Physical Sciences and Mathematics Commons^™

Applications Of Parallel Discrete Event Simulation, Erik J. Jensen

Modeling, Simulation and Visualization Student Capstone Conference

This work presents three applications of parallel discrete event simulation (PDES), which describe the motivation for and the benefits of using PDES, the kinds of synchronization algorithms that are used, and scaling behavior with these different synchronization algorithms.

Deapsecure Computational Training For Cybersecurity: Third-Year Improvements And Impacts, Bahador Dodge, Jacob Strother, Rosby Asiamah, Karina Arcaute, Wirawan Purwanto, Masha Sosonkina, Hongyi Wu

Modeling, Simulation and Visualization Student Capstone Conference

The Data-Enabled Advanced Training Program for Cybersecurity Research and Education (DeapSECURE) was introduced in 2018 as a non-degree training consisting of six modules covering a broad range of cyberinfrastructure techniques, including high performance computing, big data, machine learning and advanced cryptography, aimed at reducing the gap between current cybersecurity curricula and requirements needed for advanced research and industrial projects. By its third year, DeapSECURE, like many other educational endeavors, experienced abrupt changes brought by the COVID-19 pandemic. The training had to be retooled to adapt to fully online delivery. Hands-on activities were reformatted to accommodate self-paced learning. In this paper ...

Medical Devices And Cybersecurity, Hilary Finch

School of Cybersecurity Posters

I begin by looking at the role of cybersecurity in the medical world. The healthcare industry adopted information technology quite quickly. While the advancement was obviously beneficial and necessary to keep up with an ever-growing demand, the healthcare industry did not place any kind of pointed focus on the security of their IT department, or the sensitive information housed therein.

When rapid advancements of technology outpaced the gradual advancement of hospital cybersecurity, security concerns became a difficult issue to control. There is a serious need for more advancements in hospital security. Each interconnected medical device has its own unique security ...

Clostridioides Difficile Spore Production In Response To Antibiotic And Immune Stress, Adenrele Oludiran, Erin B. Purcell

College of Sciences Posters

Clostridioides (Clostridium) difficile, an anaerobic, spore-forming Gram-positive pathogenic bacterium, is a major cause of hospital-acquired infections and can persist as surface-attached biofilms for protection from antibiotic and immune stress. C. difficile can form biofilms as a single species or with other anaerobic intestinal bacteria. The environmental signals that cause individual cells to secrete toxins, form biofilms, or develop into spores that can spread the infection to new patients are unknown. In these studies, we investigate bacterial responses to different stress. Antimicrobial host-defense peptides (HDPs) produced by animal immune systems are promising candidates to develop novel therapies for bacterial infection because ...

Physics-Informed Neural Networks (Pinns) For Dvcs Cross Sections, Manal Almaeen, Jake Grigsby, Joshua Hoskins, Brandon Kriesten, Yaohang Li, Huey-Wen Lin, Simonetta Liuti, Sorawich Maichum

College of Sciences Posters

We present a physics informed deep learning technique for Deeply Virtual Compton Scattering (DVCS) cross sections from an unpolarized proton target using both an unpolarized and polarized electron beam. Training a deep learning model typically requires a large size of data that might not always be available or possible to obtain. Alternatively, a deep learning model can be trained using additional knowledge gained by enforcing some physics constraints such as angular symmetries for better accuracy and generalization. By incorporating physics knowledge to our deep learning model, our framework shows precise predictions on the DVCS cross sections and better extrapolation on ...

Lattice Optics Optimization For Recirculatory Energy Recovery Linacs With Multi-Objective Optimization, Isurumali Neththikumara, Todd Satogata, Alex Bogacz, Ryan Bodenstein, Arthur Vandenhoeke

College of Sciences Posters

Beamline optics design for recirculatory linear accelerators requires special attention to suppress beam instabilities arising due to collective effects. The impact of these collective effects becomes more pronounced with the addition of energy recovery (ER) capability. Jefferson Lab’s multi-pass, multi-GeV ER proposal for the CEBAF accelerator, ER@CEBAF, is a 10- pass ER demonstration with low beam current. Tighter control of the beam parameters at lower energies is necessary to avoid beam break-up (BBU) instabilities, even with a small beam current. Optics optimizations require balancing both beta excursions at high-energy passes and overfocusing at low-energy passes. Here, we discuss ...

