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Full-Text Articles in Physical Sciences and Mathematics

Draft Final Bpsou Insufficiently Reclaimed Sites Colorado Dump-West Lot Remedial Action Work Plan (Rawp), Pioneer Technical Services, Inc. Jul 2022

Draft Final Bpsou Insufficiently Reclaimed Sites Colorado Dump-West Lot Remedial Action Work Plan (Rawp), Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.


Environment And Sustainability: July 2022, Environment And Sustainability, Office Of The President Jul 2022

Environment And Sustainability: July 2022, Environment And Sustainability, Office Of The President

Environment and Sustainability

• UC Nairobi getting EDGE Advanced certified

• The President’s blog contemplates on our sustainability responsibility

• Donated electric bikes reduce emissions and local air pollution

• Impact of Earth Day and World Environment Day activities

• Related events from across the university.


Modeling Postfire Effects On Snow Albedo And Forest Recovery Over A Chronosequence Of Burned Forests In The Triple Divide Region Of The Rocky Mountains, Anton J. Surunis Jul 2022

Modeling Postfire Effects On Snow Albedo And Forest Recovery Over A Chronosequence Of Burned Forests In The Triple Divide Region Of The Rocky Mountains, Anton J. Surunis

Dissertations and Theses

Wildfires impact snow albedo, forest cover, and forest structure and thus snow melt rate and snowpack supply for as long as 15 years following burn. These effects have not been quantified at fine spatial resolutions and long time periods at a watershed scale. I modeled the effects of postfire effects on snow albedo, snow-mass energy balance, and resulting snow-water equivalent (SWE) depth over a long-time scale and at a fine spatial resolution. Using a spatially and temporally distributed snow evolution model called SnowModel, I modeled postfire effects on snow albedo and forest structure over postfire recovery within 8 forest fires …


Reconstructing Historical Earthquake-Induced Tsunamis: Case Study Of 1820 Event Near South Sulawesi, Indonesia, Taylor Jole Paskett Jul 2022

Reconstructing Historical Earthquake-Induced Tsunamis: Case Study Of 1820 Event Near South Sulawesi, Indonesia, Taylor Jole Paskett

Theses and Dissertations

We build on the method introduced by Ringer, et al., applying it to an 1820 event that happened near South Sulawesi, Indonesia. We utilize other statistical models to aid our Metropolis-Hastings sampler, including a Gaussian process which informs the prior. We apply the method to multiple possible fault zones to determine which fault is the most likely source of the earthquake and tsunami. After collecting nearly 80,000 samples, we find that between the two most likely fault zones, the Walanae fault zone matches the anecdotal accounts much better than Flores. However, to support the anecdotal data, both samplers tend toward …


Magnetic Resonance Systems Development For Point-Of-Care Mri Platforms, Eric J. Lessard Jul 2022

Magnetic Resonance Systems Development For Point-Of-Care Mri Platforms, Eric J. Lessard

Electronic Thesis and Dissertation Repository

Magnetic resonance imaging utilizes electromagnets to produce anatomical images in both clinical and research settings. In the race towards increasing performance head-optimized scanners have begun playing a significant role in providing high quality imaging of the head. However, they are implemented using smaller geometries and as such fail to allow entrance of the patient past their shoulders. This is overcome by designing asymmetric gradient coils which have their imaging region located towards one end of the gradient coil, as opposed to the geometric center, allowing brain imaging. There exists interest in compact configurations which allow imaging further into the cervical …


Design And Synthesis Of Nef:Sfk Interaction Inhibitors For Application In An Immune-Directed Hiv-1 Cure, Antony Lurie Jul 2022

Design And Synthesis Of Nef:Sfk Interaction Inhibitors For Application In An Immune-Directed Hiv-1 Cure, Antony Lurie

Electronic Thesis and Dissertation Repository

The human immunodeficiency virus type 1 (HIV-1) protein, Nef, binds and activates Src family kinases (SFKs) to reduce cell surface levels of major histocompatibility complex class I (MHC-I), thereby facilitating cytotoxic T lymphocyte (CTL) evasion. Importantly, Nef-mediated CTL evasion compromises the success of immune-directed curative approaches, underscoring Nef:SFK interaction inhibitors as promising adjuvants in an immune-directed cure. Previously, our group identified a dipeptide derivative (H3-1) which inhibits the Nef:SFK interaction and MHC-I downregulation in vitro, but is unstable in vivo. I hypothesized that H3-1’s instability is due to its proteolysis and have generated peptidomimetic analogues of H3-1 which …


