Digital Commons Network^™

Evaluating The Reliability And Accuracy Of Alchemical Binding Free Energy Methods And Calculations, Fnu Sheenam

Dissertations, Theses, and Capstone Projects

Molecular recognition plays a crucial role in various biological processes, such as enzymatic reactions, signal transduction, and genetic information processing. Investigating how proteins selectively bind to their partners is an active research area, but there is a lack of experimental details on protein structures and interactions in molecular complexes. Computational techniques based on macromolecular structures offer a way to predict protein-ligand interactions and explore their recognition mechanisms. Estimating binding affinities, particularly through alchemical binding free energy calculations, has become valuable in supporting drug discovery. This work introduces new methodologies, utilizing the Alchemical Transfer Method, to address issues like poor convergence …

Rational Design Of Peptide-Based Materials Informed By Multiscale Molecular Dynamics Simulations, Dhwanit Rahul Dave

Dissertations, Theses, and Capstone Projects

The challenge of establishing a sustainable and circular economy for materials in medicine and technology necessitates bioinspired design. Nature's intricate machinery, forged through evolution, relies on a finite set of biomolecular building blocks with through-bond and through-space interactions. Repurposing these molecular building blocks requires a seamless integration of computational modeling, design, and experimental validation. The tools and concepts developed in this thesis pioneer new directions in peptide-materials design, grounded in fundamental principles of physical chemistry. We present a synergistic approach that integrates experimental designs and computational methods, specifically molecular dynamics simulations, to gain in-depth molecular insights crucial for advancing the …

A Causal Inference Approach For Spike Train Interactions, Zach Saccomano

Dissertations, Theses, and Capstone Projects

Since the 1960s, neuroscientists have worked on the problem of estimating synaptic properties, such as connectivity and strength, from simultaneously recorded spike trains. Recent years have seen renewed interest in the problem coinciding with rapid advances in experimental technologies, including an approximate exponential increase in the number of neurons that can be recorded in parallel and perturbation techniques such as optogenetics that can be used to calibrate and validate causal hypotheses about functional connectivity. This thesis presents a mathematical examination of synaptic inference from two perspectives: (1) using in vivo data and biophysical models, we ask in what cases the …

Stereospecific Cross-Coupling Reactions Of Vinyl Triflates And An Investigation Of The Synthesis And Reactivity Of Activated Alkyltricyclohexylstannanes, Pejman Ghaemimohammadi

Dissertations, Theses, and Capstone Projects

Organic chemistry exists in all aspects of everyday life from polymers to pharmaceutics. Formation of carbon-carbon bonds is essential for the synthesis of complex organic compounds. This goal can be achieved by using transition metal catalysts. Second-row transition metals such as Pd, Pt, Rh, and Ir have shown remarkable efficacy in these reactions. Metal-catalyzed cross-coupling reactions form carbon-carbon bonds between electrophiles and nucleophiles using transition metal catalysts. Pd is mainly used in this reaction.

Transition metal-catalyzed cross-coupling reactions that form a bond between two C(sp²) carbons have been widely studied over the past decades. C(sp²)-C(sp^{3 …}

Clustering Of Patients With Heart Disease, Mukadder Cinar

Dissertations, Theses, and Capstone Projects

Heart disease, a leading cause of mortality worldwide, presents complex challenges in public health due to its varied manifestations. Accurate diagnosis and patient stratification are essential for effective management and improved outcomes. In response, this study employed machine learning techniques to analyze heart disease data obtained from UCI Machine Learning Repository, aiming to enhance patient care through advanced data analysis.

The study began with the application of K-Nearest Neighbors (KNN) classification, which categorized patients into 'Disease' and 'No Disease' groups. This preliminary step provided initial insights into the structure of the dataset. Subsequently, K-means clustering was applied in two rounds, …

Integration Of Field- And Space-Based Observations Toward Assessing Drivers Of Biogeochemical Variability Across Vulnerable Coastal Ecosystems, Alana B. Menendez

Dissertations, Theses, and Capstone Projects

This thesis uses new field datasets and satellite ocean color products to quantify biogeochemical variability in three coastal regions: Long Island Sound estuary, the coastline of the Bay of Bengal extending east to the Mekong Delta, and the Yukon River Delta. These three study regions have vastly different size domains, climates, populations, and economies, but all require enhanced coastal water monitoring in the face of climate change. These regions are all naturally dynamic and experience strong seasonal phenomena but are also subject to changing hydrological forcings and direct anthropogenic perturbations. This leaves these coastal areas vulnerable to altered biogeochemical cycling, …

Studies Of Oxidopyrylium Ylide Dimers And Their Utility In The Synthesis Of Densely Functionalized Troponoids, Daniel V. Schiavone

Dissertations, Theses, and Capstone Projects

Herein, we describe our efforts to investigate mechanistic considerations of oxidopyrylium ylides and their use in cycloadditions to form complex bicyclic structures and the advancement of these cycloadducts to the synthesis of densely functionalized tropolones. This work also describes applications of tropolones as biologically relevant structures and dynamic fluorophores.

