation Of Chaotic Resonances In Optical Microcavities, Shuai Wang, Shuai Liu, Yilin Liu, Shumin Xiao, Zi Wang, Yubin Fan, Jiecai Han, Li Ge, Qinghai Song

Publications and Research

Optical microcavities play a significant role in the study of classical and quantum chaos. To date, most experimental explorations of their internal wave dynamics have focused on the properties of their inputs and outputs, without directly interrogating the dynamics and the associated mode patterns inside. As a result, this key information is rarely retrieved with certainty, which significantly restricts the verification and understanding of the actual chaotic motion. Here we demonstrate a simple and robust approach to directly and rapidly map the internal mode patterns in chaotic microcavities. By introducing a local index perturbation through a pump laser, we report …

Weather And Crime: New York State, Yuna Kim

Student Theses

The present study assesses the degree to which temperature affects the crime rates in all 62 counties in the State of New York. Five different crimes (i.e., robbery, aggravated assault, burglary; larceny, and motor vehicle theft) for the year 2019 were selected from the Division of Criminal Justice Services of New York to be examined. The current study examined whether the rate of these crimes was associated with the changes in weather, with the assumption that higher weathers would lead to higher property and violent crimes, when controlling for the effect of various control variables. The findings suggest that the …

Evaluation Of Log P, Pka, And Log D Predictions From The Sampl7 Blind Challenge, Teresa Danielle Bergazin, Nicolas Tielker, Yingying Zhang, Junjun Mao, M. R. Gunner, Karol Francisco, Carlo Ballatore, Stefan M. Kast, David L. Mobley

Publications and Research

The Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges focuses the computational modeling community on areas in need of improvement for rational drug design. The SAMPL7 physical property challenge dealt with prediction of octanol-water partition coefficients and pK_a for 22 compounds. The dataset was composed of a series of N-acylsulfonamides and related bioisosteres. 17 research groups participated in the log P challenge, submitting 33 blind submissions total. For the pK_a challenge, 7 different groups participated, submitting 9 blind submissions in total. Overall, the accuracy of octanol-water log P predictions in the SAMPL7 challenge was …

Protein Motifs For Proton Transfers That Build The Transmembrane Proton Gradient, Divya Kaur, Umesh Khaniya, Yingying Zhang, M. R. Gunner

Publications and Research

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome …

Covid-19 Multi-Targeted Drug Repurposing Using Few-Shot Learning, Yang Liu, You Wu, Xiaoke Shen, Lei Xie

Publications and Research

The life-threatening disease COVID-19 has inspired significant efforts to discover novel therapeutic agents through repurposing of existing drugs. Although multi-targeted (polypharmacological) therapies are recognized as the most efficient approach to system diseases such as COVID-19, computational multi-targeted compound screening has been limited by the scarcity of high-quality experimental data and difficulties in extracting information from molecules. This study introduces MolGNN , a new deep learning model for molecular property prediction. MolGNN applies a graph neural network to computational learning of chemical molecule embedding. Comparing to state-of-the-art approaches heavily relying on labeled experimental data, our method achieves equivalent or superior prediction …

Defining The Basis Of Cyanine Phototruncation Enables A New Approach To Single-Molecule Localization Microscopy, Siddharth S. Matikonda, Dominic A. Helmerich, Mara Meub, Gerti Beliu, Philip Kollmannsberger, Alexander Greer, Markus Sauer, Martin J. Schnermann

Publications and Research

The light-promoted conversion of extensively used cyanine dyes to blue-shifted emissive products has been observed in various contexts. However, both the underlying mechanism and the species involved in this photoconversion reaction have remained elusive. Here we report that irradiation of heptamethine cyanines provides pentamethine cyanines, which, in turn, are photoconverted to trimethine cyanines. We detail an examination of the mechanism and substrate scope of this remarkable twocarbon phototruncation reaction. Supported by computational analysis, we propose that this reaction involves a singlet oxygeninitiated multistep sequence involving a key hydroperoxycyclobutanol intermediate. Building on this mechanistic framework, we identify conditions to improve the …

The “Knapsack Problem” Workbook: An Exploration Of Topics In Computer Science, Steven Cosares