Commutative C*-Algebras Generated By Toeplitz Operators On The Fock Space, Vishwa Nirmika Dewage Jul 2022

Commutative C*-Algebras Generated By Toeplitz Operators On The Fock Space, Vishwa Nirmika Dewage

LSU Doctoral Dissertations

The Fock space $\mathcal{F}(\mathbb{C}^n)$ is the space of holomorphic functions on $\mathbb{C}^n$ that are square-integrable with respect to the Gaussian measure on $\mathbb{C}^n$. This space plays an essential role in several subfields of analysis and representation theory. In particular, it has for a long time been a model to study Toeplitz operators. Grudsky and Vasilevski showed in 2002 that radial Toeplitz operators on $\mathcal{F}(\mathbb{C})$ generate a commutative $C^*$-algebra $\mathcal{T}^G$, while Esmeral and Maximenko showed that $C^*$-algebra $\mathcal{T}^G$ is isometrically isomorphic to the $C^*$-algebra $C_{b,u}(\mathbb{N}_0,\rho_1)$. In this thesis, we extend the result to $k$-quasi-radial symbols acting on the Fock space $\mathcal{F}(\mathbb{C}^n)$. …


Assessment Of 3d Mesh Watermarking Techniques, Neha Sharma, Jeebananda Panda Jul 2022

Assessment Of 3d Mesh Watermarking Techniques, Neha Sharma, Jeebananda Panda

Journal of Digital Forensics, Security and Law

With the increasing usage of three-dimensional meshes in Computer-Aided Design (CAD), medical imaging, and entertainment fields like virtual reality, etc., the authentication problems and awareness of intellectual property protection have risen since the last decade. Numerous watermarking schemes have been suggested to protect ownership and prevent the threat of data piracy. This paper begins with the potential difficulties that arose when dealing with three-dimension entities in comparison to two-dimensional entities and also lists possible algorithms suggested hitherto and their comprehensive analysis. Attacks, also play a crucial role in deciding a watermarking algorithm so an attack based analysis is also presented …


Experimental Investigation Of The Physical Properties Of Irmsnn (M = 1, 3 And N = 2, 4, 7), Smita Speer Jul 2022

Experimental Investigation Of The Physical Properties Of Irmsnn (M = 1, 3 And N = 2, 4, 7), Smita Speer

LSU Doctoral Dissertations

Exploration of transition metal stannides, formed from a combination of transition metals (T) and Sn, has resulted in the discovery a variety of materials with interesting physical properties, which is in part due to the complexity of interactions that can occur between the T-d orbitals and Sn-p orbitals. There have been observations of (extremely) large magnetoresistance [1-4], topological flat and nearly flat bands [5-7], superconducting behavior in 2D and 3D systems [5, 8-11], ultrahigh carrier mobility [12-13], and more attributed to d-p orbital mixing in such systems. This dissertation will address the effects of T-Sn interactions …


On A Relation Between Ado And Links-Gould Invariants, Nurdin Takenov Jul 2022

On A Relation Between Ado And Links-Gould Invariants, Nurdin Takenov

LSU Doctoral Dissertations

In this thesis we consider two knot invariants: Akutsu-Deguchi-Ohtsuki(ADO) invariant and Links-Gould invariant. They both are based on Reshetikhin-Turaev construction and as such share a lot of similarities. Moreover, they are both related to the Alexander polynomial and may be considered generalizations of it. By experimentation we found that for many knots, the third order ADO invariant is a specialization of the Links-Gould invariant. The main result of the thesis is a proof of this relation for a large class of knots, specifically closures of braids with five strands.


