Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li

Computer Science Faculty Publications

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding …

Enhancement Of The Performance And Emission Attributes For The Diesel Engine Using Diesel-Waste Cooking Oil Biodiesel And Graphene Oxide Nanofluid Blends Through Response Surface Methodology, Medhat Elkelawy, E A El Shenawy, Hagar Alm-Eldin Bastawissi, Mahmoud M. Shams

Mansoura Engineering Journal

This study examined how diesel fuel and waste-cooked oil (WCO) biodiesel blends added by various concentrations of graphene oxide (GO) nanoparticles can effect on the performance and emission characteristics of constant-speed, four-stroke, single-cylinder, water-cooled diesel engines. The GO nanoparticles concentrations are 50,100 and 150 ppm dispersed in different diesel-WCO biodiesel blends are pure diesel fuel (B0), 20% WCO biodiesel and 76% diesel fuel (B20), and 40% WCO biodiesel and 56% diesel fuel (B40). In addition 4% toluene in all blends which used as a surfactant. The diesel engine fueled with these blends and operated at various engine loads are 2, …

Carbon Dioxide Gasification Of Biochar: A Study On Utilizing Captured Co2 To Mitigate Greenhouse Gas Emission And Improving Carbon Conversion Efficiency, Nnamdi Ofuani

College of Graduate Studies: Theses & Dissertations

With rapidly growing global economies and world population, fossil fuel continues to play a major role in meeting current energy demands. Carbon capture and storage (CCS) technologies have, hence, been implemented to reduce CO₂ emissions in the atmosphere. With the implementation of CCS technologies comes the need to utilize the captured CO₂. This research, therefore, proposes CO₂ gasification of biochar as a viable carbon utilization pathway. With captured CO₂ coming at various concentrations, there is a need to understand how CO₂ concentration affects biochar conversion to useful products. This study, therefore, evaluates the effects …

Investigations Of Performance And Emissions Of A Fischer-Tropsch Gtl Sustainable Aerospace Fuel With Lubricity Improver In A Compression Ignition Engine With Butanol Port Fuel Injection, James B. Willis

College of Graduate Studies: Theses & Dissertations

As there is increasing concern over emissions of traditional fossil fuels, as well as the future of continued reliance on this dwindling resource, it is becoming increasingly evident that alternative fuels are a necessity. This research investigates the use of a Fischer-Tropsch fuel from natural gas feedstocks, S8, in an internal combustion research engine with a common rail fuel injection system. This synthetic kerosene fuel has a high DCN of 62, indicating high affinity to autoignition compared to conventional pump diesel (ULSD) at 48 DCN. However, due to the process by which it is produced, this fuel lacks the necessary …

Numerical Modeling Of Thermal Runaway In Lithium-Ion Batteries Using Decomposition Kinetics And Inter-Cell Contact Resistance, Shehzad Khan

College of Graduate Studies: Theses & Dissertations

Lithium-ion batteries (LIBs) are central in numerous high-demand applications due to their high energy density and prolonged cycle life. Despite these advantages, their susceptibility to thermal runaway (TR) poses a significant safety risk, with the potential for catastrophic failures. This study focuses on the thermal behavior of prismatic lithium-ion cells, using a finite volume-based partial differential equation (PDE) solver developed in MATLAB and JULIA to model TR behavior. This solver accurately simulates transient behaviors, convection, diffusion, and source terms across various coordinate systems. By engaging in a series of increasing complex case studies, this research aims to identify the critical …

Application Of Predictive Control Strategies For Water-Gas Shift Membrane Reactors Using Data-Driven Models, Bernardo De Oliveira Vecchio

Graduate Theses, Dissertations, and Problem Reports (ETD)

As demand for more efficient processes keeps rising and more restrictive environmental legislation requires higher levels of both yield and purity, the process industry has now, more than ever, been looking for new ways to achieve these goals. One approach has been the implementation of Process Intensification (PI). PI aims to combine multiple unit operations into a single one, promoting efficiency gains on multiple levels. This combination, however, leads to complex process dynamics, and controlling such processes, particularly when setup as multi-input-multi-output (MIMO) systems, presents a great challenge due to highly interactive complex process dynamics and the imposition of many …

Parametrization Of Fluid Models For Electrical Breakdown Of Nitrogen At Atmospheric Pressure, Shirshak K. Dhali

