Physical Sciences and Mathematics Commons^™

Dta+Vae: Drug Target Affinity Prediction With Selfies String Via Variational Autoencoder And Transformer6 Protein Model, Yakin Patel

Electronic Theses and Dissertations

A crucial step in drug discovery is identifying drug-target interactions. Over the years, there have been many computational methods to determine whether a drug and a target will interact or not. Drug-target binding affinity can also be determined by predicting the strength of the binding interaction between the drug and the target. Drug target binding affinity consider a lot of information that is left out by drug target interaction. There have been many methods to predict the binding affinity, all the methods use SMILES representation, learning accurate drug representations is essential for tasks such as computational drug repositioning, drug target …

An Improved Shallow Water Temperature Model For An Australian Tidal Wetland Environment Using Publicly Available Data, Kerry Staples, Steven Richardson, Peter J. Neville, Jacques Oosthuizen

Research outputs 2022 to 2026

Larval mosquito development is directly impacted by environmental water temperature. Shallow water less than 1 m deep is a common larval mosquito habitat. Existing mathematical models estimate water temperature using meteorological variables, and they range in complexity. We developed a modification of an existing one-layer heat balance model for estimating hourly water temperature and compared its performance with that of a model that uses only air temperature and water volume as inputs and that uses air temperature itself as an indicator of water temperature. These models were assessed against field measurements from a shallow tidal wetland—a known larval habitat—in southwest …

Drought Stress Responses Of Some Prairie Landscape C4 Grass Species For Xeric Urban Applications, Fatemeh Kazemi, Mansoure Jozay, Farzaneh Salahshoor, Eddie Van Etten, Sahar Rezaie

Research outputs 2022 to 2026

Creating xeric landscapes in lawns and prairies is a significant challenge and practical need in arid urban environments. This study examined the drought resistance of some C4 grass species for constructing urban lawns and prairies. A factorial experiment based on randomized complete block designs with four replications was conducted. Experimental treatments were two irrigation levels (100% and 50% Field Capacity (FC)) and five warm-season grass species (Andropogon gerardii Vitman, Sorghastrum nutans (L.) Nash, Panicum virgatum L., Schizachyrium scoparium (Michx.) Nash, and Bouteloua curtipendula (Michx.) Torr.). The effects of drought on physiological, morphological, and qualitative characteristics of the grass species were …

Environmental Contamination With Clostridioides (Clostridium) Difficile In Vietnam, Peng A. Khun, Long D. Phi, Huong T. T. Bui, Nguyen T. Bui, Quyen T. H. Vu, Luong D. Trinh, Deirdre A. Collins, Thomas V. Riley

Research outputs 2022 to 2026

AIMS: To investigate the prevalence, molecular type, and antimicrobial susceptibility of Clostridioides difficile in the environment in Vietnam, where little is known about C. difficile. METHODS AND RESULTS: Samples of pig faeces, soils from pig farms, potatoes, and the hospital environment were cultured for C. difficile. Isolates were identified and typed by polymerase chain reaction (PCR) ribotyping. The overall prevalence of C. difficile contamination was 24.5% (68/278). Clostridioides difficile was detected mainly in soils from pig farms and hospital soils, with 70%-100% prevalence. Clostridioides difficile was isolated from 3.4% of pig faecal samples and 5% of potato surfaces. The four …

Joint Beamforming And Phase Shift Design For Hybrid Irs And Uav-Aided Directional Modulation Networks, Rongen Dong, Hangjia He, Feng Shu, Qi Zhang, Riqing Chen, Shihao Yan, Jiangzhou Wang