A Spatially And Temporally Second Order Method For Solving Parabolic Interface Problems, Kumudu Gamage, Yan Peng

College of Sciences Posters

Parabolic interface problems have many applications in physics and biology, such as hyperthermia treatment of cancer, underground water flow, and food engineering. Here we present an algorithm for solving two-dimensional parabolic interface problems where the coefficient and the forcing term have a discontinuity across the interface. The Crank-Nicolson scheme is used for time discretization, and the direct immersed interface method is used for spatial discretization. The proposed method is second order in both space and time for both solution and gradients in maximum norm.

Active Polar Liquid Crystal Channel Flows: Analyzing The Roles Of Nematic Strength And Activation Parameter, Lacey Schenk, Ruhai Zhou

College of Sciences Posters

Suspensions of active polar liquid crystalline polymers (APLC) exhibit complex phenomena such as spontaneous flows, pattern formations and defects. Using the Kinetic Model, which couples the Smoluchowski Equation and the Navier-Stokes Equations, we conduct numerical simulations of APLC in a microfluidic channel to investigate the competitive effect among different material constants, such as the nematic concentration (the strength of the potential for nematic order) and active strength (the individual nano-rods strength of their individual movement) with and without a pressure gradient. Both Dirichlet and Neumann boundary conditions on the mathematical model are employed. Steady states, including isotropic and nematic states ...

Empirically Adjusted Weighted Ordered P-Values Method, Wimarsha Jayanetti, Sinjini Sikdar, N. Rao Chaganty

College of Sciences Posters

Recent advancements in high-throughput technologies have enabled simultaneous inference of thousands of genes. With the abundance of public databases, it is now possible to rapidly access the results of several genomic studies, each of which includes the significance testing results of a large number of genes. Researchers frequently aggregate genomic data from multiple studies in the form of a meta-analysis. Most traditional meta-analysis methods aim at combining summary results to find signals in at least one of the studies. However, often the goal is to identify genes that are differentially expressed in a consistent pattern across multiple studies. Recently, a ...

A Machine Learning Approach To Denoising Particle Detector Observations In Nuclear Physics, Polykarpos Thomadakis, Angelos Angelopoulos, Gagik Gavalian, Nikos Chrisochoides

College of Sciences Posters

With the evolution in detector technologies and electronic components used in the Nuclear Physics field, experimental setups become larger and more complex. Faster electronics enable particle accelerator experiments to run with higher beam intensity, providing more interactions per time and more particles per interaction. However, the increased beam intensities present a challenge to particle detectors because of the higher amount of noise and uncorrelated signals. Higher noise levels lead to a more challenging particle reconstruction process by increasing the number of combinatorics to analyze and background signals to eliminate. On the other hand, increasing the beam intensity can provide physics ...

Analysis Of An Existing Method In Refinement Of Protein Structure Predictions Using Cryo-Em Images, Maytha Alshammari, Jing He, Willy Wriggers, Jiangwen Sun

College of Sciences Posters

Protein structure prediction produces atomic models from its amino acid sequence. Three-dimensional structures are important for understanding the function mechanism of proteins. Knowing the structure of a given protein is crucial in drug development design of novel enzymes. AlphaFold2 is a protein structure prediction tool with good performance in recent CASP competitions. Phenix is a tool for determination of a protein structure from a high-resolution 3D molecular image. Recent development of Phenix shows that it is capable to refine predicted models from AlphaFold2, specifically the poorly predicted regions, by incorporating information from the 3D image of the protein. The goal ...

Circulation, Volume 27, No. 2, Center For Coastal Physical Oceanography, Old Dominion University

CCPO Circulation

Spring 2022 issue of CCPO Circulation featuring the article "Looking Back While Moving Forward," by Sönke Dangendorf.

A Super Fast Algorithm For Estimating Sample Entropy, Weifeng Liu, Ying Jiang, Yuesheng Xu

Mathematics & Statistics Faculty Publications

: Sample entropy, an approximation of the Kolmogorov entropy, was proposed to characterize complexity of a time series, which is essentially defined as − log(B/A), where B denotes the number of matched template pairs with length m and A denotes the number of matched template pairs with m + 1, for a predetermined positive integer m. It has been widely used to analyze physiological signals. As computing sample entropy is time consuming, the box-assisted, bucket-assisted, x-sort, assisted sliding box, and kd-tree-based algorithms were proposed to accelerate its computation. These algorithms require O(N²) or O(N²⁻ 1/m+1 ...

