Physical Sciences and Mathematics Commons^™

Structure, Dynamics, And Redox Reactivity Of An All-Purpose Flavodoxin, Sharique Khan, Ahmadullah Ansari, Monica Brachi, Debarati Das, Wassim El Housseini, Shelley Minteer, Anne Frances Miller

Chemistry Faculty Research & Creative Works

The Flavodoxin Of Rhodopseudomonas Palustris CGA009 (Rp9Fld) Supplies Highly Reducing Equivalents To Crucial Enzymes Such As Hydrogenase, Especially When The Organism Is Iron-Restricted. By Acquiring Those Electrons From Photodriven Electron Flow Via The Bifurcating Electron Transfer Flavoprotein, Rp9Fld Provides Solar Power To Vital Metabolic Processes. To Understand Rp9Fld's Ability To Work With Diverse Partners, We Solved Its Crystal Structure. We Observed The Canonical Flavodoxin (Fld) Fold And Features Common To Other Long-Chain Flds But Not All The Surface Loops Thought To Recognize Partner Proteins. Moreover, Some Of The Loops Display Alternative Structures And Dynamics. To Advance Studies Of Protein–protein Associations …

Quantum Chaos, Integrability, And Hydrodynamics In Nonequilibrium Quantum Matter, Javier Lopez Piqueres

Doctoral Dissertations

It is well-known that the Hilbert space of a quantum many-body system grows exponentially with the number of particles in the system. Drive the system out of equilibrium so that the degrees of freedom are now dynamic and the result is an extremely complicated problem. With that comes a vast landscape of new physics, which we are just recently starting to explore. In this proposal, we study the dynam- ics of two paradigmatic classes of quantum many-body systems: quantum chaotic and integrable systems. We leverage certain tools commonly employed in equilibrium many-body physics, as well as others tailored to the …

A Field-Programmable Metamaterial Using Memristor As A Stable Switcher, Taekuk Hong

Theses and Dissertations

Before the memristor was discovered, there were RLC circuits as representative passive devices. However, the fourth fundamental two-terminal circuit has been discovered by Dr. Leon Chua in 1971 and has been called a memristor. The memristor is a compound word of memory and resistor, and is an element whose resistive value is not constant and whose resistive value changes depending on the applied voltage and is recorded as a memory. It is mainly used in resistive switching and is the center of this research theme. A metamaterial is artificially created material that has never been found in nature. The theory …

Application Of Digital Twin Model In Grinding Of Bearing Rings, Hongbin Liu, Zhiqiang Shen, Yize Wang, Ming Qiu, Wenrong Lin

Journal of System Simulation

Abstract: The digital twin model can effectively promote the virtual-real interaction between the actual product and the product model. Aiming at the grinding force generated in the grinding process of spherical roller bearings, this paper constructs the bearing ring raceway grinding process by performing dynamics, contact algorithm modeling and rigid-flexible coupling treatment on the components of the grinding work area. The digital twin model completes the virtual mapping of the grinding work area of the bearing ring in the digital space. The model is used to analyze and test the process parameters such as the grinding wheel linear speed and …

The Reversible Low-Temperature Instability Of Human Dj-1 Oxidative States, Tessa Andrews, Javier Seravallic, Robert Powers

Robert Powers Publications

DJ-1 is a homodimeric protein that is centrally involved in various human diseases including Parkinson disease (PD). DJ-1 protects against oxidative damage and mitochondrial dysfunction through a homeostatic control of reactive oxygen species (ROS). DJ-1 pathology results from a loss of function, where ROS readily oxidizes a highly conserved and functionally essential cysteine (C106). The over-oxidation of DJ-1 C106 leads to a dynamically destabilized and biologically inactivated protein. An analysis of the structural stability of DJ-1 as a function of oxidative state and temperature may provide further insights into the role the protein plays in PD progression. NMR spectroscopy, circular …

Modeling The Spread Of Covid-19 In Spatio-Temporal Context, S.H. Sathish Indika, Norou Diawara, Hueiwang Anna Jeng, Bridget D. Giles, Dilini S.K. Gamage

Mathematics & Statistics Faculty Publications

This study aims to use data provided by the Virginia Department of Public Health to illustrate the changes in trends of the total cases in COVID-19 since they were first recorded in the state. Each of the 93 counties in the state has its COVID-19 dashboard to help inform decision makers and the public of spatial and temporal counts of total cases. Our analysis shows the differences in the relative spread between the counties and compares the evolution in time using Bayesian conditional autoregressive framework. The models are built under the Markov Chain Monte Carlo method and Moran spatial correlations. …

Rapidly Changing Range Limits In A Warming World: Critical Data Limitations And Knowledge Gaps For Advancing Understanding Of Mangrove Range Dynamics In The Southeastern Usa, Rémi Bardou, Michael J. Osland, Steven Scyphers, Christine Shepard, Karen E. Aerni, Jahson B. Alemu I, Robert Crimian, Richard H. Day, Nicholas M. Enwright, Laura C. Feher, Sarah L. Gibbs, Kiera O'Donnell, Savannah H. Swinea, Kalaina Thorne, Sarit Truskey, Anna R. Armitage, Ronald Baker, Josh L. Breithaupt, Kyle C. Cavanaugh, Erik S. Yando, A. Randall Hughes, Et Al.