Research outputs 2022 to 2026

Recently, intelligent reflecting surfaces (IRSs) and unmanned aerial vehicles (UAVs) have been integrated into wireless communication systems to enhance the performance of air–ground transmission. To balance performance, cost, and power consumption well, a hybrid IRS and UAV-assisted directional modulation (DM) network is investigated in this paper in which the hybrid IRS consisted of passive and active reflecting elements. We aimed to maximize the achievable rate by jointly designing the beamforming and phase shift matrix (PSM) of the hybrid IRS subject to the power and unit-modulus constraints of passive IRS phase shifts. To solve the non-convex optimization problem, a high-performance scheme …

Star-Ris-Uav-Aided Coordinated Multipoint Cellular System For Multi-User Networks, Baihua Shi, Yang Wang, Danqi Li, Wenlong Cai, Jinyong Lin, Shuo Zhang, Weiping Shi, Shihao Yan, Feng Shu

Research outputs 2022 to 2026

Different from conventional reconfigurable intelligent surfaces (RIS), simultaneous transmitting and reflecting RIS (STAR-RIS) can reflect and transmit signals to the receiver. In this paper, to serve more ground users and increase deployment flexibility, we investigate an unmanned aerial vehicle (UAV) equipped with STAR-RIS (STAR-RIS-UAV)-aided wireless communications for multi-user networks. Energy splitting (ES) and mode switching (MS) protocols are considered to control the reflection and transmission coefficients of STAR-RIS elements. To maximize the sum rate of the STAR-RIS-UAV-aided coordinated multipoint (CoMP) cellular system for multi-user networks, the corresponding beamforming vectors as well as transmitted and reflected coefficient matrices are optimized. Specifically, …

Two Rapid Power Iterative Doa Estimators For Uav Emitter Using Massive/Ultra-Massive Receive Array, Yiwen Chen, Qijuan Jie, Yiqiao Zhang, Feng Shu, Xichao Zhan, Shihao Yan, Wenlong Cai, Xuehui Wang, Zhongwen Sun, Peng Zhang, Peng Chen

Research outputs 2022 to 2026

To provide rapid direction finding (DF) for unmanned aerial vehicle (UAV) emitters in future wireless networks, a low-complexity direction of arrival (DOA) estimation architecture for massive multiple-input multiple-output (MIMO) receiver arrays is constructed. In this paper, we propose two strategies to address the extremely high complexity caused by eigenvalue decomposition of the received signal covariance matrix. Firstly, a rapid power iterative rotational invariance (RPI-RI) method is proposed, which adopts the signal subspace generated by power iteration to obtain the final direction estimation through rotational invariance between subarrays. RPI-RI causes a significant complexity reduction at the cost of a substantial performance …

Guided Rotational-Based Graph Embeddings For Error Detection In Noisy Knowledge Graphs, Regina Khalil

Electronic Theses and Dissertations

Knowledge graphs (KGs) use triples to describe real-world facts. They have seen widespread use in intelligent analysis and applications. However, the automatic construction process of KGs unavoidably introduces possible noises and errors. Furthermore, KG-based tasks and applications assume that the knowledge in the KG is entirely correct, which leads to potential deviations. Error detection is critical in KGs, where errors are rare but significant. Various error detection methodologies, primarily path ranking (PR) and representation learning, have been proposed to ad- dress this issue. In this thesis, we introduced the Enhanced Path Ranking Guided Embedding (EPRGE), which is an improved version …

The Minimum Consistent Spanning Subset Problem On Trees, Parham Khamsepour

Electronic Theses and Dissertations

Given a vertex-colored edge-weighted graph, the minimum consistent subset (MCS) problem asks for a minimum subset S of vertices such that every vertex v not in S has the same color as its nearest neighbor in S. This problem has applications in clustering and classification algorithms, specially in finding the optimal number of clusters in k-clustering algorithms. This problem is NP-complete. A recent result of Dey, Maheshwari, and Nandy (2021) gives a polynomial-time algorithm for the MCS problem on trees. In thesis we study the MCS problem on different settings, and discuss some of the shortcomings of the MCS problem …