The Influence Of Particle Concentration And Bulk Characteristics On Polarized Oceanographic Lidar Measurements, Brian L. Collister, Richard C. Zimmerman, Charles I. Sukenik, William M. Balch, Victoria J. Hill

OES Faculty Publications

Oceanographic lidar measurements of the linear depolarization ratio, δ, contain information on the bulk characteristics of marine particles that could improve our ability to study ocean biogeochemistry. However, a scarcity of information on the polarized light-scattering properties of marine particles and the lack of a framework for separating single and multiple scattering effects on δ have hindered the development of polarization-based retrievals of bulk particle properties. To address these knowledge gaps, we made single scattering measurements of δ for several compositionally and morphologically distinct marine particle assemblages. We then used a bio-optical model to explore the influence of multiple scattering ...

Empirically Derived Thermal Thresholds Of Four Coral Species Along The Red Sea Using A Portable And Standardized Experimental Approach, Nicolas R. Evensen, Christian R. Voolstra, Maoz Fine, Gabriela Perna, Carol Buitrago-López, Anny Cárdenas, Guilhem Banc-Prandi, Katherine Rowe, Daniel J. Barshis

Biological Sciences Faculty Publications

Global warming is causing an unprecedented loss of species and habitats worldwide. This is particularly apparent for tropical coral reefs, with an increasing number of reefs experiencing mass bleaching and mortality on an annual basis. As such, there is a growing need for a standardized experimental approach to rapidly assess the thermal limits of corals and predict the survival of coral species across reefs and regions. Using a portable experimental system, the Coral Bleaching Automated Stress System (CBASS), we conducted standardized 18 h acute thermal stress assays to quantitively determine the upper thermal limits of four coral species across the ...

Diabetic Foot Exam System, Stephanie Trusty

Undergraduate Research Symposium

The diabetic foot exam system aims to perform certain aspects of the dermatological and musculoskeletal assessments that are typical to a 3-minute diabetic foot exam. Utilizing the RaspberryPi computer and camera module, the system seeks to capture a series of images of the patient’s foot. It then evaluates these images for calluses, blisters, and three types of deformities: claw toe deformities, hammertoe deformities, and bunions. This evaluation is performed using a trained TensorFlow image classification model, which categorizes the image as a callus, blister, or deformity. The system was tested using six different images: four callus images, a hammertoe ...

Covid-19 Classroom Occupancy Detection System, Stephanie Trusty

Undergraduate Research Symposium

The classroom occupancy detection system aims to limit the spread of COVID-19 and support mitigation efforts advised by national and international health organizations by enforcing social distancing in classroom environments. Utilizing the RaspberryPi computer and its compatible camera module, the system accomplishes this by capturing an overhead image of a classroom and assessing the image for violations. Here, violations are defined as the presence of adjacent occupied seats. As such, for an acceptable state to be detected, there must be at least one vacant seat between all students seated in the classroom. The system communicates the classroom’s state with ...

Access To Nitrogen Heterocycles Via Borrowing Hydrogen Catalysis, Robert P. Reynolds, Kellen P. Mcguire, Conor T. Mccormick, Kyle M. Lambert

Undergraduate Research Symposium

Nitrogen heterocycles are ubiquitous motifs which occur as the core structure of several alkaloid natural products exhibiting inherent biological activity against an array of bacteria, fungi, viruses, and cancer cell lines. These azacycles serve as key synthetic building blocks for medicinal chemists to access more structurally complex and diverse compounds with tunable biological properties. A synthetic approach to these valuable motifs employing intramolecular borrowing hydrogen catalysis has been developed. The utility of the developed chemistry will be applied to synthetic efforts towards the recently isolated Cylicomorphins A-E.

Two-Stage Transfer Learning For Facial Expression Classification In Children, Gregory Hubbard, Megan Witherow, Khan Iftekharuddin

Undergraduate Research Symposium

Studying facial expressions can provide insight into the development of social skills in children and provide support to individuals with developmental disorders. In afflicted individuals, such as children with Autism Spectrum Disorder (ASD), atypical interpretations of facial expressions are well-documented. In computer vision, many popular and state-of-the-art deep learning architectures (VGG16, EfficientNet, ResNet, etc.) are readily available with pre-trained weights for general object recognition. Transfer learning utilizes these pre-trained models to improve generalization on a new task. In this project, transfer learning is implemented to leverage the pretrained model (general object recognition) on facial expression classification. Though this method, the ...

