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Full-Text Articles in Entire DC Network
Myceli-Yum: Elucidating Structure-Property Relationships For Polymer Degradation By Mycelial Digestion, Jordan Scott Ford
Myceli-Yum: Elucidating Structure-Property Relationships For Polymer Degradation By Mycelial Digestion, Jordan Scott Ford
Master's Theses
Since the industrial entrance of polymer plastic materials, plastic has become ubiquitous in both everyday use and waste. Due to inefficiencies and knowledge gaps, current recycling methods are not able to account for the high scale of plastic waste, resulting in the bulk of this waste being landfilled, mishandled, and deposited in the environment. Mycelium, the microorganism responsible for fruiting mushroom bodies and mold growth, holds potential to reduce plastic waste and can potentially be utilized as a method of industrial recycling. Following a drug-design approach, the active site of mycelial enzymes responsible for natural biopolymer degradation have been assessed …
An Inquiry Into The Physics Of Mixing And Floc Filtration, Andrew P. Pennock
An Inquiry Into The Physics Of Mixing And Floc Filtration, Andrew P. Pennock
Dissertations
Flocculation and clarification are two essential processes to deliver safe water at a reasonable cost to consumers. There are two major thrusts to the research presented in this dissertation. The first is to better characterize the physics and mixing parameters used for the design of hydraulic flocculators in the context of drinking water treatment plants. The second major thrust is to investigate floc filtration as a mechanism for the removal of primary particles during floc blanket clarification.
The intensity of mixing in environmental and chemical engineering applications is often characterized by the Camp and Stein velocity gradient. This parameter has …
Strongly Confined Bi2se3 Quantum Dots Via Pulsed Laser Ablation In Liquids, Gregory Guisbiers, Rajendra Subedi, Burningham Burningham, Francisco Francisco Ruiz-Zepeda, Qiaohui Zhou, Xin Lu
Strongly Confined Bi2se3 Quantum Dots Via Pulsed Laser Ablation In Liquids, Gregory Guisbiers, Rajendra Subedi, Burningham Burningham, Francisco Francisco Ruiz-Zepeda, Qiaohui Zhou, Xin Lu
Faculty Scholarship
Bismuth selenide (Bi2Se3) is a binary compound displaying a strong spin−orbit coupling, resulting in a narrow bulk bandgap material with a gapless metallic surface. By shrinking the size of Bi2Se3 within the strong confinement regime, its optoelectronic properties changed drastically. To achieve this goal, strongly confined Bi2Se3 quantum dots (QDs) were produced by pulsed laser ablation in liquids (PLAL). The laser used for the synthesis was a nanosecond Nd/YAG laser emitting at 1064 nm and pulsing at ∼13 mJ/pulse. The irradiation of the bulk target was performed at 1 kHz in acetone and lasted 5 min. Finally, the Bi2Se3 QDs …
Preparation And Modification Of Mxene Composites For Application In Electrochemical Energy Storage, Zhang-Hai You, Ding-Ze Lu, Kiran Kumar Kondamareddy, Wen-Ju Gu, Peng-Fei Cheng, Jing-Xuan Yang, Rui Zheng, Hong-Mei Wang
Preparation And Modification Of Mxene Composites For Application In Electrochemical Energy Storage, Zhang-Hai You, Ding-Ze Lu, Kiran Kumar Kondamareddy, Wen-Ju Gu, Peng-Fei Cheng, Jing-Xuan Yang, Rui Zheng, Hong-Mei Wang
Journal of Electrochemistry
With the acceleration of advanced industrialization and urbanization, the environment is deteriorating rapidly, and non-renewable energy resources are depleted. The gradual advent of potential clean energy storage technologies is particularly urgent. Electrochemical energy storage technologies have been widely used in multiple fields, especially supercapacitors and rechargeable batteries, as vital elements of storing renewable energy. In recent years, two-dimensional material MXene has shown great potential in energy and multiple application fields thanks to its excellent electrical properties, large specific surface area, and tunability. Based on the layered materials of MXene, researchers have successfully achieved the dual functions of energy storage and …