Electrical & Computer Engineering Faculty Publications

In the transient phase of an atmospheric pressure discharge, the avalanche turns into a streamer discharge with time. Hydrodynamic fluid models are frequently used to describe the formation and propagation of streamers, where charge particle transport is dominated by the creation of space charge. The required electron transport data and rate coefficients for the fluid model are parameterized using the local mean energy approximation (LMEA) and the local field approximation (LFA). In atmospheric pressure applications, the excited species produced in the electrical discharge determine the subsequent conversion chemistry. We performed the fluid model simulation of streamers in nitrogen gas at …

Characterization Of Antibody Repertoires Developed From Naive And Recall Responses, Nicholas C. Curtis

Dartmouth College Ph.D Dissertations

Adaptive immunity, comprised in part by the antibody repertoire, is the cornerstone of our ability to remain healthy amongst the plethora of pathogenic challenges we encounter daily. Despite the importance of understanding antibody repertoire development, much remains unknown about the composition and evolution of circulating antibodies in response to viral challenges. To better understand antibody repertoire development, we profiled the serum antibody repertoire using a combination of next-generation sequencing and serum antibody proteomics in the predominantly naïve response against SARS-CoV-2 spike and the recalled response to influenza hemagglutinin. The response to SARS-CoV-2 spike in four convalescent individuals was diverse (consisting …

Development Of Probabilistic Dynamic Model Building And Bayesian Machine Learning Approaches, Samuel Oladayo Adeyemo

Graduate Theses, Dissertations, and Problem Reports (ETD)

Abstract

Development of Probabilistic Dynamic Model Building and Bayesian Machine Learning Approaches

Samuel Adeyemo

The recent years have seen a tremendous increase in the use of artificial intelligence (AI) and machine learning (ML) for the development of data-driven mathematical models needed for performing real-time optimization, model-based control, performance optimization, dynamic data reconciliation, and process performance monitoring. However, the development of data-driven models is faced with some challenges including lack of model interpretability, sensitivity of algorithm to noise in training data, limited extrapolation capabilities and violation of conservation laws. Drawing motivation from these existing gaps, this work aims to develop robust …

State Estimation And Economic Analysis For Electrochemical Sensor-Based Corrosion Monitoring, Chandra Sekhar Somayajula

Graduate Theses, Dissertations, and Problem Reports (ETD)

Coal is currently the third-largest source of electricity production in the U.S. However, renewables are projected to be the primary source of electricity production in the future. Though coal-fired power plants (CFPPs) are rapidly retiring in the U.S., many CFPPs worldwide are expected to stay operational for a while due to factors like easy and cheap access to comparatively inexpensive coal. Therefore, non-renewable sources like coal are still expected to be prevalent and be used to ensure the stability of the electric grid in the foreseeable future. The existing coal-fired power plants generally designed to operate at base-loaded conditions are …

Design And Development Of Biocompatible Mofs And Silica-Based Nanocarriers With Controlled Pharmacokinetics For Drug Delivery Applications, Neila Pederneira

Doctoral Dissertations

"In the past decade, a big interest has drawn into nanoporous metal-organic frameworks (MOFs) and silica-based materials as nanocarriers for drug delivery applications, owing to their exceptionally high surface area and highly structured porous network. The overall goal of this research was to optimize the pharmacokinetic behavior of several highly porous biocompatible drug carriers that have the potential to carry Ibuprofen, 5-Fluorouracil, and Curcumin to the desired tissue without creating a burst effect and minimizing the amount of dosage and size that conventional capsules require. The specific objectives of this study are to (i) assess the effect of drug solubility …

Effect Of Various Irrigation Protocols And Antioxidant Application On Bonding Performance Of Two Adhesive Systems To Coronal Dentin, Nada Omar, Haidy N. Salem, Ahmed Abdou, Lamiaa M. Moharam

Chemical and Biochemical Engineering Faculty Research & Creative Works

Background: The aim was to evaluate the effect of different irrigation protocols and antioxidants application on the shear bond strength (SBS) of two different adhesive systems to deep coronal dentin at different temperature. Material and Methods: One hundred and twenty human premolar teeth were cut longitudinally in two halves, then the prepared specimens were allocated into four main groups according to the irrigation protocols; Distilled water (control), Sodium hypochlorite (NaOCl) + Ethylenediamine Tetra-acetic Acid (EDTA), and NaOCl + Editronate (HEDP), two subgroups according to irrigation solutions temperature; 4°C and 37°C, two divisions according to grape seed extract (GSE) application (with …