Objective Measure Of Working Memory Capacity Using Eye Movements, James Owens, Gavindya Jayawardena, Yasasi Abeysinghe, Vikas G. Ashok, Sampath Jayarathna

Undergraduate Research Symposium

Human-autonomy teaming (HAT) has become an important area of research due to the autonomous systems being developed for different applications, such as remotely controlled aircraft. Many remotely controlled vehicles will be controlled by automated systems, with a human monitor that may be monitoring multiple vehicles simultaneously. The attention and working memory capacity of operators of remote-controlled vehicles must be maintained at appropriate levels during operation. However, there is currently no direct method of determining working memory capacity, which is important because it is a measure for how memory is being stored for a short term and interacting with long term ...

Oxidation Of Thiols To Disulfides Using An Environmentally “Green” Organocatalyst And New Mechanistic Insights, Kosta V. Vlasakakis, Olivia M. White, Robert P. Reynolds, Shayne M. Weierbach, Shannon M. Weaver, Ramsey T. Ritter, Nishi H. Patel, Eric C. Hayes, Sydney Dunmire, Kyle M. Lambert

Undergraduate Research Symposium

The selective oxidation of thiols to disulfides is an area of great importance in the areas of materials and medicinal chemistry research. The production of polymers, rubber, pharmaceuticals, and the folding of proteins in biological systems all rely on the formation of disulfide bonds. Herein, we introduce a stoichiometric and electrocatalytic method for the oxidation of various pharmaceutically and biologically relevant thiols into their respective disulfides in more environmentally benign solvents such as water and alcohol solvents. The scope of the transformation was evaluated and a detailed mechanistic study involving control experiments, experimental kinetic studies, and computational investigations led to ...

Natural Phaeosphaeride A Derivatives Overcome Drug Resistance Of Tumor Cells And Modulate Signaling Pathways, Victoria Abzianidze, Natalia Moiseeva, Diana Suponina, Sofya Zakharenkova, Nadezhda Rogovskaya, Lidia Laletina, Alvin A. Holder, Denis Krivorotov, Alexander Bogachenkov, Alexander Garabadzhiu, Anton Ukolov, Vyacheslav Kosorukov

Chemistry & Biochemistry Faculty Publications

n the present study, natural phaeosphaeride A (PPA) derivatives are synthesized. Anti-tumor studies are carried out on the PC3, K562, HCT-116, THP-1, MCF-7, A549, NCI-H929, Jurkat, and RPMI8226 tumor cell lines, and on the human embryonic kidney (HEK293) cell line. All the compounds synthesized turned out to have better efficacy than PPA towards the tumor cell lines listed. Among them, three compounds exhibited an ability to overcome the drug resistance of tumor cells associated with the overexpression of the P-glycoprotein by modulating the work of this transporter. Luminex xMAP technology was used to assess the effect of five synthesized compounds ...

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 ...

Habitat Restoration Restores Underwater Soundscapes And Larval Recruitment, Jack Butler, Emily R. Anderson, Mark J. Butler

Biological Sciences Faculty Publications

Habitat degradation alters many ecosystem processes, and the potential for the reestablishment of ecosystem function through restoration is an area of active research. Among marine systems, coastal habitats are particularly vulnerable to anthropogenic degradation and, in response, are the focus of marine ecological restoration. One of the crucial functions of structurally complex coastal habitats (e.g., saltmarshes, seagrass meadows, kelp forests, coral reefs) are as nurseries to coastal and offshore species, many of whose larvae utilize sound to locate suitable nursery habitat. However, the effect of habitat degradation and subsequent restoration on underwater soundscapes and their function as navigational cues ...

A Laser Frequency Transverse Modulation Might Compensate For The Spectral Broadening Due To Large Electron Energy Spread In Thomson Sources, Vittoria Petrillo, Illya Drebot, Geoffrey Krafft, Cesare Maroli, Andrea R. Rossi, Marcello Rossetti Conti, Marcel Ruijter, Balša Terzić

Physics Faculty Publications

Compact laser plasma accelerators generate high-energy electron beams with increasing quality. When used in inverse Compton backscattering, however, the relatively large electron energy spread jeopardizes potential applications requiring small bandwidths. We present here a novel interaction scheme that allows us to compensate for the negative effects of the electron energy spread on the spectrum, by introducing a transverse spatial frequency modulation in the laser pulse. Such a laser chirp, together with a properly dispersed electron beam, can substantially reduce the broadening of the Compton bandwidth due to the electron energy spread. We show theoretical analysis and numerical simulations for hard ...