Three-Dimensional Melamine Carbon Sponge/Nai As Cathode Materials For Sodium-Ion Batteries, Qian-Ying Huang, Yue Liu, Zi-Xin Lin, Shu-Yi Zheng, Ting-Ting Mei, Yu-Ting Tang, Ying-He Zhang, Jun Liu
Three-Dimensional Melamine Carbon Sponge/Nai As Cathode Materials For Sodium-Ion Batteries, Qian-Ying Huang, Yue Liu, Zi-Xin Lin, Shu-Yi Zheng, Ting-Ting Mei, Yu-Ting Tang, Ying-He Zhang, Jun Liu
Journal of Electrochemistry
The sodium-iodine (Na-I) battery exhibits significant potential as an alternative energy storage device to the lithium-ion battery. However, its development is hindered by inadequate electrical and thermal stability, as well as the dissolution and shuttling of polyiodide. In this study, we report a preparation method for melamine carbon sponge (MC) via carbonizing a commercially available kitchen sponge. It was revealed that the as-prepared MC, composed of unique self-growing carbon nanotubes, could provide both physical and chemical adsorption capabilities for intermediate polyiodides to improve the electrochemical performance of NaI. Consequently, the NaI/MC electrode effectively minimized polyiodide dissolution and reduced the electrochemical …
Understanding The Morphology And Mass Transport Resistance Of Mesoporous Carbon-Supported Pemfc Based On Modeling Analysis, Hao Deng, Jia Liu, Zhong-Jun Hou
Understanding The Morphology And Mass Transport Resistance Of Mesoporous Carbon-Supported Pemfc Based On Modeling Analysis, Hao Deng, Jia Liu, Zhong-Jun Hou
Journal of Electrochemistry
Mesoporous carbon supports mitigate Pt sulfonic poisoning through nanopore-confined Pt deposition, yet their morphological impacts on oxygen transport remain unclear. This study integrates carbon support morphology simulation with an enhanced agglomerate model to establish a mathematical framework elucidating pore evolution, Pt utilization, and oxygen transport in catalyst layers. Results demonstrate dominant local mass transport resistance governed by three factors: (1) active site density dictating oxygen flux; (2) ionomer film thickness defining shortest transport path; (3) ionomer-to-Pt surface area ratio modulating practical pathway length. At low ionomer-to-carbon (I/C) ratios, limited active sites elevate resistance (Factor 1 dominant). Higher I/C ratios improve …
Optimization Of Renewable Energy Systems: Comparative Analysis Of Advanced Algorithms And Photovoltaic-Electrolyzer Performance For Cost Reduction And Efficiency Enhancement, Mohamed-Amine Babay, Mustapha Adar, Ahmed Chebak, Mustapha Mabroukia
Optimization Of Renewable Energy Systems: Comparative Analysis Of Advanced Algorithms And Photovoltaic-Electrolyzer Performance For Cost Reduction And Efficiency Enhancement, Mohamed-Amine Babay, Mustapha Adar, Ahmed Chebak, Mustapha Mabroukia
Journal of Electrochemistry
The increasing demand for cost-effective and efficient renewable energy solutions presents significant optimization challenges in hybrid energy systems. This paper addresses these challenges by conducting a comparative analysis of three advanced optimization algorithms—Lévy Flight Optimization (LFO), Archimedean Optimization (AO), and Quantum Gorilla Optimization (QGO)—to minimize the Total Net Present Cost (TNPC) and Levelized Cost of Energy (LCOE) in hybrid renewable energy systems. The study integrates critical cost parameters such as Capital Expenditure (CAPEX), Operational Expenditure (OPEX), replacement costs, and salvage values into an advanced optimization framework. Three system configurations are evaluated: Wind Turbines and Fuel Cells (WT/FC), Photovoltaic Systems and …