The Comprehensive Study Of High Viscosity Friction Reducers In High-Tds And High-Temperature Environments, Xiaojing Ge

Doctoral Dissertations

"High viscosity friction reducers (HVFRs) have been recently gaining more attention and increasing in use, not only as friction-reducing agents but also as proppant carriers. Reusing of produced water has also been driven by both environmental and economic benefits. Currently, most friction reducers on the market are anionic friction reducers, which are fully compatible with most produced water with low to medium level of Total Dissolved Solids (TDS) but show a significant drop at high TDS conditions in term of their friction reduction performance in most cases. On the contrary, cationic friction reducers are believed to have better TDS tolerance …

Investigating The Potential Of Blended Feedstocks For Biofuel Production Via Pyrolysis Process: Experimental And Aspen Simulation Approach, Hasan Jawad Hammood Al-Abedi

Doctoral Dissertations

"The development of renewable energy sources has become increasingly urgent considering the climate crisis and the need to reduce greenhouse gas emissions. Pyrolysis, which is decomposition of an organic feedstock without oxygen, is a thermo-chemical process that has garnered significant attention as a promising technology for sustainable energy production, capable of converting biomass and waste materials into biofuels.

The primary objective of this study is to investigate the pyrolysis and co-pyrolysis behaviors of corn stover (CS), refuse-derived fuel (RDF), and oil shale (OS) in equal mass ratios. Utilizing a thermogravimetric analyzer and differential scanning calorimetry (DSC), the co-pyrolysis process is …

Investigation Of Operational Parameter Differences Between The Standard Ron Test Method And Knock-Limited Modern Spark-Ignition Engine Operation, Alexander Hoth

Dissertations, Master's Theses and Master's Reports

Octane numbers (ONs) are used worldwide to rate the knock propensity of gasoline-like fuels for spark-ignition engines, making ONs the leading indicator of fuel quality for commercial distribution. The ONs were established 90 years ago and have only received minor changes compared to significant advancements in modern engine operation and fuel composition. This has resulted in discrepancies between knock-limited modern engine operation and standard ON ratings. This dissertation used a standard CFR octane rating engine at Argonne National Laboratory that was instrumented with modern combustion research tools to investigate key differences between the Research Octane Number (RON) rating conditions and …

Continuous, Platform Purification Of Viral Products Using Aqueous Two-Phase Extraction, Natalie M. Nold

Dissertations, Master's Theses and Master's Reports

Cell and gene therapies, a ground-breaking class of drugs that can heal genetic diseases and cure cancer, often have treatment costs over $1 million. Most cell and gene therapies are delivered using virus-based delivery vectors, which are incredibly expensive to manufacture. Liquid chromatography is the favored method of viral vector purification since it is easily scalable and can be functionalized to purify by biospecificity, charge, hydrophobicity, or size. However, chromatography-based purification processes are highly expensive and usually only recover 20-50% of the viral vectors. There is currently no platform purification strategy for viral vectors due to differences in their surface …

Sustainable Materials For Environment − Multifunctional Material Made From Dead Leaves And Nanostructured Materials For Antibiotic Degradation, Siyuan Fang

Dissertations, Master's Theses and Master's Reports

As environmental pollution from industrial processes and human activities continues to rise, finding efficient approaches to recycle waste materials and degrade persistent contaminants becomes increasingly critical. Dead leaves, an abundant but underutilized biomass, present an opportunity for creating value-added materials if their biocomponents can be preserved and transformed. Simultaneously, antibiotics such as tetracycline are widely found in water bodies but pose serious ecological and health risks, necessitating effective degradation methods. This dissertation addresses these challenges by leveraging natural and nanostructured materials to develop multifunctional products and advanced photocatalytic processes.

Chapter 3 of this dissertation addresses the challenge of converting waste …

Optimizing Diabetes Diagnostics: Electrophoretic Separation And Detection Of Hemoglobin A1c With Boronate, Rixlie Fozilova

Dissertations, Master's Theses and Master's Reports

Diabetes affects 537 million people worldwide, while 136 million Americans have diabetes or prediabetes; roughly 22.6% of individuals are undiagnosed. Diabetes is the inability to regulate blood sugar levels. Hemoglobin A1c (HbA1c) is glycosylated hemoglobin and indicates average blood sugar levels over the past three months.