Jones Polynomial Obstructions For Positivity Of Knots, Lizzie Buchanan

Dartmouth College Ph.D Dissertations

The fundamental problem in knot theory is distinguishing one knot from another. We accomplish this by looking at knot invariants. One such invariant is positivity. A knot is positive if it has a diagram in which all crossings are positive. A knot is almost-positive if it does not have a diagram where all crossings are positive, but it does have a diagram in which all but one crossings are positive. Given a knot with an almost-positive diagram, it is in general very hard to determine whether it might also have a positive diagram. This work provides positivity obstructions for three …

Apatite Reference Materials For Sims Microanalysis Of Isotopes And Trace Elements, James L. Crowley, Mark Schmitz

Geosciences Faculty Publications and Presentations

Twelve apatite samples have been tested as secondary ion mass spectrometry (SIMS) reference materials. Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) analysis shows that the SLAP, NUAN and GR40 apatite gems are internally homogeneous, with most trace element mass fractions having 2 standard deviations (2s) ≤ 2.0%. BR2, BR5, OL2, AFG2 and AFB1, which have U > 63 μg g^-1, ²⁰⁶Pb/²⁰⁴Pb > 283, and homogeneous SIMS U-Pb data, have respective isotope dilution thermal ionisation mass spectrometry (ID-TIMS) ages of 2053.83 ± 0.21 Ma, 2040.34 ± 0.09 Ma, 868.87 ± 0.25 Ma, 478.71 ± 0.22 Ma and …

Earth Steward: Will Steffen's Contributions To Earth System Science, Governance And Law, W.J. Boonstra, P. Magalhães, B. J. Preston, J. Taylor Rockström

Research Collection Yong Pung How School Of Law

In January 2023, the world lost one of its most influential environmental scientists, Will Steffen. Recognised by his peers as the ‘Father of Earth System Science’, Steffen exemplified the ethic of planetary stewardship (Stockholm Resilience Centre 2023; Fig. 1). This ethic was especially evident, not only in Steffen’s scholarship, but also in his contributions to creating institutions that respect the reality of a single integrated Earth System and aim to govern human behaviour accordingly (Steffen 2016). This article commemorates Will Steffen’s scientific work in Earth System Science, and places it in the larger context of his contributions to governance and …

Trust And Robotics: A Multi-Staged Decision-Making Approach To Robots In Community, Wenxi Zhang, Willow Wong, Mark Findlay

Research Collection Yong Pung How School Of Law

With the desired outcome of social good within the wider robotics ecosystem, trust is identified as the central adhesive of the human–robot interaction (HRI) interface. However, building trust between humans and robots involves more than improving the machine’s technical reliability or trustworthiness in function. This paper presents a holistic, community-based approach to trust-building, where trust is understood as a multifaceted and multi-staged looped relation that depends heavily on context and human perceptions. Building on past literature that identifies dispositional and learned stages of trust, our proposed decision to trust model considers more extensively the human and situational factors influencing how …

Beyond Covid-19: Designing Inclusive Public Health Surveillance By Including Wastewater Monitoring, Rochelle H. Holm, Na'taki Osborne Jelks, Rebecca Schneider, Ted Smith

Faculty and Staff Scholarship

Wastewater-based epidemiology is a promising and expanding public health surveillance method. The current wastewater testing trajectory to monitor primarily at community wastewater treatment plants was necessitated by immediate needs of the pandemic. Going forward, specific consideration should be given to monitoring vulnerable and underserved communities to ensure inclusion and rapid response to public health threats. This is particularly important when clinical testing data are insufficient to characterize community virus levels and spread in specific locations. Now is a timely call to action for equitably protecting health in the United States, which can be guided with intentional and inclusive wastewater monitoring.