Theoretical Insights Into The Atomic And Electronic Structures Of Polyperyleneimide: On The Origin Of Photocatalytic Oxygen Evolution Activity, Yi-Qing Wang, Zhi Lin, Ming-Tao Li, Shao-Hua Shen
Theoretical Insights Into The Atomic And Electronic Structures Of Polyperyleneimide: On The Origin Of Photocatalytic Oxygen Evolution Activity, Yi-Qing Wang, Zhi Lin, Ming-Tao Li, Shao-Hua Shen
Journal of Electrochemistry
Polymeric perylene diimide (PDI) has been evidenced as a good candidate for photocatalytic water oxidation, yet the origin of the photocatalytic oxygen evolution activity remains unclear and needs further exploration. Herein, with crystal and atomic structures of the self-assembled PDI revealed from the X-ray diffraction pattern, the electronic structure is theoretically illustrated by the first-principles density functional theory calculations, suggesting the suitable band structure and the direct electronic transition for efficient photocatalytic oxygen evolution over PDI. It is confirmed that the carbonyl O atoms on the conjugation structure serve as the active sites for oxygen evolution reaction by the crystal …
The Nitrogen-Vacancy-Nitrogen Color Center: A Ubiquitous Visible And Near-Infrared-Ii Quantum Emitter In Nitrogen-Doped Diamond, Brett C. Johnson, Mitchell O. De Vries, Alexander J. Healey, Marco Capelli, Anjay Manian, Giannis Thalassinos, Amanda N. Abraham, Harini Hapuarachchi, Tingpeng Luo, Vadym N. Mochalin, Jan Jeske, Jared H. Cole, Salvy Russo
The Nitrogen-Vacancy-Nitrogen Color Center: A Ubiquitous Visible And Near-Infrared-Ii Quantum Emitter In Nitrogen-Doped Diamond, Brett C. Johnson, Mitchell O. De Vries, Alexander J. Healey, Marco Capelli, Anjay Manian, Giannis Thalassinos, Amanda N. Abraham, Harini Hapuarachchi, Tingpeng Luo, Vadym N. Mochalin, Jan Jeske, Jared H. Cole, Salvy Russo
Chemistry Faculty Research & Creative Works
Photoluminescent defects in diamond, such as the nitrogen-vacancy (NV) color center, are at the forefront of emerging optical quantum technologies. Most emit in the visible and near-infrared spectral region below 1000 nm (NIR-I), limiting their applications in photonics, fiber communications, and biology. Here, we show that the nitrogen-vacancy-nitrogen (N2V) center, which emits in the visible and near-infrared-II (NIR-II, 1000-1700 nm), is ubiquitous in as-synthesized and processed nitrogen-doped diamond, ranging from bulk samples to nanoparticles. We demonstrate that N2V is also present in commercially available state-of-the-art NV diamond sensing chips made via chemical vapor deposition (CVD). In high-pressure high-temperature (HPHT) diamonds, …
Nuclear Magnetic Resonance Dynamics Of Pyrazole-Litfsi Eutectic Solvents As Promising Electrolytes, Emilia Pelegano-Titmuss, Giselle De Araujo Lima E Souza, Muhammad Zulqarnain, Ramez Elgammal, Thomas Zawodzinski, Steven Greenbaum
Nuclear Magnetic Resonance Dynamics Of Pyrazole-Litfsi Eutectic Solvents As Promising Electrolytes, Emilia Pelegano-Titmuss, Giselle De Araujo Lima E Souza, Muhammad Zulqarnain, Ramez Elgammal, Thomas Zawodzinski, Steven Greenbaum
Undergraduate Research
Deep Eutectic Solvents (DESs) have emerged as promising candidates to replace conventional organic solvents in various technological applications due to their low vapor pressure, non-flammability, and ease of preparation at low costs. In particular, Type IV DESs, which are composed of metal salts and hydrogen bond donors, are possible replacements for lithium-ion battery electrolytes due to their potential of having high lithium transference numbers. In this study, we investigated solvents of Pyrazole and LiTFSI at varying molar ratios using Fast Field Cycling (FFC) NMR Relaxometry. Notably, the 1:2 LiTFSI: Pyrazole sample shows distinct behavior, exhibiting enhanced relaxation rates for 1 …