Learning From Machines: Insights In Forest Transpiration Using Machine Learning Methods, Morgan Tholl Jul 2022

Learning From Machines: Insights In Forest Transpiration Using Machine Learning Methods, Morgan Tholl

Dissertations and Theses

Machine learning has been used as a tool to model transpiration for individual sites, but few models are capable of generalizing to new locations without calibration to site data. Using the global SAPFLUXNET database, 95 tree sap flow data sites were grouped using three clustering strategies: by biome, by tree functional type, and through use of a k-means unsupervised clustering algorithm. Two supervised machine learning algorithms, a random forest algorithm and a neural network algorithm, were used to build machine learning models that predicted transpiration for each cluster. The performance and feature importance in each model were analyzed and compared …


Control And Planning For Mobile Manipulators Used In Large Scale Manufacturing Processes, Joshua T. Nguyen Jul 2022

Control And Planning For Mobile Manipulators Used In Large Scale Manufacturing Processes, Joshua T. Nguyen

LSU Master's Theses

Sanding operations in industry is one of the few manufacturing tasks that has yet to achieve automation. Sanding tasks require skilled operators that have developed a sense of when a work piece is sufficiently sanded. In order to achieve automation in sanding with robotic systems, this developed sense, or intelligence, that human operators have needs to be understood and implemented in order to achieve, at the minimum, the same quality of work. The system will also need to have the equivalent reach of a human operator and not be constrained to a single, small workspace. This thesis developed solutions for …


Sulfuric Acid Speleogenesis And Surface Landform Evolution Along The Vienna Basin Transfer Fault: Plavecký Karst, Slovakia, Pavel Bella, Helena Hercman, Šimon Kdýr, Petr Mikysek, Petr Pruner, Juraj Littva, Jozef Minár, Michal Gradzinski, Wojciech Wróblewski, Marek Velšmid, Pavel Bosak Jul 2022

Sulfuric Acid Speleogenesis And Surface Landform Evolution Along The Vienna Basin Transfer Fault: Plavecký Karst, Slovakia, Pavel Bella, Helena Hercman, Šimon Kdýr, Petr Mikysek, Petr Pruner, Juraj Littva, Jozef Minár, Michal Gradzinski, Wojciech Wróblewski, Marek Velšmid, Pavel Bosak

International Journal of Speleology

Hypogene caves in the Plavecký hradný vrch Hill (Western Slovakia, Central Europe) were formed by waters ascending along faults in fractured Triassic carbonates related to the horst-graben structure at the contact of the Malé Karpaty Mountains and the NE part of the Vienna Basin. The Plavecká jaskyňa and Pec caves mostly contain horizontal passages and chambers with flat corrosion bedrock floors, fissure discharge feeders, wall water-table notches, replacement pockets, as well as a few other speleogens associated with sulfuric acid speleogenesis. The low-temperature sulfuric acid development phases of the Plavecká Jaskyňa are also indicated by the presence of sulfate minerals …


Reference Database Of Teeth Images From The Family Bovidae, Juliet K. Brophy, Gregory J. Matthews Jul 2022

Reference Database Of Teeth Images From The Family Bovidae, Juliet K. Brophy, Gregory J. Matthews

Mathematics and Statistics: Faculty Publications and Other Works

Researchers typically rely on fossils from the Family Bovidae to generate African paleoenvironmental reconstructions due to their strict ecological tendencies. Bovids have dominated the southern African fauna for the past four million years and, therefore, dominate the fossil faunal assemblages, especially isolated teeth. Traditionally, researchers reference modern and fossil comparative collections to identify teeth. However, researchers are limited by the specific type and number of bovids at each institution. B.O.V.I.D. (Bovidae Occlusal Visual IDentification) is a repository of images of the occlusal surface of bovid teeth. The dataset currently includes extant bovids from 7 tribes and 20 species (~3900). B.O.V.I.D. …


Control Implemented On Quantum Computers: Effects Of Noise, Nondeterminism, And Entanglement, Kip Nieman, Keshav Kasturi Rangan, Helen Durand Jul 2022

Control Implemented On Quantum Computers: Effects Of Noise, Nondeterminism, And Entanglement, Kip Nieman, Keshav Kasturi Rangan, Helen Durand

Chemical Engineering and Materials Science Faculty Research Publications

Quantum computing has advanced in recent years to the point that there are now some quantum computers and quantum simulators available to the public for use. In addition, quantum computing is beginning to receive attention within the process systems engineering community for directions such as machine learning and optimization. A logical next step for its evaluation within process systems engineering is for control, specifically for computing control actions to be applied to process systems. In this work, we provide some initial studies regarding the implementation of control on quantum computers, including the implementation of a single-input/single-output proportional control law on …


Improving The Factual Accuracy Of Abstractive Clinical Text Summarization Using Multi-Objective Optimization, Amanuel Alambo, Tanvi Banerjee, Krishnaprasad Thirunarayan, Mia Cajita Jul 2022