We adapted the selective boronic acid binding to the HbA1c sugar moieties from boronate affinity chromatography and translated it into a portable microchip paper-based electrophoresis platform. We explored a range of boronate concentrations at a steady voltage and sample volume to determine the optimal HbA1c binding and subsequent electrophoretic separation. A pH above 11 …

Analytical And Machine Learning Modeling Of Direct Carbonation Of Natural Silicate Minerals, William Hanson

Dissertations, Master's Theses and Master's Reports

The climate-altering effects of atmospheric CO₂ make it necessary to develop innovative technologies that can remove it from the atmosphere. Mineral carbonation is a scalable technology to sequestrate and store CO2 in a stable carbonate mineral form. The efficiency of the mineral carbonation process depends on both feed mineralogy and process parameters. Comprehensive modeling and prediction of mineral carbonation efficiency for different CO₂ – reactive rocks has not been achieved in the past. In this thesis work, analytical and machine learning models are developed to predict the carbonation efficiency of dunite reactions. It is found that random forest …

Lithospheric Drip And Mantle Thermal Upwelling Beneath Central Asia And The Southern Great Plains Of North America: Evidence From Receiver Function Imaging, Yangyang Liao

Doctoral Dissertations

"Investigating the depth of mantle transition zone (MTZ) discontinuities provides insights into mantle dynamics, including regional-scale downwelling of mantle lithosphere (i.e., lithospheric drip) and upwelling of thermal materials (i.e., mantle plume). In our study, we employ receiver functions to image the 410 km (d410) and 660 km (d660) mantle discontinuities and to ascertain thickness of the MTZ beneath Central Asia and the Great Plains in United States. The findings unveil a significantly thickened transition zone, exhibiting an average thickness of 284 km beneath East Sayan. When considered alongside geochemical observations, our results indicate that the descent of the lithosphere is …

Exploring Seismic Anisotropy In The Crust And Mantle Of The Tibetan Plateau And Analyzing Seismic Velocity Variations In Yellowstone, Cong Shen

Doctoral Dissertations

"Seismology is a scientific discipline that utilizes seismic waves to investigate the deep structures within the Earth's interior, which are otherwise inaccessible to direct observation by humans. These seismic waves can be categorized into two types: body waves and surface waves, each with distinct propagation modes and behaviors, carrying valuable information about their travel paths. The first paper concentrates on the analysis and inversion of body waves produced by large seismic events. It employs shear wave splitting and receiver function methods to explore the geodynamic structure of the south-central Tibetan Plateau, near the plate boundary. The investigation covers the depth …

Improving Syngas Quality In A Downdraft Biomass Gasifier With Blended Feedstocks, Rania Almusafir

Doctoral Dissertations

"Biomass gasification is the greatest potential renewable energy source and will play an important role in the energy mix of the future. To achieve a high quality of produced synthesis gas (syngas) in the gasification system, the syngas cleaning and cooling processes pose challenges. The main objectives of the present work are advancing the knowledge of the gasification process and producing syngas in the studied pilot-scale downdraft biomass gasifier.

A Thermogravimetric analysis (TGA) has been developed and utilized to experimentally investigate the impact of biomass feedstock diversity on the performance of the gasification process of hardwood (HW), softwood (SW) pellets, …

Topography Of The 410 And 660 Km Discontinuities Beneath The Tibetan Plateau And Adjacent Areas, Zexin Miao

Doctoral Dissertations

"The Tibetan Plateau represents the ongoing geotectonic aftermath of a continental collision initiated approximately 65 million years ago. Despite numerous seismological studies, controversies remain regarding the structure, evolution, and dynamics of the crust and mantle beneath Tibetan Plateau. In this study, we used teleseismic broadband data to investigate the topography of the mantle transition zone (MTZ) discontinuities. A total of ~655,000 receiver functions from 735 stations was utilized to image the 410 and 660 km discontinuities bordering the MTZ. Combining the observed and velocity corrected results, several areas in the central Tibet exhibit a typical d410 and an anomalously deep …

Paleoecological And Paleoclimatic Reconstructions Based On Holocene Sediment Cores, Lake Izabal, Eastern Guatemala, Erdoo Mongol

Doctoral Dissertations

"The Maya Region in Central America is characterized by pronounced discrepancies in precipitation, resulting in high precipitation gradients that support large-scale differences in vegetation across the region. Several lake deposits and other paleoclimate archives in the region have been studied to reconstruct past climates and palaeoecological conditions. However, actual data from proxy records have not been qualitatively and quantitatively utilized to interpret the behavior of the vegetation in moister areas within the Maya Region, such as the Lake Izabal Basin (LIB). The palynomorphs from two sediment cores in the LIB provided a good opportunity to infer the patterns of past …