Computational Approach: 3d-Qsar, Molecular Docking, Molecular Dynamics Simulation Investigations, Drug- Like-Ness, And Dft Score Evaluation Of A Potential Novel And Retrosynthesis Of Some Tr-H Derivatives As Streptococcus Pneumoniae Drug., Belaidi Mustapha, Tchouar Noureddine, Djelilate Mohammed, Saleh Bufarwa, Dalal K. Thbayh
Computational Approach: 3d-Qsar, Molecular Docking, Molecular Dynamics Simulation Investigations, Drug- Like-Ness, And Dft Score Evaluation Of A Potential Novel And Retrosynthesis Of Some Tr-H Derivatives As Streptococcus Pneumoniae Drug., Belaidi Mustapha, Tchouar Noureddine, Djelilate Mohammed, Saleh Bufarwa, Dalal K. Thbayh
Karbala International Journal of Modern Science
Streptococcus pneumoniae is the main source of hospital-acquired pneumonia and meningococcal pneumonia in children, adults, and the elderly, especially the immunocompromised. Recently, it has attracted the attention of many research studies around the world as a potential target for remediation. TR-H are considered SP antibacterial agents, as they can inhibit. To describe their mode of action and to identify new antibacterial drugs against Streptococcus pneumoniae exhibiting the TR-H scaffold, the present work included 3D-QSAR, in- silico pharmacokinetic evaluation and molecular simulation modelling of TR-H. Using an atom-based method for quantitative structure-activity relationship (QSAR) study, a comprehensive 3D-QSAR model …
Integrative Computational Modeling Of Distinct Binding Mechanisms For Broadly Neutralizing Antibodies Targeting Sars-Cov-2 Spike Omicron Variants: Balance Of Evolutionary And Dynamic Adaptability In Shaping Molecular Determinants Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker
Integrative Computational Modeling Of Distinct Binding Mechanisms For Broadly Neutralizing Antibodies Targeting Sars-Cov-2 Spike Omicron Variants: Balance Of Evolutionary And Dynamic Adaptability In Shaping Molecular Determinants Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker
Mathematics, Physics, and Computer Science Faculty Articles and Research
In this study, we conducted a comprehensive analysis of the interactions between the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and four neutralizing antibodies—S309, S304, CYFN1006, and VIR-7229. Using integrative computational modeling that combined all-atom molecular dynamics (MD) simulations, mutational scanning, and MM-GBSA binding free energy calculations, we elucidated the structural, energetic, and dynamic determinants of antibody binding. Our findings reveal distinct dynamic binding mechanisms and evolutionary adaptation driving the broad neutralization effect of these antibodies. We show that S309 targets conserved residues near the ACE2 interface, leveraging synergistic van der Waals and electrostatic interactions, while S304 focuses on …
Protein Stability Retention Under Harsh Conditions, Kaylen Su
Protein Stability Retention Under Harsh Conditions, Kaylen Su
Student Theses and Dissertations
Plastic waste is a growing environmental concern due to its resistance to natural degradation, leading to long-term accumulation in landfills and oceans. One potential solution is enzymatic degradation, where specific enzymes break down plastic into smaller, biodegradable components. However, enzymes often lose their effectiveness under the extreme conditions plastics experience during manufacturing, such as high temperatures, mechanical stress, and dehydration. This study explores whether small molecules, known as ligands, can help stabilize enzymes and improve their ability to break down plastics.