X17 Boson And The ³H(P, E⁺E⁻) ⁴He And ³He(N,E⁺E⁻) ⁴He Processes: A Theoretical Analysis, M. Viviani, E. Filandri, C. Gustavino, A. Kievsky, L. E. Marcucci, Rocco Schiavilla

Physics Faculty Publications

The present work deals with e⁺−e⁻ pair production in the four-nucleon system. We first analyze the process as a purely electromagnetic one in the context of a state-of-the-art approach to nuclear strong-interaction dynamics and nuclear electromagnetic currents, derived from chiral effective field theory (χEFT). Next, we examine how the exchange of a hypothetical low-mass boson would impact the cross section for such a process. We consider several possibilities, that this boson is either a scalar, pseudoscalar, vector, or axial particle. The ab initio calculations use exact hyperspherical-harmonics methods to describe the bound state and low-energy spectrum of the A ...

Formal Modeling And Verification Of A Blockchain-Based Crowdsourcing Consensus Protocol, Hamra Afzaal, Muhammad Imran, Muhammad Umar Janjua, Sarada Prasad Gochhayat

VMASC Publications

Crowdsourcing is an effective technique that allows humans to solve complex problems that are hard to accomplish by automated tools. Some significant challenges in crowdsourcing systems include avoiding security attacks, effective trust management, and ensuring the system’s correctness. Blockchain is a promising technology that can be efficiently exploited to address security and trust issues. The consensus protocol is a core component of a blockchain network through which all the blockchain peers achieve an agreement about the state of the distributed ledger. Therefore, its security, trustworthiness, and correctness have vital importance. This work proposes a Secure and Trustworthy Blockchain-based Crowdsourcing ...

Variability And Dynamics Of Along‐Shore Exchange On The West Antarctic Peninsula (Wap) Continental Shelf, Xin Wang, Carlos Moffat, Michael S. Dinniman, John M. Klinck, David A. Sutherland, Borja Aguiar-Gonzáles

CCPO Publications

The continental shelf of the West Antarctic Peninsula (WAP) is characterized by strong along-shore hydrographic gradients resulting from the distinct influences of the warm Bellingshausen Sea to the south and the cold Weddell Sea water flooding Bransfield Strait to the north. These gradients modulate the spatial structure of glacier retreat and are correlated with other physical and biochemical variability along the shelf, but their structure and dynamics remain poorly understood. Here, the magnitude, spatial structure, seasonal-to-interannual variability, and driving mechanisms of along-shore exchange are investigated using the output of a high-resolution numerical model and with hydrographic data collected in Palmer ...

Point Cloud-Based Mapper For Qcd Analysis, Tareq Alghamdi, Yasir Alanazi, Manal Almaeen, Nobuo Sato, Yaohang Li

The Graduate School Posters

In many scientific applications, Inverse problems are challenging. An inverse problem is the process of inferring unknown parameters from observable ones. In this poster, we present our prototype using Point Cloud-based Variational Autoencoder mapping. Data that connects parameters to detector level events is used to train the proposed model. A point cloud is used to describe a series of events that keeps the permutation invariant property and geometric correlations of the events while being flexible with the number of events in the input. The trained Point Cloud-based Variational Autoencoder functions as an effective inverse function from detector level events to ...

Experimental Study Of The Behavior Of The Bjorken Sum At Very Low Q², A. Deur, J. P. Chen, S. E. Kuhn, C. Peng, M. Ripani, V. Sulkosky, K. Adhikari, M. Battaglieri, V. D. Burkert, G. D. Cates, R. De Vita, G.E. Dodge, L. El Fassi, F. Garibaldi, H. Kang, M. Osipenko, J. T. Singh, K. Slifer, J. Zhang, X. Zheng

Physics Faculty Publications

We present new data on the Bjorken sum ^-Γ ^p-n₁ (Q²) at 4-momentum transfer 0.021 ≤ Q² ≤ 0.496 GeV². The data were obtained in two experiments performed at Jefferson Lab: EG4 on polarized protons and deuterons, and E97110 on polarized ³He from which neutron data were extracted. The data cover the domain where chiral effective field theory (χEFT), the leading effective theory of the Strong Force at large distances, is expected to be applicable. We find that our data and the predictions from χEFT are only in marginal agreement. This is somewhat ...