Biological Sciences Faculty Publications

Climate change is altering species’ range limits and transforming ecosystems. For example, warming temperatures are leading to the range expansion of tropical, cold-sensitive species at the expense of their cold-tolerant counterparts. In some temperate and subtropical coastal wetlands, warming winters are enabling mangrove forest encroachment into salt marsh, which is a major regime shift that has significant ecological and societal ramifications. Here, we synthesized existing data and expert knowledge to assess the distribution of mangroves near rapidly changing range limits in the southeastern USA. We used expert elicitation to identify data limitations and highlight knowledge gaps for advancing understanding of …

Investigating The Dynamics And Fragmentation Of Nitroaromatic Radical Cations Through Femtosecond Time-Resolved Mass Spectrometry And Computational Chemistry, Hugo Andres Lopez Pena

Theses and Dissertations

Chemists have sought to control molecular dissociation with lasers for decades. Effective control of unimolecular dissociation was only achieved with the development of high-intensity ultrashort pulsed lasers and coherent control techniques that operate on timescales faster than vibrational energy redistribution. In view of this, our lab has specialized in the study of polyatomic radical cations using femtosecond time-resolved mass spectrometry (FTRMS). The interest in radical cations stems from the fact that they are highly reactive species that contribute to many physical, chemical, and biological processes. For instance, radical cations participate in shock initiation of detonated energetic materials used as explosives …

Impact Of Sample Conditions On Dna Phosphodiester Backbone Bi/Bii Conformational Equilibrium Dynamics, Autumn C. Pilarski

MSU Graduate Theses

DNA damage, such as single base lesions and mismatches, is highly prevalent within cells. If these DNA damage events are not repaired, they could lead to mutations and thus disease and cancer. Intricate repair mechanisms are in place to fix these damage events, one such being Base Excision Repair (BER) and associated enzyme: Thymine DNA Glycosylase (TDG). The first step of this repair process, recognition of the lesion by TDG, is not well understood. The following thesis presents results to better understand the fundamental biophysical question of how a DNA lesion within a mismatch context is recognized in a million …

The Exploration Of Small Molecules, Lanthanide Complexes, And Catalysis Using Electronic Structure Theory, Dynamics, And Machine Learning, Gavin Mccarver

Doctoral Dissertations

With the ever increasing availability of computational resources, more challenging chemical systems can be studied. Among these challenges are the rotational and vibrational spectra of diatomic molecules within spectroscopic accuracy, the environmental perturbations induced on a rotating water molecule, the prediction of free binding energies of lanthanide complexes using machine learning, and the study of catalytic mechanisms through a theoretical framework. High levels of electronic structure theory were combined with a rigorous treatment of either the anharmonic vibrational wave functions to study diatomic molecules or the rotational wave functions to study H₂O-pH₂ interactions. The former was initially …

An Entropic Approach To Dynamics, Pedro Henrique Moreira Pessoa

Legacy Theses & Dissertations (2009 - 2024)

The present thesis deals with different aspects of probability, the method of maximum entropy, information geometry, and dynamical systems and their applications to statistical physics and complex systems. Those topics come together in the framework for dynamics termed entropic dynamics. Work on the topic was initiated by my PhD advisor Professor Ariel Caticha and many colleagues at University at Albany as a method for explaining the dynamical processes in quantum mechanics from first principles of probability theory.

Stabilizing Controlled Systems In The Presence Of Time-Delays, Isaac Becker Pardo

Theses and Dissertations

A dynamical system's state evolves over time, and when the system stays near a particular state this state is known as a stable state of the system. Through control methods, dynamical systems can be manipulated such that virtually any state can be made stable. Although most real systems evolve continuously in time the application of digital control methods to these systems is inherently discrete. States are sampled (with sensors) and fed back into the system in discrete-time to determine the input needed to control the continuous system. Additionally, dynamical systems often experience time delays. Some examples of time delays are …

Concurrent Identification, Characterization, And Reconstruction Of Protein Structure And Mixed-Mode Dynamics From Rdc Data Using Redcraft, Hanin Rafiq Omar

Theses and Dissertations

A complete understanding of the structure-function relationship of proteins requires an analysis of their dynamic behaviors and the static structure. However, all current approaches to studying dynamics in proteins have their shortcomings. A conceptually attractive and alternative approach simultaneously characterizes a protein's structure and its intrinsic dynamics⁠. Ideally, such an approach could solely rely on RDC data-carrying both structural and dynamical information. The major bottleneck in utilizing RDC data in recent years has been attributed to a lack of RDC analysis tools capable of extracting the pertinent information embedded within this complex data source.

