Physical Sciences and Mathematics Commons^™

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 …

Outstanding Advantages, Current Drawbacks, And Significant Recent Developments In Mechanochemistry: A Perspective View, Silvina Pagola

Chemistry & Biochemistry Faculty Publications

Although known since antiquity, mechanochemistry has remained dormant for centuries. Nowadays, mechanochemistry is a flourishing research field at the simultaneous stages of gathering data and (often astonishing) observations, and scientific argumentation toward their analysis, for which the combination of interdisciplinary expertise is necessary. Mechanochemistry’s implementation as a synthetic method is constantly increasing, although it remains far from being fully exploited, or understood on the basis of fundamental principles. This review starts by describing many remarkable advantages of mechanochemical reactions, simplifying and “greening” chemistry in solutions. This description is followed by an overview of the current main weaknesses to be addressed …

More On The Demons Of Thermodynamics, Daniel P. Sheehan, Garret Moddel, James W. Lee

Chemistry & Biochemistry Faculty Publications

No abstract provided.

4,6-O-Phenylethylidene Acetal Protected D-Glucosamine Carbamate-Based Gelators And Their Applications For Multi-Component Gels, Pooja Sharma, Guijun Wang

Chemistry & Biochemistry Faculty Publications

The self-assembly of carbohydrate-based low molecular weight gelators has led to useful advanced soft materials. The interactions of the gelators with various cations and anions are important in creating novel molecular architectures and expanding the scope of the small molecular gelators. In this study, a series of thirteen new C-2 carbamates of the 4,6-O-phenylethylidene acetalprotected D-glucosamine derivatives has been synthesized and characterized. These compounds are rationally designed from a common sugar template. All carbamates synthesized were found to be efficient gelators and three compounds are also hydrogelators. The resulting gels were characterized using optical microscopy, atomic force microscopy, …

Recent Advancements In Electrochemical Conversion Of Carbon Dioxide, Nandan Nag, Amit Kumar, Sumit Sharma, Sandeep Kumar, Amit K. Thakur

Civil & Environmental Engineering Faculty Publications

Electrochemical reduction of carbon dioxide into eco-friendly and clean products is a promising approach to eradicate pollution. Although carbon dioxide emission is inhibited by the advent of renewable sources of energy, it is present in the atmosphere and needs to be cleaned. The reduction of carbon dioxide from atmospheric gases can be accomplished by its adsorption and subsequent transportation to electrolytic chambers, where it is reduced to hydrocarbons, organic acids or carbonates. This review focuses on developing a three compartment electrochemical cell to reduce carbon dioxide used as a catholyte. Various factors affecting the electrochemical reduction of carbon dioxide and …

Reducing Print Time While Minimizing Loss In Mechanical Properties In Consumer Fdm Parts, Long Le, Mitchel A. Rabsatt, Hamid Eisazadeh, Mona Torabizadeh

Mechanical & Aerospace Engineering Faculty Publications

Fused deposition modeling (FDM), one of various additive manufacturing (AM) technologies, offers a useful and accessible tool for prototyping and manufacturing small volume functional parts. Polylactic acid (PLA) is among the commonly used materials for this process. This study explores the mechanical properties and print time of additively manufactured PLA with consideration to various process parameters. The objective of this study is to optimize the process parameters for the fastest print time possible while minimizing the loss in ultimate strength. Design of experiments (DOE) was employed using a split-plot design with five factors. Analysis of variance (ANOVA) was employed to …

A Local Mode Study Of Ring Puckering Effects In The Infrared Spectra Of Cyclopentane, Edwin L. Sibert Iii, Peter F. Bernath

Chemistry & Biochemistry Faculty Publications

We report and interpret recently recorded high-resolution infrared spectra for the fundamentals of the CH₂ scissors and CH stretches of gas phase cyclopentane at −26.1 and −50 ^○C, respectively. We extend previous theoretical studies of this molecule, which is known to undergo barrierless pseudorotation due to ring puckering, by constructing local mode Hamiltonians of the stretching and scissor vibrations for which the frequencies, couplings, and linear dipoles are calculated as functions of the pseudorotation angle using B3LYP/6-311++(d,p) and MP2/cc-pVTZ levels of theory. Symmetrization (D_5h) of the vibrational basis sets leads to simple vibration/pseudorotation Hamiltonians whose solutions …

Broadband Dielectric Spectroscopic Detection Of Ethanol: A Side-By-Side Comparison Of Zno And Hkust-1 Mofs As Sensing Media, Papa K. Amoah, Zeinab Mohammed Hassan, Pengtao Lin, Engelbert Redel, Helmut Baumgart, Yaw S. Obeng