Open Educational Resources

This workbook provides discussions, programming assignments, projects, and class exercises revolving around the “Knapsack Problem” (KP), which is widely a recognized model that is taught within a typical Computer Science curriculum. Throughout these discussions, we use KP to introduce or review topics found in courses covering topics in Discrete Mathematics, Mathematical Programming, Data Structures, Algorithms, Computational Complexity, etc. Because of the broad range of subjects discussed, this workbook and the accompanying spreadsheet files might be used as part of some CS capstone experience. Otherwise, we recommend that individual sections be used, as needed, for exercises relevant to a course in …

My Interdisciplinary Perspective On Climate Change [Natural Sciences], Richa Gupta, Tuli Chatterji, Tao Chen, Rebecca Schwartz

Open Educational Resources

This assignment titled “My Interdisciplinary Perspective on Climate Change” was developed in Fall 2020 as the signature assignment of the STEM Learning Community LC50 for students enrolled in the Biology program of the Natural Sciences department, at LaGuardia Community College, CUNY. The assignment targets Integrative Learning and Global Learning Core Competencies, and Digital/Oral Communication Abilities.

For this STEM Cluster, “Climate Change” is the shared theme that connects learning from the different disciplines and helps build students’ overall knowledge on an imperative issue that our planet currently faces. Work on this assignment entails a narrated digital student presentation on the various …

Iron And Iodine-Mediated Reactions, Xiaochen Liu

Dissertations, Theses, and Capstone Projects

This thesis work focuses on developing facile, low-cost, and environmentally friendly reactions, specifically the iron and iodine-mediated reactions, including (1) iron-catalyzed reductive ring-opening of 3,5-disubstituted isoxazoles and isoxazolines in aged N-methyl-2-pyrrolidone (NMP*), (2) iodine-mediated C-N bond cross-coupling reactions between amides and aldehydes, and (3) ICl-mediated functionalization of β-alkoxy alkynes – synthesis of α-iodo-γ-chloro-ketones.

Chapter I provides a background introduction on previous synthesis and applications of β-enaminones and 1,3-diketones that play as synthons or ligands. Ring-openings of heterocycles, such as isoxazoles and isoxazolines have attracted great attentions. A newly developed iron-catalyzed reductive system was established upon our previous palladium-catalyzed research. …

Computational Modeling Of Water And Proteins In Drug Discovery, Anthony Cruz Balberdy

Dissertations, Theses, and Capstone Projects

This thesis aims to improve how structural and thermodynamic properties of water on protein surfaces can be exploited to aid early stage drug discovery and lead optimization. We first discuss our development of SSTMap, a public domain software suite that maps out the properties of water on biomolecular surfaces. We then show the utility of these maps in describing differences in binding affinities between congeneric pairs of ligands. We then discuss our use of solvation maps in the prospective discovery of novel binders to cytochrome C peroxidase. Finally, we present our creation and validation of a homology model of Interleukin-24 …

Synthetic And Biological Studies On Benzazepine Derivatives As Dopamine Receptor Ligands, Rajan Giri

Dissertations, Theses, and Capstone Projects

Dopamine (DA) receptors, members of the G-protein coupled receptors (GPCRs) family, are divided in two groups based on their transmembrane structural homology domains: D1R-like (D1R, D5R sub-types) and D2R-like DA receptors (D2R, D3R and D4R sub-types). Disturbances in dopaminergic neurotransmission are associated with several CNS disorders. Hence, DA receptor selective ligands have been sought as pharmacological agents to normalize perturbations in the dopaminergic system. Despite several notable efforts, the discovery of highly selective ligands for dopamine receptor sub-types has proved challenging due to close transmembrane structural similarity, especially between DA receptor sub-types within the same group.

The 1-phenylbenzazepine scaffold is …

Hierarchical Hyperbolicity Of Graph Products And Graph Braid Groups, Daniel James Solomon Berlyne

Dissertations, Theses, and Capstone Projects

This thesis comprises three original contributions by the author concerning hierarchical hyperbolicity, a coarse geometric tool developed by Behrstock, Hagen, and Sisto to provide a common framework for studying aspects of non-positive curvature in a wide variety of groups and spaces.