Here we present a comprehensive strategy …

In Silico Identification Of Vaccine Candidates Against Viral Infections, Prabin Baral

FIU Electronic Theses and Dissertations

There are many viral diseases without effective treatments or vaccines. These viruses can cause catastrophic epidemics such as the Lassa, Ebola, and Marburg viruses. Similarly, the recent coronavirus pandemic is of great concern as new variants are continuously emerging with decreased susceptibility to antibodies and vaccines that were developed for earlier strains. A critical step in the immune system’s fight against viruses involves an immunological protein molecule binding to a viral protein molecule. I investigate the atomic and molecular details of binding site recognition and binding interactions and dynamics for three important viruses.

Antigens are molecules, such as viral proteins, …

Problems Of Formation And Evolution Of Bulges Of Spiral Galaxies, Farkhodjon Botirov, Salakhutdin Nuritdinov

Bulletin of National University of Uzbekistan: Mathematics and Natural Sciences

In this work, we develop the theory of the origin of galactic bulges, and gravitational instability of the bending, as well as modes of perturbation based on the background of a nonlinear non-stationary model. As a result, here, we propose critical diagrams and determine increments of instabilities for such types of perturbations. In addition, we also consider relationships between the masses of the bulge and the central black hole, which is of great importance in studying the evolution of the bulges of spiral galaxies. Moreover, problems on the evolution of bulges in spiral galaxies, together with discussions of their main …

On The Use Of High-Frequency Surface Wave Oceanographic Research Radars As Bistatic Single-Frequency Oblique Ionospheric Sounders, Stephen R. Kaeppler, Ethan S. Miller, Daniel Cole, Teresa Updyke

CCPO Publications

We demonstrate that bistatic reception of high-frequency oceanographic radars can be used as single-frequency oblique ionospheric sounders. We develop methods that are agnostic of the software-defined radio system to estimate the group range from the bistatic observations. The group range observations are used to estimate the virtual height and equivalent vertical frequency at the midpoint of the oblique propagation path. Uncertainty estimates of the virtual height and equivalent vertical frequency are presented. We apply this analysis to observations collected from two experiments run at two locations in different years, but utilizing similar software-defined radio data collection systems. In the first …

Monitoring And Modelling The Dynamics Of The Cellular Glycolysis Pathway: A Review And Future Perspectives, Nitin Patil, Hugh Byrne, Orla L. Howe, Paul A. Cahill

Articles

Background

The dynamics of the cellular glycolysis pathway underpin cellular function and dysfunction, and therefore ultimately health, disease, diagnostic and therapeutic strategies. Evolving our understanding of this fundamental process and its dynamics remains critical.

Scope of review

This paper reviews the medical relevance of glycolytic pathway in depth and explores the current state of the art for monitoring and modelling the dynamics of the process. The future perspectives of label free, vibrational microspectroscopic techniques to overcome the limitations of the current approaches are considered.

Major conclusions

Vibrational microspectroscopic techniques can potentially operate in the niche area of limitations of other …

Indoor Air Quality Through The Lens Of Outdoor Atmospheric Chemistry, Jonathan P.D. Abbatt, Douglas B. Collins

Faculty Contributions to Books

Outdoor atmospheric chemistry and air quality have been the topic of research that intensified in earnest around the mid-20^th century, while indoor air quality research has only been a key focus of chemical researchers over the last 30 years. Examining practices and approaches employed in the outdoor atmospheric chemistry research enterprise provides an additional viewpoint from which we can chart new paths to increase scientific understanding of indoor chemistry. This chapter explores our understanding of primary chemical sources, homogeneous and multiphase reactivity, gas-surface partitioning, and the coupling between the chemistry and dynamics of indoor air through the lens of …

Video Snapshot: Single Image Motion Expansion Via Invertible Motion Embedding, Qianshu Zhu, Chu Han, Guoqiang Han, Tien-Tsin Wong, Shengfeng He

Research Collection School Of Computing and Information Systems

Unlike images, finding the desired video content in a large pool of videos is not easy due to the time cost of loading and watching. Most video streaming and sharing services provide the video preview function for a better browsing experience. In this paper, we aim to generate a video preview from a single image. To this end, we propose two cascaded networks, the motion embedding network and the motion expansion network. The motion embedding network aims to embed the spatio-temporal information into an embedded image, called video snapshot. On the other end, the motion expansion network is proposed to …