In Chapter 1, we expand upon previous studies done in the Murelli Lab describing the ability of 3-hydroxy-4-pyrone derived oxidopyrylium dimers to revert back to ylides in situ and as result can be used as a clean oxidopyrylium ylide source in accessing oxabicyclic compounds. Intermolecular cycloadditions of these ylides can be …

Low Shear In Short-Term Impacts Endothelial Cell Traction And Alignment In Long-Term, Mohanish Chandurkar, Nikhil Mittal, Shaina P. Royer-Weeden, Steven D. Lehmann, Yeonwoo Rho, Sangyoon J. Han

Michigan Tech Publications

Within the vascular system, endothelial cells (ECs) are exposed to fluid shear stress (FSS), a mechanical force exerted by blood flow that is critical for regulating cellular tension and maintaining vascular homeostasis. The way ECs react to FSS varies significantly; while high, laminar FSS supports vasodilation and suppresses inflammation, low or disturbed FSS can lead to endothelial dysfunction and increase the risk of cardiovascular diseases. Yet, the adaptation of ECs to dynamically varying FSS remains poorly understood. This study focuses on the dynamic responses of ECs to brief periods of low FSS, examining its impact on endothelial traction-a measure of …

Local Habitat Composition And Complexity Outweigh Seascape Effects On Fish Distributions Across A Tropical Seascape, Molly Moustaka, Richard D. Evans, Gary A. Kendrick, Glenn A. Hyndes, Michael V. W. Cuttler, Tahlia J. Bassett, Michael J. O’Leary, Shaun K. Wilson

Research outputs 2022 to 2026

Context: The distribution of animals is influenced by a complex interplay of landscape, environmental, habitat, and anthropogenic factors. While the effects of each of these forces on fish assemblages have been studied in isolation, the implications of their combined influence within a seascape remain equivocal. Objectives: We assessed the importance of local habitat composition, seascape configuration, and environmental conditions for determining the abundance, diversity, and functional composition of fish assemblages across a tropical seascape. Methods: We quantified fish abundance in coral, macroalgal, mangrove, and sand habitats throughout the Dampier Archipelago, Western Australia. A full-subsets modelling approach was used that incorporated …

Low Shear In Short-Term Impacts Endothelial Cell Traction And Alignment In Long-Term, Mohanish K. Chandurkar, Nikhil Mittal, Shaina P. Royer-Weeden, Steven D. Lehmann, Yeonwoo Rho, Sangyoon J. Han

Michigan Tech Publications

Within the vascular system, endothelial cells (ECs) are exposed to fluid shear stress (FSS), a mechanical force exerted by blood flow that is critical for regulating cellular tension and maintaining vascular homeostasis. The way ECs react to FSS varies significantly; while high, laminar FSS supports vasodilation and suppresses inflammation, low or disturbed FSS can lead to endothelial dysfunction and increase the risk of cardiovascular diseases. Yet, the adaptation of ECs to dynamically varying FSS remains poorly understood. This study focuses on the dynamic responses of ECs to brief periods of low FSS, examining its impact on endothelial traction—a measure of …

College Of Natural Sciences 2023 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 1 Dean's Message
Page 3 Department Highlights
Page 4 One Day for State
Page 5 Noble Prize Winner Speaks on Campus
Page 6-7 Faculty Excellence
Page 8-9 Student Excellence
Page 10 Outreach Program
Page 10 Events and Traditions
Page 11 Connections Abroad
Page 12 Student Spotlight
Page 13 Alumni Spotlight
Page 14 First Ever Drone Day
Page 15 Grand Opening of POET Bioproducts Center
Page 16 Work Anniversaries

Salmonella In The Environment: A Review On Ecology, Antimicrobial Resistance, Seafood Contaminations, And Human Health Implications, Mohammad Maruf Billah, Md Saydur Rahman