Using molecular dynamics simulations, we tested four ligands—poly(ethylene glycol) (PEG), 6-hydroxyhexanoic acid (HHA), benzalkonium chloride (BC), and 6-aminohexanoic acid …
Application Of Quechers Extraction Method For Optimization Of Organic Matters In Oil Sand By Ultrahigh Fourier Transform Infrared Orbitrap-Mass Spectrometry, Gbenga Aladekoyi, Emmanuel G. Olumayede, Samuel O. Olusanya, Simeon Schum
Application Of Quechers Extraction Method For Optimization Of Organic Matters In Oil Sand By Ultrahigh Fourier Transform Infrared Orbitrap-Mass Spectrometry, Gbenga Aladekoyi, Emmanuel G. Olumayede, Samuel O. Olusanya, Simeon Schum
Michigan Tech Publications
This work focuses on the performance of composite solvents using the QuEchERs extraction (quick, easy, cheap, effective, rugged, and safe) method in bitumen recovery and determination of organic matters present in the oil sands of the Okitipupa area of southwestern Nigeria. Different correlated parameters, such as extraction time (h), stirring time (r/ min), change in temperature (°C), and type of solvent (heptane—toluene and dichloromethane—toluene), solvent ratios (2: 8, 3: 7, 5: 5, 7: 3, and 8: 2) were used to optimize dissolved organic matters from the oil sands using QuEchERs extraction method. Ratios 1 g/2.5 ml for each solvent mix …
Sequence Conservation Of Suppressor Of Ikk Epsilon Phosphorylation Sites, Kaydence M. Isaacs
Sequence Conservation Of Suppressor Of Ikk Epsilon Phosphorylation Sites, Kaydence M. Isaacs
Undergraduate Honors Theses
Suppressor of IKK epsilon (SIKE) is a protein that is implicated in immune response signaling pathways. SIKE interaction networks suggest roles in cell motility and macromolecular complexes mediating kinase/phosphatase activity. In this project, we aim to better understand the function of SIKE by analyzing amino acid sequences across different species. In human SIKE, viral infection leads to phosphorylation of SIKE at defined serine residues. Comparing SIKE sequences, and specifically these phosphorylation sites, allows us to discover its ancestral connections to innate immune function. This has particular applications in bridging the evolutionary gap between fungi and metazoa SIKE sequences. Multiple sequence …
Asymmetric, Carboxy And Ester Functionalized Fluorophthalocyanines: Synthesis, Adsorption, And Reactivity, Sean J. Scally
Asymmetric, Carboxy And Ester Functionalized Fluorophthalocyanines: Synthesis, Adsorption, And Reactivity, Sean J. Scally
Seton Hall University Dissertations and Theses (ETDs)
Strong electron-deficient compounds, fluorinated metal phthalocyanines (FxPcM), exhibit enhanced photosensitizing properties, making them optimal candidates for photocatalytic studies. Perfluoroalkyl-substituted phthalocyanines are notably thermally robust materials that are chemically inert and resistant to electrophilic, nucleophilic, and radical, including reactive oxygen species (ROS) attacks. These properties can be attributed to their ‘Teflon-like’ inert organic shield that surrounds a reactive metal center, as well as their complete (x = 16, 40, 64), or almost complete (x = 48) lack of C-H bonds. Third-generation, functionalized, asymmetric phthalocyanines are of interest due to their ability to bind to oxidic supports via a carboxyl …
Complementary Design Of Optical And Photochemical Systems, Joshua Plank
Complementary Design Of Optical And Photochemical Systems, Joshua Plank
Chemistry Theses and Dissertations
The ability to manipulate chemical systems has been prized through history as the bridge between the macroscopic and microscopic worlds. As an example, the camera obscura has arguably existed since the earliest days of humanity; however, it was the discovery of early silver halide chemistry that lead to the ability to fix these images into the earliest photographs. In modern photolithography employed in electronics manufacturing, the primary resolution limits arise not from the chemistry of the molecules involved, but from the limits of the systems used to project light. Thus, as much as photochemistry advances, optical imaging and projection techniques …
A Computational Method For Detecting Compound Promiscuity In Early-Stage Pharmaceutical Discovery, John Allen Ringer
A Computational Method For Detecting Compound Promiscuity In Early-Stage Pharmaceutical Discovery, John Allen Ringer
Computer Science ETDs