Improving The Factual Accuracy Of Abstractive Clinical Text Summarization Using Multi-Objective Optimization, Amanuel Alambo, Tanvi Banerjee, Krishnaprasad Thirunarayan, Mia Cajita

Computer Science and Engineering Faculty Publications

While there has been recent progress in abstractive summarization as applied to different domains including news articles, scientific articles, and blog posts, the application of these techniques to clinical text summarization has been limited. This is primarily due to the lack of large-scale training data and the messy/unstructured nature of clinical notes as opposed to other domains where massive training data come in structured or semi -structured form. Further, one of the least explored and critical components of clinical text summarization is factual accuracy of clinical summaries. This is specifically crucial in the healthcare domain, cardiology in particular, where an …


Dual Isotopic (O & N) Approach In The Assessment Of No3- Pollution In An Urban River, Abongwa T. Pride, Walter Den, Aarin Teague Jul 2022

Dual Isotopic (O & N) Approach In The Assessment Of No3- Pollution In An Urban River, Abongwa T. Pride, Walter Den, Aarin Teague

Water Resources Science and Technology Faculty Publications

Deterioration of urban waterways has become a major environmental concern as management and recreational goals are often hampered by poor water quality. The San Antonio River (TX, USA), whose upper reaches, including its headwaters, pass through a highly urbanized community, is vulnerable to pollution from a myriad of anthropogenic activities within its initial 17-km stretch. This investigation applied a dual-isotope approach to characterize water samples collected during the wet season (May–June, 2019) in order to assess the potential sources of nitrate in the urban stretch of river. The δ15N-NO3 and δ18O-NO3 values ranged from …


Neutron Interferometry Using A Single Modulated Phase Grating, Ivan J. Hidrovo Giler Jul 2022

Neutron Interferometry Using A Single Modulated Phase Grating, Ivan J. Hidrovo Giler

LSU Master's Theses

Neutron grating interferometry provides information on phase and small-angle scatter in addition to attenuation. Previously, phase grating moiré interferometers (PGMI) with two or three phase gratings have been developed. These phase-grating systems use the moiré far-field technique to avoid the need for high-aspect absorption gratings used in Talbot-Lau interferometers (TLI) which reduce the neutron flux reaching the detector. We demonstrate through simulations a novel phase grating interferometer system for cold neutrons that requires a single modulated phase grating (MPG) for phase-contrast imaging, as opposed to the two or three phase gratings in previously employed PGMI systems. We compare the MPG …


Local And State Climate Initiatives In Louisiana Since 2005: Content And Thematic Analyses, Jessie F. Parrott Jul 2022

Local And State Climate Initiatives In Louisiana Since 2005: Content And Thematic Analyses, Jessie F. Parrott

LSU Master's Theses

Louisiana is uniquely exposed to severe weather because of its geography and climate. Louisiana’s extreme weather is exacerbated by anthropogenic climate change, which will worsen in the future. The risks its population and environment are exposed to has generated several policies and planning documents, nine of which are analyzed in this thesis. Three plans are from the state level, three are from the parish level, and three are from the urban (New Orleans) level. These planning documents pose various adaptation and mitigation actions to ameliorate and address multiple climate issues. These actions utilize specific mitigation strategies. The content and thematic …


Impact Of Oil And A Tropical Cyclone On An Omnivore And Herbivore Population In Salt Marshes Of Louisiana, Hannah K. Gordon Jul 2022

Impact Of Oil And A Tropical Cyclone On An Omnivore And Herbivore Population In Salt Marshes Of Louisiana, Hannah K. Gordon

LSU Master's Theses

Terrestrial arthropods are the ideal ecological indicators for the health of a salt marsh. Salt marshes are under extreme continuous stressors including climate change, land loss, oil spills, and tropical cyclones. Such stressors impact trophic and species level interactions, food resources, dispersal and population size of insects. In the present study, we collected terrestrial arthropods from eleven sites around Barataria Bay, five sites were oiled and five sites were unoiled, to determine the impact of the redistribution of oil from the Deepwater Horizon oil spill. Site C6 was excluded from the oiled and unoiled data because it was in close …


Fairness In Information Access Systems, Michael D. Ekstrand, Anubrata Das, Robin Burke, Fernando Diaz Jul 2022

Fairness In Information Access Systems, Michael D. Ekstrand, Anubrata Das, Robin Burke, Fernando Diaz

Computer Science Faculty Publications and Presentations

Recommendation, information retrieval, and other information access systems pose unique challenges for investigating and applying the fairness and non-discrimination concepts that have been developed for studying other machine learning systems. While fair information access shares many commonalities with fair classification, there are important differences: the multistakeholder nature of information access applications, the rank-based problem setting, the centrality of personalization in many cases, and the role of user response all complicate the problem of identifying precisely what types and operationalizations of fairness may be relevant.