School of Earth, Environmental, & Marine Sciences Faculty Publications

Salmonella is a genus of Gram-negative bacteria that is responsible for numerous food poisoning outbreaks worldwide. With 93.8 million food-borne illnesses and 155,000 fatalities annually, it has emerged as a significant global public health issue. There are currently more than 2,500 distinct Salmonella serotypes, and more than half of them are associated with Salmonella enterica. An increasing global public health concern for humans and animals is antimicrobial resistance by Salmonella species worldwide. Salmonella infections can be lethal; conditioned with an increased prevalence of multi-drug resistant (MDR) strains in the future. The emergence of MDR Salmonella serotypes is considerably …

Trends In Catch Rates Of Sawfish On The Australian North West Shelf, C. Wakefield, S. J. Newman, M. Braccini, A. Harry

Fisheries Research Articles

Northwestern Australia is thought to have some of the world’s last remaining viable sawfish populations, although little quantitative data exists on their status or trends. This study examined 17 years of logbook bycatch records (n = 815) for green sawfish Pristis zijsron and narrow sawfish Anoxypristis cuspidata from a trawl fishery operating on the Australian North West Shelf. Incidental sawfish captures by the fishery are rare, occurring approximately once every 75 trawls (~199 trawl hours). To standardize catch rates and account for excess zeros in the data, we employed generalized additive models for location, scale, and shape (GAMLSSs) using a …

Sparse Bayesian Variable Selection In High‐Dimensional Logistic Regression Models With Correlated Priors, Zhuanzhuan Ma, Zifei Han, Souparno Ghosh, Liucang Wu, Min Wang

School of Mathematical & Statistical Sciences Faculty Publications

In this paper, we propose a sparse Bayesian procedure with global and local(GL) shrinkage priors for the problems of variable selection and classification in high-dimensional logistic regression models. In particular, we consider two types of GL shrinkage priors for the regression coefficients, the horseshoe (HS)prior and the normal-gamma (NG) prior, and then specify a correlated prior for the binary vector to distinguish models with the same size. The GL priors are then combined with mixture representations of logistic distribution to construct a hierarchical Bayes model that allows efficient implementation of a Markov chain Monte Carlo (MCMC) to generate samples from …

An Overview Of The Second-Previous Memory Effect In The Strictlyalternating Donation Game, Mohamed Zayet, Essam El-Seidy, Amira Abdel-Malek, Aya Rabie

Basic Science Engineering

Game theory delves into the examination of strategic behaviour across diverse domains such as insurance, business, military, biology, andmore,with the aim of deriving optimal decisions. Recent research focusing on the alteration of memory in the donation game with simultaneous iterated rounds has spurred our interest in investigating this phenomenon within the realm of the strictly alternating donation game. This study proposes a novel decision-making approach, utilising the previous unit instead of the most recent one. Thescopenarrowsdownto16employedstrategies,each definedbyfinitetwo-stateautomata,whileaccountingforpotentialimplementationerrorsinthe computationofstrategypayoffs.Dominant strategies are determined by assessing the interaction payoffs among strategy pairs. This article centres on the calculation of equilibrium points among heteroclinic …

Biomolecular Crystals As Functional Materials, Fahmeed Khan Sheehan

Dissertations, Theses, and Capstone Projects

The field of supramolecular chemistry has undergone significant evolution over the last few decades, progressing from fundamental studies of self-assembling systems to the rational design of functional materials with exceptional properties. Among these materials, short peptides have emerged as a chemically simple yet highly versatile class of biomimetic compounds. Initially, short peptides were used as model systems to understand larger protein interactions. As the field progressed, short peptides were found to have exceptional functionality, and are now explored as functional nanomaterials for diverse applications. In many cases, short peptide materials have displayed properties not found in biology, in some cases …

Towards Sociobiogeochemistry: Critical Perspectives On Anthropogenic Alterations To Soil Nitrogen Chemistry Via U.S. Urban And Suburban Development, Christopher D. Ryan

Dissertations, Theses, and Capstone Projects

The ecological impacts of changes to land use are relevant to concerns about climate change, eutrophication of waterbodies, and reductions in biodiversity. As a foundational component of ecosystem functioning, changes to soil biogeochemistry have significant effects on overall ecosystem health. With cities continuing to grow and develop in extent, the impacts of urbanization and suburbanization on soils are of particular concern. Despite a wide range of natural climatic and geologic conditions, several factors have driven similar patterns of land transformation and management across the United States. In particular, federal initiatives including the Home Owners Loan Corporation, the Federal Housing Administration, …

Investigating The Mass Mortality Induced Factors Of Pearl Oyster (Pinctada Radiata) At Abu Dhabi Pearls Farm, Uae, Hamad Ahmed Almansoori