Electrical & Computer Engineering Faculty Publications

The most common gas sensors are based on chemically induced changes in electrical resistivity and necessarily involve making imperfect electrical contacts to the sensing materials, which introduce errors into the measurements. We leverage thermal- and chemical-induced changes in microwave propagation characteristics (i.e., S-parameters) to compare ZnO and surface-anchored metal-organic-framework (HKUST-1 MOF) thin films as sensing materials for detecting ethanol vapor, a typical volatile organic compound (VOC), at low temperatures. We show that the microwave propagation technique can detect ethanol at relatively low temperatures (<100 >°C), and afford new mechanistic insights that are inaccessible with the traditional dc-resistance-based measurements. In addition, …

Efficient Removal Of Lead Ions From Aqueous Media Using Sustainable Sources On Marine Algae, Hannah Namkoong, Erik Biehler, Gon Namkoong, Tarek M. Abdel-Fattah

Electrical & Computer Engineering Faculty Publications

The goal of this project is to explore a new method to efficiently remove Pb(II) ions from water by processing Undaria pinnatifida into immobilized beads using sodium alginate and calcium chloride. The resulting biosorbent was characterized by Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy (SEM-EDS). Using immobilized U. pinnatifida, we investigated the effect of various factors on Pb(II) ion removal efficiency such as temperature, pH, ionic strength, time, and underlying biosorption mechanisms. For Pb(II) ion biosorption studies, Pb(II) ion biosorption data were obtained and analyzed using Langmuir and Freundlich adsorption models. It …

Oxygen Harvesting From Carbon Dioxide: Simultaneous Epoxidation And Co Formation, Han Xu, Muhammad Shaban, Sui Wang, Anas Alkayal, Dingxin Liu, Michael G. Kong, Felix Plasser, Benjamin R. Buckley, Felipe Iza

Bioelectrics Publications

Due to increasing concentrations in the atmosphere, carbon dioxide has, in recent times, been targeted for utilisation (Carbon Capture Utilisation and Storage, CCUS). In particular, the production of CO from CO₂ has been an area of intense interest, particularly since the CO can be utilized in Fischer–Tropsch synthesis. Herein we report that CO₂ can also be used as a source of atomic oxygen that is efficiently harvested and used as a waste-free terminal oxidant for the oxidation of alkenes to epoxides. Simultaneously, the process yields CO. Utilization of the atomic oxygen does not only generate a valuable product, …

Advanced Raman Spectroscopy Detection Of Oxidative Damage In Nucleic Acid Bases: Probing Chemical Changes And Intermolecular Interactions In Guanosine At Ultralow Concentration, Francesca Ripanti, Claudia Fasolato, Flavia Mazzarda, Simonetta Palleschi, Marina Ceccarini, Chunchun Li, Margherita Bignami, Enrico Bodo, Steven E.J. Bell, Filomena Mazzei, Paolo Postorino

Bioelectrics Publications

DNA/RNA synthesis precursors are especially vulnerable to damage induced by reactive oxygen species occurring following oxidative stress. Guanosine triphosphates are the prevalent oxidized nucleotides, which can be misincorporated during replication, leading to mutations and cell death. Here, we present a novel method based on micro-Raman spectroscopy, combined with ab initio calculations, for the identification, detection, and quantification of oxidized nucleotides at low concentration. We also show that the Raman signature in the terahertz spectral range (<100 >cm(-1)) contains information on the intermolecular assembly of guanine in tetrads, which allows us to further boost the oxidative damage detection limit. Eventually, we …

Interface Model Of Pem Fuel Cell Membrane Steady-Dtate Behavior, Russell L. Edwards, Ayodeji Demuren

Mechanical & Aerospace Engineering Faculty Publications

Modeling works which simulate the proton-exchange membrane fuel cell with the computational fluid dynamics approach involve the simultaneous solution of multiple, interconnected physics equations for fluid flows, heat transport, electrochemical reactions, and both protonic and electronic conduction. Modeling efforts vary by how they treat the physics within and adjacent to the membrane-electrode assembly (MEA). Certain approaches treat the MEA not as part of the computational domain, but rather an interface connecting the anode and cathode computational domains. These approaches may lack the ability to consistently model catalyst layer losses and MEA ohmic resistance. This work presents an upgraded interface formulation …

Analyzing The Spectral Energy Cascade In Turbulent Channel Flow, João Rodrigo Andrade, Ramon Silva Martins, Gilmar Mompean, Laurent Thais, Thomas B. Gatski