Pedagogical Prisms: Toward Domain Isomorphic Analogy Design For Relevance And Engagement In Computing Education, Briana Christina Bettin, Linda Ott

Michigan Tech Publications, Part 2

Analogy is a frequently leveraged pedagogical tool used across many disciplines, with computing being no exception. Computing education researchers, however, have raised concerns regarding the limitations of analogy. One obvious concern is the relevance of any given analogy to learners. Designing relevant analogies can greatly increase student engagement with the problem space by centering examples on their lived experiences. Relevant analogies can also facilitate learners in building appropriate connections as they explore novel concepts. Designing relevant analogies is an ongoing process which requires understanding the learners' context. It is unlikely that any given analogy will be "universally"relevant across learners, problems, …

Neuroevolution Application To Collaborative And Heuristics-Based Connected And Autonomous Vehicle Cohort Simulation At Uncontrolled Intersection, Frederic Jacquelin, Jungyun Bae, Bo Chen, Darrell Robinette

Michigan Tech Publications, Part 2

Artificial intelligence is gaining tremendous attractiveness and showing great success in solving various problems, such as simplifying optimal control derivation. This work focuses on the application of Neuroevolution to the control of Connected and Autonomous Vehicle (CAV) cohorts operating at uncontrolled intersections. The proposed method implementation’s simplicity, thanks to the inclusion of heuristics and effective real-time performance are demonstrated. The resulting architecture achieves nearly ideal operating conditions in keeping the average speeds close to the speed limit. It achieves twice as high mean speed throughput as a controlled intersection, hence enabling lower travel time and mitigating energy inefficiencies from stop-and-go …

More (Sema|Meta)Phors: Additional Perspectives On Analogy Use From Concurrent Programming Students, Briana Christina Bettin, Linda Ott, Julia Hiebel

Michigan Tech Publications, Part 2

A concurrent computing course is filled with challenges for upper-level programming students. Understanding concurrency provides deeper insight into many modern computing and programming language behaviors, but the subject matter can be difficult even for relatively proficient students. It can be a challenge to help students navigate and understand these unfamiliar topics. While there is a difference in general programming familiarity, teaching this novel material is not unlike some challenges faced when engaging introductory students with first programming concepts. In this work, we explore the use of analogy by students while learning a novel programming methodology. We investigate perceptions of the …

Addressing The Embeddability Problem In Transition Rate Estimation, Curtis Goolsby, James Losey, Ashkan Fakharzadeh, Yuchen Xu, Marie-Christine Düker, Mila Getmansky Sherman, David S. Matteson, Mahmoud Moradi

Chemistry & Biochemistry Faculty Publications and Presentations

Markov State Models (MSM) and related techniques have gained significant traction as a tool for analyzing and guiding molecular dynamics (MD) simulations due to their ability to extract structural, thermodynamic, and kinetic information on proteins using computationally feasible MD simulations. The MSM analysis often relies on spectral decomposition of empirically generated transition matrices. This work discusses an alternative approach for extracting the thermodynamic and kinetic information from the so-called rate/generator matrix rather than the transition matrix. Although the rate matrix itself is built from the empirical transition matrix, it provides an alternative approach for estimating both thermodynamic and kinetic quantities, …

Lightning: An X-Ray To Submillimeter Galaxy Sed-Fitting Code With Physically Motivated Stellar, Dust, And Agn Models, Keith Doore, Erik B. Monson, Rafael T. Eufrasio, Bret D. Lehmer, Kristen Garofali, Antara Basu-Zych

Physics Faculty Publications and Presentations

We present an updated version of Lightning, a galaxy spectral energy distribution (SED) fitting code that can model X-ray to submillimeter observations. The models in Lightning include the options to contain contributions from stellar populations, dust attenuation and emission, and active galactic nuclei (AGNs). X-ray emission, when utilized, can be modeled as originating from stellar compact binary populations with the option to include emission from AGNs. We have also included a variety of algorithms to fit the models to observations and sample parameter posteriors; these include adaptive Markov Chain Monte Carlo (MCMC), affine-invariant MCMC, and Levenberg–Marquardt gradient-descent (MPFIT) algorithms. To …