Theses

The aquaculture of shellfish plays a crucial role in enhancing maritime environments by mitigating algal blooms and improving water quality through the filtration of organic matter, nutrients, and bacteria. This study investigated the environmental factors influencing oyster (Pinctada radiata) mortalities through a comprehensive analysis of water quality in Al Mirfa and Al Mughirah farming sites of Abu Dhabi (UAE), from February 2021 to February 2022. To reach such understanding of the main factors led to mass mortalities of cultivated oysters, different monthly sampling and both chemical and biological analyses of the farm water, sediments as well as for both living …

Accessing Reactive Metal Hydrides Through Designed Heterometallic Bridges, Fernando Gonzalez, Edgardo De Leon, Manar M. Shoshani

School of Integrative Biological & Chemical Sciences Faculty Publications

A methodology to access reactive hydride moieties is highly desirable, yet limited. Multimetallic hydride fragments are notable for their heightened reactivity and catalysis, but deliberate access to these species is lacking. In this highlight, we discuss recent developments by our group in the design of a new heterometallic complex that invokes an architecture designed to provide modular access to reactive hydride moieties by leveraging metal hydrides in combination with pendent donors to a model heterotrimetallic Ni–(Al–H)2 complex. An amplification of insertion-based reactivity has been examined in the hydrofunctionalization of quinolines, and our complex substantially outperformed the parent aluminum hydride LAlH …

Experimental Sars-Cov-2 Infection Of Elk And Mule Deer, Stephanie M. Porter, Airn E. Hartwig, Helle Bielefeldt-Ohmann, Jeffrey M. Marano, J. Jeffrey Root, Angela M. Bosco-Lauth

United States Department of Agriculture Wildlife Services: Staff Publications

To assess the susceptibility of elk (Cervus canadensis) and mule deer (Odocoileus hemionus) to SARS-CoV-2, we performed experimental infections in both species. Elk did not shed infectious virus but mounted low-level serologic responses. Mule deer shed and transmitted virus and mounted pronounced serologic responses and thus could play a role in SARS-CoV-2 epidemiology.

Probing Central Spin Decoherence Dynamics Of Electronic Point Defects In Diamond And Silicon, Ethan Que Williams

Dartmouth College Ph.D Dissertations

Electron spins of point defects in diamond and silicon can exhibit long coherence times, making them attractive platforms for the physical implementation of qubits for quantum sensing and quantum computing. To realize these technologies, it is essential to understand the mechanisms that limit their coherence. Decoherence of these systems is well described by the central spin model, wherein the central electron spin weakly interacts with numerous electron and nuclear spins in its environment. The dynamics of the resultant dephasing can be probed with pulse electron paramagnetic resonance (pEPR) experiments.

Using a 2.5 GHz pEPR spectrometer built in-house, we performed multi-pulse …

Fisheries Research Report No. 339: Assessment Of The Status Of The South Coast Demersal Scalefish Resource, Jeffrey V. Norriss, Sybrand A. Hesp, David V. Fairclough, Rubie Evans-Powell, B. Hancock, Emily A. Fisher, Tim Leary, Nick Jarvis

Fisheries Research Reports

This document provides the 2023 risk-based weight of evidence stock assessments for snapper, Bight redfish, hapuku, blue morwong, and Western blue groper for 2023 in the South Coast Bioregion (SCB).

Containerization Of Seafarers In The International Shipping Industry: Contemporary Seamanship, Maritime Social Infrastructures, And Mobility Politics Of Global Logistics, Liang Wu

Dissertations, Theses, and Capstone Projects

This dissertation discusses the mobility politics of container shipping and argues that technological development, political-economic order, and social infrastructure co-produce one another. Containerization, the use of standardized containers to carry cargo across modes of transportation that is said to have revolutionized and globalized international trade since the late 1950s, has served to expand and extend the power of international coalitions of states and corporations to control the movements of commodities (shipments) and labor (seafarers). The advent and development of containerization was driven by a sociotechnical imaginary and international social contract of seamless shipping and cargo flows. In practice, this liberal, …

Making Sense Of Making Parole In New York, Alexandra Mcglinchy

Dissertations, Theses, and Capstone Projects

For many individuals incarcerated in New York, the initial step toward freedom begins with an interview with the Board of Parole. This process, however, is frequently a complex and challenging one, characterized by repeated denials and extended incarcerations. The disparity in outcomes – where one individual may receive over 20 denials and another is granted parole on their first attempt – highlights the ambiguity and inconsistency in the parole decision-making process. This project aims to clarify the factors that influence parole decisions by concentrating on measurable variables. These include age, race, duration of sentence served, proportion of sentence served, type …