CCPO Publications

An analysis of the spectral turbulent kinetic energy budget in a fully developed turbulent plane channel flow is performed. Direct numerical simulation data are evaluated at friction Reynolds numbers Re_τ of 180 and 1000. The analysis is focused on the influence of the Reynolds number on the spectral cascade of energy and the corresponding energy cascade in physical space in the presence of inhomogeneity and anisotropy. The turbulent kinetic energy distribution is compared for both Reynolds numbers, and the relevant characteristics of the energy transfer process in a wall-bounded turbulent flow are described. Differences in energy cascade are noted …

Plasma Processes And Polymers Third Special Issue On Plasma And Cancer, Mounir Laroussi, Annemie Bogaerts, Nazir Barekzi

Electrical & Computer Engineering Faculty Publications

(First paragraph) This issue of Plasma Processes and Polymers is the third in a series on the applications of low temperature plasma (LTP) against cancer, or “plasma oncology.” The papers in this issue are inspired from the talks given at the third International Workshop on Plasma for Cancer Treatment (IWPCT) which took place on April 11–12, 2016 in Washington, DC, USA. IWPCT is an international workshop that was created in 2014 as a venue to share cutting edge plasma oncology research. The first IWPCT was held in Washington DC, under the co-chairmanship of Prof. Mounir Laroussi (Old Dominion University) and …

Characterization Of Biochars Produced From Peanut Hulls And Pine Wood With Different Pyrolysis Conditions, James W. Lee, Bob Hawkins, Michelle K. Kidder, Barbara R. Evans, A. C. Buchanan, Danny Day

Chemistry & Biochemistry Faculty Publications

Background

Application of modern biomass pyrolysis methods for production of biofuels and biochar is potentially a significant approach to enable global carbon capture and sequestration. To realize this potential, it is essential to develop methods that produce biochar with the characteristics needed for effective soil amendment.

Methods

Biochar materials were produced from peanut hulls and pine wood with different pyrolysis conditions, then characterized by cation exchange (CEC) capacity assays, nitrogen adsorption–desorption isotherm measurements, micro/nanostructural imaging, infrared spectra and elemental analyses.

Results

Under a standard assay condition of pH 8.5, the CEC values of the peanut hull-derived biochar materials, ranging from …

Plasma Processes And Cancer - Special Topical Cluster Of The 2nd Iwpct Meeting, Masaru Hori, Mounir Laroussi, Kai Masur, Yuzuru Ikehara

Electrical & Computer Engineering Faculty Publications

(First paragraph) Although the emerging multidisciplinary field of plasma medicine has been around for nearly two decades important advances have already taken place that could one day revolutionize healthcare and the way various challenging diseases can be treated.1-3Amongst these advances the effects of low temperature plasma (LTP) on cancer cells in vitro and in vivo stand out.4-13Current cancer treatment modalities, such as chemotherapy and radiation therapy, have serious side effects and tend to lose their benefits to the patients after a while. Therefore, novel and improved therapies that can be used alone …

Rheological Signatures In Limit Cycle Behaviour Of Dilute, Active, Polar Liquid Crystalline Polymers In Steady Shear, M. Gregory Forest, Panon Phuworawong, Qi Wang, Ruhai Zhou

Mathematics & Statistics Faculty Publications

We consider the dilute regime of active suspensions of liquid crystalline polymers (LCPs), addressing issues motivated by our kinetic model and simulations in Forest et al. (Forest et al. 2013 Soft Matter 9, 5207-5222 (doi:10.1039/c3sm27736d)). In particular, we report unsteady two-dimensional heterogeneous flow-orientation attractors for pusher nanorod swimmers at dilute concentrations where passive LCP equilibria are isotropic. These numerical limit cycles are analogous to longwave (homogeneous) tumbling and kayaking limit cycles and two-dimensional heterogeneous unsteady attractors of passive LCPs in weak imposed shear, yet these states arise exclusively at semi-dilute concentrations where stable equilibria are nematic. The results in Forest …

Plasma Processes And Polymers Special Issue On: Plasma And Cancer, Mounir Laroussi, Michael Keidar

Electrical & Computer Engineering Faculty Publications

During the last two decades, research efforts on the application of low temperature plasmas in biology and medicine have positioned nonequilibrium lowtemperature plasmas as a technology that has the potential of revolutionizing healthcare.[1,2] Low temperature plasmas can be applied in direct contact with living tissues to inactivate bacteria,[3] to disinfect wounds and accelerate wound healing,[4] and to induce damage in some cancer cells.[5–11]

Review Of Us And Eu Initiatives Toward Development, Demonstration, And Commercialization Of Lignocellulosic Biofuels, Venkatesh Balan, David Chiaramonti, Sandeep Kumar