Modern drug discovery and chemical biology research relies heavily on analyzing bioassay data. One of the many challenges in bioassay data analysis is identifying false trails, i.e., chemical compounds which initially appear to have desirable activity but are found to be problematic upon further investigation. Badapple (the BioAssay-Data Associative Promiscuity Pattern Learning Engine) was created over ten years ago to help researchers identify promiscuous compounds and thus avoid a common source of these false trails. Through an effort involving software engineering, cheminformatics, and biomedical data science we have developed Badapple 2.0, which incorporates updated assay records and expanded data semantics. …
Fe/Co/Ni-Doped Mos2 An Electrocatalyst For Overall Water Splitting, Himanshi Lnu
Fe/Co/Ni-Doped Mos2 An Electrocatalyst For Overall Water Splitting, Himanshi Lnu
Electronic Theses & Dissertations
Electrochemical water splitting is a promising method for sustainable hydrogen production, addressing global energy challenges. However, its practical application is limited by the need for efficient and durable electrocatalysts for both the hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). In this study, MoS₂ was doped with Co, Ni, and Fe at varying concentrations (5:0.5, 5:1, and 5:1.5) using a hydrothermal synthesis method to evaluate their potential as electrocatalysts for water splitting. Characterization revealed that metal doping significantly altered the electronic and morphological properties of MoS₂, enhancing its catalytic performance. Electrochemical evaluations in alkaline media demonstrated that Co-doped MoS₂ …
Trade-Off Between Limonene & Geraniol-Based Reprocessable And Non-Reprocessable Epoxy Thermosets: Role Of Aliphatic Diamines In Polymer Networks Design, Priyankkumar Kanubhai Patel
Trade-Off Between Limonene & Geraniol-Based Reprocessable And Non-Reprocessable Epoxy Thermosets: Role Of Aliphatic Diamines In Polymer Networks Design, Priyankkumar Kanubhai Patel
Electronic Theses & Dissertations
The growing demand for sustainable materials, driven by environmental concerns and the rapid depletion of fossil fuels, has garnered significant attention in the fabrication of bio-based epoxy thermosets as renewable alternatives to petroleum-derived thermosetting polymers. The present study focuses on the synthesis and characterization of epoxy prepolymer resins derived from limonene and geraniol via a two-step process, followed by the fabrication of thermally cross-linked flexible epoxy thermoset films using various traditional aliphatic diamine curing agents, namely 1,2-ethylenediamine (EDA), 1,4-butylenediamine (BDA), and 1,6-hexamethylenediamine (HDA). Additionally, the incorporation of cystamine, a disulfide-containing diamine, enabled the formation of a covalent adaptable network through …
The Effects Of Reprocessing, Post-Processing Conditions, And Environmental Exposure On The Physical Properties Of Post-Industrial And Post-Consumer Polyethylene, Grant M. Howard
Electronic Theses & Dissertations
THE EFFECTS OF REPROCESSING, POST-PROCESSING CONDITIONS, AND ENVIRONMENTAL EXPOSURE ON THE PHYSICAL PROPERTIES OF POST-INDUSTRIAL AND POST-CONSUMER POLYETHYLENE
An Abstract of the Thesis by
Grant Howard
Plastic pollution is a rapidly growing problem. Globally, millions of tons of plastic waste are produced, and that amount is projected to increase each year. To address this, recycling of commodity thermoplastics like polyethylene, polypropylene, and polyethylene terephthalate, have become a point of emphasis in industry. Companies have started to investigate the use of recycled plastics instead of virgin plastics in their products. The advantages of using recycled material are to receive tax breaks, …
Development Of Non-Precious Iron-Cobalt Alloy Catalyst For Electrocatalytic Reaction, Harsh Panchal
Development Of Non-Precious Iron-Cobalt Alloy Catalyst For Electrocatalytic Reaction, Harsh Panchal
Electronic Theses & Dissertations
The development of a FeCo alloy catalyst with tunable Fe/Co ratios is examined to improve electrocatalytic performance in reactions like the oxygen evolution reaction (OER), hydrogen evolution reaction (HER), and oxygen reduction reaction (ORR). Many energy conversion devices, such as fuel cells, metal-air batteries, and water-splitting systems, depend on these interactions to function. These technologies have huge potential to meet the increasing need for hydrogen production and renewable energy sources worldwide, which are critical to attaining a sustainable energy future. When compared with noble metal-based catalysts, the FeCo alloy catalyst shows much higher catalytic activity, according to previous studies. Hydrothermal …