In this monograph, we present a taxonomy of the various dimensions of fair information access and …


Relating Plant Community Structure To Carbon Dynamics In Semiarid Grasslands, Theodore D. Roper Jul 2022

Relating Plant Community Structure To Carbon Dynamics In Semiarid Grasslands, Theodore D. Roper

Biology ETDs

Understanding how fine-scale changes in soil characteristics and plant community composition affect ecosystem functioning is key to predicting how biome shifts will affect regional and global carbon cycling. This is crucial in the dryland biomes of the US Southwest, projected to be one of the regions most affected by climate change. We examined fine-scale drivers of ecosystem function within two biomes – a Chihuahuan Desert grassland and Plains/Chihuahuan Desert ecotone – via long-term vegetation data, micrometeorological data, eddy covariance carbon flux measurements, and soil water and texture, finding that the ecotone site had over 30% higher soil water content, over …


To License Or Not To License Reexamined: An Updated Report On Licensing Of Digital Examiners Under State Private Investigator Statutes, Thomas Lonardo, Alan Rea, Doug White Jul 2022

To License Or Not To License Reexamined: An Updated Report On Licensing Of Digital Examiners Under State Private Investigator Statutes, Thomas Lonardo, Alan Rea, Doug White

Journal of Digital Forensics, Security and Law

In this update to the 2015 study, the authors examine US state statutes and regulations relating to licensing and enforcement of Digital Examiner functions under each state’s private investigator/detective statute. As with the prior studies, the authors find that very few state statutes explicitly distinguish between Private Investigators (PI) and Digital Examiners (DE), and when they do, they either explicitly require a license or exempt them from the licensing statute. As noted in the previous 2015 study there is a minor trend in which some states are moving to exempt DE from PI licensing requirements. We examine this trend as …


Climate Change And Weather Extremes In The Eastern Mediterranean And Middle East, G. Zittis, M. Almazroui, P. Alpert, P. Ciais, W. Cramer, Y. Dahdal, M. Fnais, D. Francis, P. Hadjinicolaou, F. Howari, A. Jrrar, D. G. Kaskaoutis, M. Kulmala, G. Lazoglou, N. Mihalopoulos, X. Lin, Y. Rudich, J. Sciare, G. Stenchikov, E. Xoplaki, J. Lelieveld Jul 2022

Climate Change And Weather Extremes In The Eastern Mediterranean And Middle East, G. Zittis, M. Almazroui, P. Alpert, P. Ciais, W. Cramer, Y. Dahdal, M. Fnais, D. Francis, P. Hadjinicolaou, F. Howari, A. Jrrar, D. G. Kaskaoutis, M. Kulmala, G. Lazoglou, N. Mihalopoulos, X. Lin, Y. Rudich, J. Sciare, G. Stenchikov, E. Xoplaki, J. Lelieveld

All Works

Observation‐based and modeling studies have identified the Eastern Mediterranean and Middle East (EMME) region as a prominent climate change hotspot. While several initiatives have addressed the impacts of climate change in parts of the EMME, here we present an updated assessment, covering a wide range of timescales, phenomena and future pathways. Our assessment is based on a revised analysis of recent observations and projections and an extensive overview of the recent scientific literature on the causes and effects of regional climate change. Greenhouse gas emissions in the EMME are growing rapidly, surpassing those of the European Union, hence contributing significantly …


The Impact Of Human Activity On Coastal Zones With Elise Granek, Elise F. Granek Jul 2022

The Impact Of Human Activity On Coastal Zones With Elise Granek, Elise F. Granek

PDXPLORES Podcast

In this episode of PDXPLORES, Professor Elise Granek discusses the coastal zone- transition zones between land, sea, and atmosphere. These ecosystems provide vital ecological, cultural, and commercial benefits. Around the world, they are home to a vast number of species, support critical industries, and sustain the cultural heritage of the people who have called them home. As with all ecosystems, they are vulnerable. Given the intense human dependence on the continued viability of these coastal ecosystems, understanding the impact of human activity on the species that inhabit them is essential to identifying solutions to address the suite of impacts. What …