A Typological And Chemical Analysis Of Roman Oil Lamps From Poggio Del Molino, Brandon Tejo

Dissertations, Theses, and Capstone Projects

Terracotta lamps, known to the Romans as lucernae, are small, handheld, often decorated objects which provided ancient people light. To modern researchers, they serve as tools for dating stratigraphy and iconographic studies. Beyond their immediately apparent aesthetic and symbolic value, the chemical compositions of the clay of these lamps reflect their origin. This study complements archaeological typologies with chemometric analyses to describe 16 Late Republican and Imperial Roman lamps recovered from the villa at Poggio del Molino (PdM), Tuscany. These finds were recovered from the 2021 and 2022 PdM excavations. The combined approach of typology with X-ray Diffraction (XRD) …

The Development Of Novel Radioimmunoconjugates For The Pet Imaging And Radioimmunotherapy Of Cancer, Samantha M. Sarrett

Dissertations, Theses, and Capstone Projects

Antibodies have long played a vital role in nuclear medicine for both the diagnosis and therapy of various malignancies. The role and development of antibodies in nuclear medicine can be broadly separated into three different categories: 1) bioconjugation strategies, 2) immunoPET imaging, and 3) radioimmunotherapy. This dissertation will attempt to comprehensively cover each of these categories through a series of studies, protocols, and reviews. For the bioconjugation strategies, we will describe the development of a novel site-selective bioconjugation strategy using an innovative lysine-targeting reagent, PFP-bisN₃, to prepare [⁸⁹Zr]Zr-^SSKDFO-pertuzumab for visualizing HER2+ breast cancer. Further, …

An Explicit Construction Of Sheaves In Context, Tyler A. Bryson

Dissertations, Theses, and Capstone Projects

This document details the body of theory necessary to explicitly construct sheaves of sets on a site together with the development of supporting material necessary to connect sheaf theory with the wider mathematical contexts in which it is applied. Of particular interest is a novel presentation of the plus construction suitable for direct application to a site without first passing to the generated grothendieck topology.

Pairings In A Ring Spectrum-Based Bousfield-Kan Spectral Sequence, Jonathan Toledo

Dissertations, Theses, and Capstone Projects

Bousfield and Kan traditionally formulated their homotopy spectral sequence over a simplicial set X resolved with respect to a ring R. By considering an adequate category of ring spectra, one can take a ring spectrum E, create from it a functor of a triple on the category of simplicial sets, and build a cosimplicial simplicial set EX. The homotopy spectral sequence can then be formed over such cosimplicial spaces by a similar construction to the original. Pairings can be established on these spectral sequences, and, for nice enough spaces, these pairings on the E₂-terms coincide with certain …

Quantifying Separability In Limit Groups, Keino Brown

Dissertations, Theses, and Capstone Projects

We show that for any finitely generated non-abelian subgroup H of a limit group L, there exists a finite-index subgroup K which is fully residually H. This generalizes the result of Wilton that limit groups admit local retractions. We also show that for any finitely generated subgroup of a limit group, there is a finite-dimensional representation of the limit group which separates the subgroup in the induced Zariski topology. As a corollary, we establish a polynomial upper bound on the size of the quotients used to separate a finitely generated subgroup in a limit group. This generalizes results of Louder, …

Sers For The Detection Of Trace Materials, Omari Kirkland

Dissertations, Theses, and Capstone Projects

In this dissertation are presented three projects that contribute to the body of research on SERS in the forensic, heritage, and semiconductor fields. The first project, Charge-Transfer mapping on GaN/Ag, a silver-decorated nanopillar semiconductor substrate fabricated from the GaN is used with the Raman probe Rhodamine 6 G (R6G) to map the effect of the nanofeatures on the CT resonance. The second project, in collaboration with Marco Leona from the Metropolitan Museum of Art, explores the use of AgNIFs to identify colorants used on textile fiber samples from four 19th century works of Japanese art. The final project analyzes the …