Soybean Oil-Derived Acrylate/Methacrylate Ether For High Resolution Additive Manufacturing (3d Printing) Technology, Tanuj Patel
Soybean Oil-Derived Acrylate/Methacrylate Ether For High Resolution Additive Manufacturing (3d Printing) Technology, Tanuj Patel
Electronic Theses & Dissertations
Additive Manufacturing is one of the rapidly developing techniques, as industries continue to explore new ways to create prototypes and end-use parts, one of the significant challenges that remains is the reliance on petroleum-based plastics for 3D printing, especially in the production of photocurable resins. that may be used to prototype complex structures and sophisticated geometries that are typically challenging to produce with conventional methods. Thus, replacing petroleum-based plastics with renewable resources is increasingly important for additive manufacturing (3D printing) of photocurable resins. The use of bio-based renewable resources in AM is a feasible alternative to traditional petroleum-based plastics. Henceforth, …
Probing Binding And Allosteric Mechanisms Of The Kras Interactions With Monobodies And Affimer Proteins : Ensemble-Based Mutational Profiling And Thermodynamic Analysis Of Binding Energetics And Allostery Reveal Diversity Of Functional Hotspots And Cryptic Pockets Linked By Conserved Communication Network, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Guang Hu, Gennady M. Verkhivker
Probing Binding And Allosteric Mechanisms Of The Kras Interactions With Monobodies And Affimer Proteins : Ensemble-Based Mutational Profiling And Thermodynamic Analysis Of Binding Energetics And Allostery Reveal Diversity Of Functional Hotspots And Cryptic Pockets Linked By Conserved Communication Network, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Guang Hu, Gennady M. Verkhivker
Mathematics, Physics, and Computer Science Faculty Articles and Research
KRAS, a historically "undruggable" oncogenic driver, has eluded targeted therapies due to its lack of accessible binding pockets in its active state. This study investigates the conformational dynamics, binding mechanisms, and allosteric communication networks of KRAS in complexes with monobodies (12D1, 12D5) and affimer proteins (K6, K3, K69) to characterize the binding and allosteric mechanisms and hotspots of KRAS binding. Through molecular dynamics simulations, mutational scanning, binding free energy analysis and network-based analyses, we identified conserved allosteric hotspots that serve as critical nodes for long-range communication in KRAS. Key residues in β-strand 4 (F78, L80, F82), α-helix 3 (I93, H95, …
Impact Of Unconventional Gas Extraction On Tributaries Of Tenmile Creek, Greene County, Pennsylvania: A 12-Year Perspective, Christian L. Beall
Impact Of Unconventional Gas Extraction On Tributaries Of Tenmile Creek, Greene County, Pennsylvania: A 12-Year Perspective, Christian L. Beall
Electronic Theses and Dissertations
Much of southwestern Pennsylvania has been central to a rapid increase in development for unconventional natural gas extraction in the past two decades. The continued monitoring of streams over their lifetime as extraction sites is pivotal to understanding the effects of fracking on local waterways and their ability to provide for wildlife and human use. Here, using multiple indices of biotic integrity (IBI), I perform analyses of fish and macroinvertebrate communities as well as water chemistry on two streams, Bates Fork (with shale wells) and Fonner Run (without), as part of a follow-up to work performed there from 2010-2012. Fish …
Structure Determination Of Mg2tihn And Mg3tihn (N=1-25) Clusters, Meagan Dobbs
Structure Determination Of Mg2tihn And Mg3tihn (N=1-25) Clusters, Meagan Dobbs
Honors College Theses
Fossil fuels are a resource that is used in everyday life. A major problem with the reliance on fossil fuels lies in their major contributor to global warming. When fossil fuels are burned, they release greenhouse gases into the atmosphere and warm the Earth. In order to decrease the amount of greenhouse gases being emitted new fuel sources are being considered, and a leading candidate is hydrogen. This project looks at magnesium hydride clusters doped with a titanium atom. Specifically, the Mg2TiHn (n =1-25) and Mg3TiHn (n =1-25) clusters are considered. The …