We show that any graph product of finitely generated groups is hierarchically hyperbolic relative to its vertex groups. We apply this to answer two questions of Genevois about the electrification of a graph product of finite groups. We also answer two questions of Behrstock, Hagen, and Sisto: we show that the syllable metric on a graph product forms a …

Mechanistic And Synthetic Studies Of Oxidopyrylium Cycloaddition Reactions, Lauren P. Bejcek

Dissertations, Theses, and Capstone Projects

Cycloaddition chemistry has historically served as a robust route to stereo-rich and highly functionalized cyclic and heterocyclic compounds. Herein we describe our examination of 3-hydroxy-4-pyrone-derived oxidopyrylium cycloadditions in both mechanistic considerations as well as the unique synthetic advancements of their corresponding cycloadducts. Chapter 1 is a literature review where we specifically outline the use of oxidopyrylium cycloadditions in the synthesis of natural products. This includes the mention of previous syntheses prior to 2008, and a more thorough examination of the natural products synthesized from 2008 to present. The work exploits this chemistry as a facile route to highly complex 7-membered …

Mechanism Design And Modeling To Analyze Complex Social Systems For Public Policy, Haripriya Chakraborty

Dissertations, Theses, and Capstone Projects

The study of complex systems is an important area of research. Many scenarios require the ability to simulate large multi-agent systems with minimal artificial assumptions. We are currently living in a world where the adoption of artificial intelligence (AI) in various areas is increasing rapidly. This, in turn, has serious consequences from a computational and policy perspective. The focus needs to be on designing systems that are not only computationally elegant and efficient but also ethical. The goal of this thesis is to examine some of the ways AI can be used to simulate complex social systems. In addition, we …

Optimization Of Materials For Magnetic Refrigeration And Thermomagnetic Power Generation, Anthony N. Tantillo

Dissertations, Theses, and Capstone Projects

The magnetocaloric effect, by which a magnetic material experiences a change in temperature due to an applied magnetic field, can be used for refrigeration. The corollary to the magnetocaloric effect -- known as the pyromagnetic effect -- is the phenomenon by which a magnetic material experiences a thermally-induced change in magnetization that can be used to harvest thermal energy. This dissertation has two main parts: one focusing on novel materials for energy harvesting; and another focusing on methods of materials discovery for refrigeration purposes. Thermomagnetic power generation (TMG) is the process by which magnetic flux, which comes from a temperature-driven …

Emergent Photophysics In Diketopyrrolopyrrole Superstructures, Andrew Levine

Dissertations, Theses, and Capstone Projects

Organic semiconductors have received substantial attention as active components in optoelectronic devices because of their processability and customizable electronic properties. Tailoring the organic active layer in these devices to exhibit desirable optoelectronic properties requires understanding the complex and often subtle structure-property relationships governing their photophysical response to light. Both structural organization and frontier molecular orbitals (FMO) play pivotal roles in energy relaxation processes, and complex interplay between organization and orbital energies are difficult to anticipate based upon the molecular structure of the components alone, especially in systems comprised of multiple components. In pursuit of design rules, there is a need …

Skyrmions And Biskyrmions In Magnetic Films, Daniel Capic

Dissertations, Theses, and Capstone Projects

Skyrmions have garnered significant attention in condensed matter systems in recent years. In principle, they are topologically protected, so there is a large energy barrier preventing their annihilation. Furthermore, they can exist at the nanoscale, be manipulated with very small currents, and be created by a number of different methods. This makes them attractive for use in potential computing applications. This work studies ferromagnetic skyrmions. In particular, it highlights our small contributions to the field of skyrmions in condensed matter systems, specifically in thin-film ferromagnets.

Photosensitization And Analytical Study On Reactive Oxygen Intermediates: Self-Sorting Surface Radicals And “On-Off” Sensitizer Function Mechanisms, Sarah J. Belh

Dissertations, Theses, and Capstone Projects

This thesis consists of four chapters which are detailed below. Chapter 1 is an introductory chapter, which lays out the background and purpose of the research.

Chapter 2 describes a study of the mobility of alkoxy radicals on a surface by detection of their recombination product. A novel method called symmetrical product recombination (SRP) utilizes an unsymmetrical peroxide that upon sensitized homolysis recombines to a symmetrical product [R'OOR → R'O•↑ + •OR → ROOR]. This allows for self-sorting of the radical to enhance the recombination path to a symmetrical product, which has been used to deduce surface migratory aptitude. SPR …