Design, Synthesis, And Kinetic Study Of The First Generation Phenyloxadiazole Compounds And The Second Generation Phenyloxadiazole Compounds And Highly Selective Hydroboration Of Alkenes, Ketones And Aldehydes Catalyzed By A Well-Defined Manganese Complex, Haisu Zeng

Dissertations, Theses, and Capstone Projects

This thesis focuses on two projects. In the first project, my goal was to discover a new variant of phenyloxadiazole compounds that could exhibit increased thiol-reactivity during bioconjugation processes. To achieve this, I synthesized several phenyloxadiazole derivatives and subjected them to NMR kinetic studies to assess their reactivity with a model thiol. Based on the results, I was able to identify a phenyloxadiazole analog that demonstrated enhanced reactivity, which included a chlorine atom located in the meta-position of the phenyl ring.

I provided a detailed description of the synthesis and characterization of the newly discovered phenyloxadiazole analog and demonstrate its …

The Study Of Excitons In 2d Novel Materials And Their Van Der Waals Heterostructures In The Magnetic Field, Anastasia Spiridonova

Dissertations, Theses, and Capstone Projects

This research focuses on the direct and indirect excitons in Rydberg states in monolayers, bilayers, and van der Waals heterostructures composed of 2D semiconductors in the presence of the external magnetic field. In our work, we report binding energies of direct and indirect excitons in Rydberg states, the energy contribution from the magnetic field to the binding energies of magnetoexcitons, and diamagnetic coefficients (DMCs) of magnetoexcitons.

We study isotropic materials: transition metal dichalcogenides, TMDCs (WSe₂, WS₂, MoSe₂, MoS₂), and Xenes (silicene, germanene, stanene), and anisotropic materials: phosphorene and transition metal trichalcogenides, TMTCs …

Phantom Shootings, Allan Ambris

Dissertations, Theses, and Capstone Projects

This capstone is a website designed to critique NYC Open Data reporting with respect to shootings through a series of visualizations and discoveries. The NYPD Shooting Incidents datasets (Historic and Year to Date) introduce themselves to the user by claiming to be a “list of every shooting incident that occurred in NYC.” The supplied documentation reveals that this is not the case.

After understanding the supporting materials, there are still undisclosed truths. My exploration of the data revealed that a single victim may be represented across multiple entries. Additionally, multiple victims may be represented by a single entry. It is …

Untangling The Nature And Timescales Of Magmatic Processes Driving Eruptions At Quiescent Volcanoes: Examples From Momotombo, Nicaragua, And Cumbre Vieja, Canary Islands, Samantha Tramontano

Dissertations, Theses, and Capstone Projects

Across all scales of human relationships (i.e. person-to-person, country-to-country, etc.), qualms can take the form of long-standing wars, quick and intense bouts, or petty exchanges. While our understanding of human behavior is ever increasing, reactions and behaviors of self and others may still come as a surprise. Expressions of disagreement can occur suddenly or following years to centuries of accumulated grievances. The solid earth is also a system that behaves (like human emotion) predictably at times and unpredictably at other times. Some volcanoes, a tangible surface expression of solid earth processes, exhibit precursory signals prior to eruption (e.g. the bulging …

Deep Learning Recommendations For The Acl2 Interactive Theorem Prover, Robert K. Thompson, Robert K. Thompson

Master's Theses

Due to the difficulty of obtaining formal proofs, there is increasing interest in partially or completely automating proof search in interactive theorem provers. Despite being a theorem prover with an active community and plentiful corpus of 170,000+ theorems, no deep learning system currently exists to help automate theorem proving in ACL2. We have developed a machine learning system that generates recommendations to automatically complete proofs. We show that our system benefits from the copy mechanism introduced in the context of program repair. We make our system directly accessible from within ACL2 and use this interface to evaluate our system in …