Prediction Of Cultivation Areas For The Commercial And An Early Flowering Wild Accession Of Salvia Hispanica L. In The United States, Mohammad Hassani, Thomas Piechota, Hagop S. Atamian Jul 2022

Prediction Of Cultivation Areas For The Commercial And An Early Flowering Wild Accession Of Salvia Hispanica L. In The United States, Mohammad Hassani, Thomas Piechota, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Salvia hispanica L., commonly known as chia, is a plant-based alternative to seafood and is rich in heart-healthy omega-3 fatty acid, protein, fiber, and antioxidants. In the Northern Hemisphere, chia flowering is triggered by the fall equinox (12-h light and dark, early October) and the seeds mature after approximately three months. Chia is sensitive to frost and end of season moisture which limits its cultivation to small areas in regions with temperate climate. The U.S. chia import has increased considerably over the years; however, chia is not widely cultivated in the United States. This study used the historical U.S. temperature …


A Closed Form Formula For The Stochastic Exponential Of A Matrix-Valued Semimartingale, Peter Kern, Christian Müller Jul 2022

A Closed Form Formula For The Stochastic Exponential Of A Matrix-Valued Semimartingale, Peter Kern, Christian Müller

Journal of Stochastic Analysis

No abstract provided.


Science Of The Total Environment, Benjamin Linhoff Jul 2022

Science Of The Total Environment, Benjamin Linhoff

United States Geological Survey: Staff Publications

Recently, the subsoils of ephemeral stream(arroyos) floodplains in the northern Chihuahuan Desert were discovered to contain large naturally occurring NO3 reservoirs (floodplain:~38,000 kg NO3-N/ha; background:~60 kg NO3-N/ha). These reservoirs may be mobilized through land use change or natural stream channel migration which makes differentiating between anthropogenic and natural groundwaterNO3sources challenging. In this study, the fate and sources of NO3 were investigated in an area with multiple NO3 sources such as accidental sewer line releases and sewage lagoons aswell as natural reservoirs of subsoil NO3. …


The Message Design Of Raiders Of The Lost Ark On The Atari 2600 & A Fan’S Map, Quick Start, And Strategy Guide, Miguel Ramlatchan, William I. Ramlatchan Jul 2022

The Message Design Of Raiders Of The Lost Ark On The Atari 2600 & A Fan’S Map, Quick Start, And Strategy Guide, Miguel Ramlatchan, William I. Ramlatchan

Distance Learning Faculty & Staff Books

The message design and human performance technology in video games, especially early video games have always been fascinating to me. From an instructional design perspective, the capabilities of the technology of the classic game consoles required a careful balance of achievable objectives, cognitive task analysis, guided problem solving, and message design. Raiders on the Atari is an excellent example of this balance. It is an epic adventure game, spanning 13+ distinct areas, with an inventory of items, where those hard to find items had to be used by the player to solve problems during their quest (and who would have …


Integrating Conformational Dynamics And Perturbation-Based Network Modeling For Mutational Profiling Of Binding And Allostery In The Sars-Cov-2 Spike Variant Complexes With Antibodies: Balancing Local And Global Determinants Of Mutational Escape Mechanisms, Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan Jul 2022

Integrating Conformational Dynamics And Perturbation-Based Network Modeling For Mutational Profiling Of Binding And Allostery In The Sars-Cov-2 Spike Variant Complexes With Antibodies: Balancing Local And Global Determinants Of Mutational Escape Mechanisms, Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan

Mathematics, Physics, and Computer Science Faculty Articles and Research

n this study, we combined all-atom MD simulations, the ensemble-based mutational scanning of protein stability and binding, and perturbation-based network profiling of allosteric interactions in the SARS-CoV-2 spike complexes with a panel of cross-reactive and ultra-potent single antibodies (B1-182.1 and A23-58.1) as well as antibody combinations (A19-61.1/B1-182.1 and A19-46.1/B1-182.1). Using this approach, we quantify the local and global effects of mutations in the complexes, identify protein stability centers, characterize binding energy hotspots, and predict the allosteric control points of long-range interactions and communications. Conformational dynamics and distance fluctuation analysis revealed the antibody-specific signatures of protein stability and flexibility of the …