Machine Learning For Refining Knowledge Graphs: A Survey, Budhitama Subagdja, D. Shanthoshigaa, Zhaoxia Wang, Ah-Hwee Tan

Research Collection School Of Computing and Information Systems

Knowledge graph (KG) refinement refers to the process of filling in missing information, removing redundancies, and resolving inconsistencies in knowledge graphs. With the growing popularity of KG in various domains, many techniques involving machine learning have been applied, but there is no survey dedicated to machine learning-based KG refinement yet. Based on a novel framework following the KG refinement process, this paper presents a survey of machine learning approaches to KG refinement according to the kind of operations in KG refinement, the training datasets, mode of learning, and process multiplicity. Furthermore, the survey aims to provide broad practical insights into …

Epigenetic Regulation In Cancer, Minzhi Gu, Bo Ren, Yuan Fang, Jie Ren, Xiaohong Liu, Xing Wang, Feihan Zhou, Ruiling Xiao, Xiyuan Luo, Lei You, Yupei Zhao

Faculty, Staff and Student Publications

Epigenetic modifications are defined as heritable changes in gene activity that do not involve changes in the underlying DNA sequence. The oncogenic process is driven by the accumulation of alterations that impact genome's structure and function. Genetic mutations, which directly disrupt the DNA sequence, are complemented by epigenetic modifications that modulate gene expression, thereby facilitating the acquisition of malignant characteristics. Principals among these epigenetic changes are shifts in DNA methylation and histone mark patterns, which promote tumor development and metastasis. Notably, the reversible nature of epigenetic alterations, as opposed to the permanence of genetic changes, positions the epigenetic machinery as …

The Early Late Miocene Cessation Of Deep And Intermediate Water Circulation Through The Central American Seaway, Benjamin Stanley Kwiatkowski

Dissertations, Theses, and Capstone Projects

The state of the middle late Miocene global ocean circulations which regulated climate and affected deep ocean chemical environments were impacted by geographic changes. During the Miocene, cirum-equatorial circulations slowly decreased, which included through the seaway between the Americas called the Central American Seaway (CAS). Its shoaling and ultimate closing led to the onset of modern day oceanic circulation as characterized by the global thermohaline circulation. However, this seaway has a long hotly debated history concerning the timing of its restriction and shallowing owing in part to the shifting of tectonic plates.

The goal of this research focuses on investigating …

Mathematicians Going East, Pasha Zusmanovich

Journal of Humanistic Mathematics

I survey emigration of mathematicians from Europe, before and during WWII, to Russia. The emigration started at the end of 1920s, the time of “Great Break”, and accelerated in 1930s, after the introduction in Germany of the “non-Aryan laws”. Not everyone who wanted to emigrate managed to do so, and most of those who did spent a relatively short time in Russia, being murdered or deported, or fleeing the Russian regime. After 1937, the year of “Great Purge”, only a handful of emigrant mathematicians remained, and even fewer managed to leave a trace in the scientific milieu of their new …

Thin-Film Nanocomposite Membranes With Alumina Nanoparticles For Textile Wastewater Treatment Applications, Amr Mohamed Tayel

Theses and Dissertations

Thin-film nanocomposite (TFN) membranes are gaining great interest in industrial wastewater treatment due to their superior performance, especially for higher water flux and pollutants’ rejection, as well as improved chemical, thermal and mechanical stabilities, compared to other types of membranes. The performance of TFN membranes can be enhanced using different types of nanofillers, among which ceramic nanomaterials, such as Al2O3, offer a promising potential for applications involving treatment of industrial wastewater such as textile effluents, and this is due to their stability, hydrophilicity, and relative low cost. The study of the TFN membrane properties and structure allows the optimization and …

Heavy Metals Analysis And Physicochemical Characterization Of Groundwater At A Battery Recycling Site In South-Western Nigeria, Adeniyi T. Adeleke, Rasaki K. Odunaike, Shamsideen K. Alausa, Idris O. Olayiwola, Adetoro T. Talabi, Qasim A. Adeniji, Adejumobi C. Adeniyi

Tanzania Journal of Science

Indiscriminate dumping of battery waste is a huge issue that endangers human health and the environment. This study aimed at analysing the health impacts of exposure to pollution from spent battery recycling in Ogun State, which houses a diverse range of battery recycling industries. At this study site, forty water samples were studied over the Wet and Dry seasons to assess the impact of battery recycling waste on groundwater. Except for the TSS, the physiochemical parameters of the groundwater vary with season and are within the permissible limits. The electrical conductivity (EC), turbidity, Phosphorus, Biochemical oxygen demand (BOD), Dissolve oxygen …