Civil & Environmental Engineering Faculty Publications

Advanced biofuels produced from lignocellulosic biomass offer an exciting opportunity to produce renewable liquid transportation fuels, biochemicals, and electricity from locally available agriculture and forest residues. The growing interest in biofuels from lignocellulosic feedstock in the United States (US) and the European Union (EU) can provide a path forward toward replacing petroleum-based fuels with sustainable biofuels which have the potential to lower greenhouse gas (GHG) emissions. The selection of biomass conversion technologies along with feedstock development plays a crucial role in the commercialization of next-generation biofuels. There has been synergy and, even with similar basic process routes, diversity in the …

Fourier Transform Emission Spectroscopy Of Yh And Yd: Observation Of New A¹Δ And B¹Π Electronic States, R. S. Ram, G. Li, P. F. Bernath

Chemistry & Biochemistry Faculty Publications

The emission spectra of YH and YD molecules have been investigated in the 3600–12 000 cm⁻¹ region using a Fourier transform spectrometer. Molecules were formed in an yttrium hollow cathode lamp operated with a continuous flow of a mixture of Ne and Ar gases, and YH and YD were observed together in the same spectra. A group of bands observed near 1 μm have been identified as 0-0 and 1-1 bands of the A¹Δ-X¹Σ⁺ and B¹Π-X¹Σ⁺ transitions of YH and the 0-0 bands of the same two transitions …

Scaling Properties At Freeze-Out In Relativistic Heavy-Ion Collisions, M. M. Aggarwal, Z. Ahammed, A. V. Alakhverdyants, I. Alekseev, J. Alford, B. D. Anderson, S. Bueltmann, I. Koralt, D. Plyku, Star Collaboration

Physics Faculty Publications

Identified charged pion, kaon, and proton spectra are used to explore the system size dependence of bulk freeze-out properties in Cu+Cu collisions at √sNN=200 and 62.4 GeV. The data are studied with hydrodynamically motivated blast-wave and statistical model frameworks in order to characterize the freeze-out properties of the system. The dependence of freeze-out parameters on beam energy and collision centrality is discussed. Using the existing results from Au + Au and pp collisions, the dependence of freeze-out parameters on the system size is also explored. This multidimensional systematic study furthers our understanding of the QCD phase diagram revealing the importance …

Sublethal And Killing Effects Of Atmospheric-Pressure, Nonthermal Plasma On Eukaryotic Microalgae In Aqueous Media, Ying Zhong Tang, Xin Pei Lu, Mounir Laroussi, Fred C. Dobbs

OES Faculty Publications

In-depth studies on the interaction of nonthermal plasmas with microorganisms usually focus on bacteria; only little attention has been given to their effects on more complex eukaryotic cells. We report here nonthermal plasma's effects on cell motility, viability staining, and morphology of eukaryotic microalgae, with three marine dinoflagellates and a marine diatom as major targets. The effects on motility and viability staining depended on the time of exposure to plasma and the species of microalgae. We observed a strong pH decrease in aqueous samples (marine and freshwater algal cultures, their culture media, and deionized water) after exposure to plasma, and …

Plasma Medicine, Mounir Laroussi, Alexander Fridman

Electrical & Computer Engineering Faculty Publications

Recent demonstrations of plasma technology in the treatment of living cells, tissues, and organs are creating a newfield at the intersection of plasma science and technology with biology and medicine - Plasma Medicine.

The Shape Of Pulverized Bituminous Vitrinite Coal Particles, Jonathan P. Mathews, Patrick G. Hatcher, Alan W. Scaroni

Chemistry & Biochemistry Faculty Publications

The shape of pulverized bituminous coal particles (vitrinites) was determined by optical and laser light scattering. Vitrain samples were collected from obvious tree remains located in the ceilings of two Appalachian coal mines. Wet sieving produced narrow size cuts. The particles were determined to be oblong or blocky in shape, with average length-to-width ratio of 1.7 and sphericity of 0.78. They were analogous in shape to a square ended, rectangular "house brick". The two bituminous coals and different size cuts of each coal had essentially the same shape parameters. Characteristic heating times and terminal velocities were higher by 22 and …

Entropy Generation Method To Quantify Thermal Comfort, S. C. Boregowda, S. N. Tiwari, S. K. Chaturvedi

Mechanical & Aerospace Engineering Faculty Publications

The present paper presents a thermodynamic approach to assess the quality of human-thermal environment interaction and quantify thermal comfort. The approach involves development of entropy generation term by applying second law of thermodynamics to the combined human-environment system. The entropy generation term combines both human thermal physiological responses and thermal environmental variables to provide an objective measure of thermal comfort. The original concepts and definitions form the basis for establishing the mathematical relationship between thermal comfort and entropy generation term. As a result of logic and deterministic approach, an Objective Thermal Comfort Index (OTCI) is defined and established as a …