Synthesis Of Sensitive Oligodeoxynucleotides Containing Acylated Cytosine, Adenine, And Guanine Nucleobases, Komal Chillar, Rohith Awasthy, Marina Tanasova, Shiyue Fang
Synthesis Of Sensitive Oligodeoxynucleotides Containing Acylated Cytosine, Adenine, And Guanine Nucleobases, Komal Chillar, Rohith Awasthy, Marina Tanasova, Shiyue Fang
Michigan Tech Publications
Background/Objective: Oligodeoxynucleotides (ODNs) containing base-labile modifications such as N4-acetyldeoxycytidine (4acC), N6-acetyladenosine (6acA), N2- acetylguanosine (2acG), and N4-methyoxycarbonyldeoxycytidine (4mcC) are highly challenging to synthesize because standard ODN synthesis methods require deprotection and cleavage under strongly basic and nucleophilic conditions, and there is a lack of ideal alternative methods to solve the problem. The objective of this work is to explore the capability of the recently developed 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) method for the incorporation of multiple 4acC modifications into a single ODN molecule and the feasibility of using the method for the incorporation of the 6acA, 2acG and 4mcC modifications into ODNs. Methods: …
Preparation, And Characterization Of Gypsum-Levan Composites And Evaluation Of Their Preliminary In Vitro And Antibacterial Characteristics, Jamileh Sultan El Arab
Preparation, And Characterization Of Gypsum-Levan Composites And Evaluation Of Their Preliminary In Vitro And Antibacterial Characteristics, Jamileh Sultan El Arab
Thesis/ Dissertation Defenses
Orthopedic surgery has to contend with a myriad of issues with bones, injuries such as fractures as well as chronic ailments, like osteoporosis. There is a widespread understanding and execution of polymethylmethacrylate (PMMA) bone cement and calcium phosphate cements (CPCs), however their drawbacks like being non-biodegradable, generating heat, low bioactivity, and other issues reserve the development of better substitutes This study intends to develop and incorporate microbial levan squaring as a β-2,6-linked fructan polysaccharide into gypsum-based formulations of bone cements to make them biodegradable, bioactive and amplify their mechanical properties. The research aims to address the performance drawbacks of traditional …
High-Quality Factor Phase Gradient Metasurfaces With Dynamic Reconfigurability, Lin Lin
High-Quality Factor Phase Gradient Metasurfaces With Dynamic Reconfigurability, Lin Lin
Arts & Sciences Graduate Student Theses and Dissertations
Free-space optical communication holds immense potential for surpassing the bandwidth limitations of conventional physically defined channels. Achieving flexible and efficient communication in free space requires compact, robust optical components capable of dynamically tuning laser light without relying on bulky lenses or mechanically driven mirrors. Metasurfaces, or flat optics, have garnered significant attention due to their densely arranged subwavelength nano-resonators, which impart phase, amplitude, and polarization changes comparable to those of traditional bulky optics. However, conventional phase gradient metasurfaces are constrained by passive designs based on geometric configurations and the weak light-matter interaction inherent in most dielectric materials, limiting their applicability …
California Red Hummingbird Flowers: Color Convergence Across Four Biochemical Categories, Melissa León-Osper, Victor Rossi, Katie Conrad, Josephine Hernandez Mena, Elaine Meslow, Amelia A. Fuller, Eduardo Narbona, Justen B. Whittall
California Red Hummingbird Flowers: Color Convergence Across Four Biochemical Categories, Melissa León-Osper, Victor Rossi, Katie Conrad, Josephine Hernandez Mena, Elaine Meslow, Amelia A. Fuller, Eduardo Narbona, Justen B. Whittall
Chemistry and Biochemistry
There are 129 red-flowered species in western North America that fit the hummingbird pollination syndrome. Theory predicts that these flowers should produce a specific red color that is conspicuous to hummingbirds but not to bees. In a few well-studied cases, red flowers can be produced with pelargonidin, cyanidin, or both—sometimes complemented with the addition of yellow carotenoids and sometimes not. Which pigment combinations are most common in California and whether they affect conspicuousness to hummingbirds and bees remain unknown. To determine the taxonomic distribution of the pigments responsible for red hummingbird-pollinated flowers, we quantified the color of 36 red-flowered species …