Investigation Wettability Contact Angle Using 2d Imaging Technology, Saleh Alsayegh

Doctoral Dissertations

"Investigation wetting preference of tight carbonate reservoir rocks and several other unconventional reservoir rocks, and their relation to oil production, is becoming noticeably important for field development in Kuwait, as in many future unconventional tight carbonate reservoirs in the Middle East. The overall objective of this investigating and modeling study is to discover many fundamental relationships from totality wettability preference as a tool for reservoir recovery predictions and management. The investigation includes advancing position of water wet preference into smaller capillaries of the matrix voids and incrementally more oil-wet into larger capillaries of natural fractures (NF). Also, investigating water/ oil …

High Viscosity Friction Reducer Evaluation At High Temperature And High Tds Environments, Ghith Ali Ahmed Biheri

Doctoral Dissertations

"In unconventional reservoirs, proppant transport during hydraulic fracturing treatments could be successful when the proppant is placed further within the reservoir's fracture networks. This could increase the reservoir formation conductivities and improve the productivity of the wells. This job of improving the reservoir conductivity by distributing and transporting proppant can be conducted by reliable fracture fluids with excellent fluid rheology (e.g., viscosity and elasticity). However, several challenges, including the high temperatures and the presence of high TDS in produced water, may limit the capability of fracture fluids to transport proppant. Additionally, the use of fracture fluid has raised fears regarding …

Novel Supercritical Biodiesel Plant Design & Process Scale-Up, Ghana Shyam Paudel

Doctoral Dissertations

"Current energy prices, national energy security, and global climate change fuel our momentum to find efficient advanced fuels choices. In this study, biodiesel processing, and a novel design for next generation biodiesel plants are explored. During a National Science Foundation (NSF) I-Corps project we identified three creative and profitable improvements to the process: 1. Incorporating Energy intensive separations and reactions 2. Utilizing Low commodity glycerol and 3. Applying process intensification principles.

Current biodiesel processes are catalyzed processes using continuous stir reactors with distillation systems to separate material constituents. We tested a lab-scale nocatalyst supercritical biodiesel process using waste cooking oil …

Sustainable Cementitious Materials For Building And Sorption Applications, Sukanta Kumar Mondal

Doctoral Dissertations

"Ordinary Portland Cement (OPC) is the most widely used cement material, but it contributes over 8% of the global CO₂ emission and the process is energy intensive. Moreover, OPC faces durability challenges, particularly in aggressive environments. Hence, there is rapidly increasing interest in sustainable alternative cements with lower carbon footprint, lower energy consumption, and those that offer superior properties that are beneficial for specific applications. Two sustainable cementitious materials that are frequently researched as an alternative to OPC are calcium sulfoaluminate (CSA) cement and alkali-activated materials (AAMs). CSA cement lowers CO₂ emission by over 40% compared to OPC, …

Investigation Of Asphaltene Instability Under Gas Injection In Unconventional Reservoirs And Its Impact On Oil Recovery Performance, Mukhtar Elturki

Doctoral Dissertations

"Unconventional reservoirs, such as shale gas and tight oil formations, have become an important source of energy in recent years. However, these reservoirs often contain high levels of asphaltenes, which can lead to deposition and blockages in production wells and reduce the flow of hydrocarbons during gas enhanced oil recovery (GEOR) techniques. This study aims to experimentally evaluate the impact of miscible and immiscible carbon dioxide (CO₂) and nitrogen (N₂) on asphaltene deposition and its impact on oil recovery performance in unconventional shale reservoirs.

This research began with a comprehensive literature review and data analysis of GEOR methods in unconventional …

The Effects Of Uv-Radiation On The Removal Of Microplastics In Water Using Agglomeration-Micro-Flotation, Palot Srichonphaisarn

Chulalongkorn University Theses and Dissertations (Chula ETD)

Microplastics, plastic particles with diameter 1 micrometer to 5 millimeters, can disturb marine ecosystems due to their small size and surface properties which can be a carrier for hazardous matters. While wastewater treatment plants could remove some microplastics but some of them remain. Among the various removal techniques, flotation is a potential method due to the hydrophobic nature of microplastics. This study investigates the effects of ultraviolet radiation on the surface wettability of microplastics and removal efficiency of microplastics. The 6 types of microplastics were prepared from plastic boards. After the ultraviolet radiation, the results showed that ultraviolet radiation could …