Data-Driven Learning For Robot Physical Intelligence, Leidi Zhao

Dissertations

The physical intelligence, which emphasizes physical capabilities such as dexterous manipulation and dynamic mobility, is essential for robots to physically coexist with humans. Much research on robot physical intelligence has achieved success on hyper robot motor capabilities, but mostly through heavily case-specific engineering. Meanwhile, in terms of robot acquiring skills in a ubiquitous manner, robot learning from human demonstration (LfD) has achieved great progress, but still has limitations handling dynamic skills and compound actions. In this dissertation, a composite learning scheme which goes beyond LfD and integrates robot learning from human definition, demonstration, and evaluation is proposed. This method tackles …

Using An Analytical Approach Of The Kuramoto Model To Stimulate 3d Neural Activity Of The Stomach, Morteza Al Rabya

Undergraduate Student Research Internships Conference

No abstract provided.

12 C(E,E'Pn) Measurements Of Short Range Correlations In The Tensor-To-Scalar Interaction Transition Region, I. Korover, J. R. Pybus, A. Schmidt, F. Hauenstein, M. Duer, O. Hen, E. Piasetzky, L. B. Weinstein, D. W. Higinbotham, S. Adhikari, K. Adhikari, M. J. Amaryan, Giovanni Angelini, H. Atac, L. Barion, M. Battaglieri, A. Beck, I. Bedlinkskiy, Fatiha Benmokhtar, Steffen Strauch, Ralf W. Gothe, Krishna Chandra Neupane, Et. Al.

Faculty Publications

High-momentum configurations of nucleon pairs at short-distance are probed using measurements of the C-12(e, e' p) and C-12(e, e' pN) reactions (where N is either n or p), at high-Q(2) and x(B) > 1.1. The data span a missing-momentum range of 300-1000 MeV/c and are predominantly sensitive to the transition region of the strong nuclear interaction from a Tensor to Scalar interaction. The data are well reproduced by theoretical calculations using the Generalized Contact Formalism with both chiral and phenomenological nucleon-nucleon (NN) interaction models. This agreement suggests that the measured high missing-momentum protons up to 1000 MeV/c predominantly belong to short-ranged …

An Operational Overview Of The Export Processes In The Ocean From Remote Sensing (Exports) Northeast Pacific Field Deployment, David A. Siegel, Ivona Cetinic, Jason R. Graff, Craig M. Lee, Norman Nelson, Mary Jane Perry, Inia Soto Ramos, Deborah K. Steinberg, Ken Buesseler, Roberta Hamme, Andrea J. Fassbender, David Nicholson, Melissa M. Omand, Marie Robert, Andrew Thompson, Vinicius Amaral, Michael Behrenfeld, Claudia R. Benitez-Nelson, Kelsey Bisson, Emmanuel Boss, Et. Al.

Faculty Publications

The goal of the EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) field campaign is to develop a predictive understanding of the export, fate, and carbon cycle impacts of global ocean net primary production. To accomplish this goal, observations of export flux pathways, plankton community composition, food web processes, and optical, physical, and biogeochemical (BGC) properties are needed over a range of ecosystem states. Here we introduce the first EXPORTS field deployment to Ocean Station Papa in the Northeast Pacific Ocean during summer of 2018, providing context for other papers in this special collection. The experiment was conducted with …

Disjointness Of Linear Fractional Actions On Serre Trees, Henry W. Talbott

Rose-Hulman Undergraduate Mathematics Journal

Serre showed that, for a discrete valuation field, the group of linear fractional transformations acts on an infinite regular tree with vertex degree determined by the residue degree of the field. Since the p-adics and the polynomials over the finite field of order p act on isomorphic trees, we may ask whether pairs of actions from these two groups are ever conjugate as tree automorphisms. We analyze permutations induced on finite vertex sets, and show a permutation classification result for actions by these linear fractional transformation groups. We prove that actions by specific subgroups of these groups are conjugate only …

Effect Of Different Storage Period On Nutrional Ingredient Of Forage, Jie Qiao, Qingyan Zhou, Dan Zheng, Yujie Lou

IGC Proceedings (1997-2023)

No abstract provided.

The Diurnal Variation In Stratospheric Ozone From Macc Reanalysis, Era-Interim, Waccm, And Earth Observation Data: Characteristics And Intercomparison, Ansgar Schanz, Klemens Hocke, Niklaus Kämpfer, Simon Chabrillat, Antje Inness, Mathias Palm, Justus Notholt, Ian Boyd, Alan Parrish, Yasuko Kasai

Astronomy Department Faculty Publication Series

In this study, we compare the diurnal variation in stratospheric ozone of the MACC (Monitoring Atmospheric Composition and Climate) reanalysis, ECMWF Reanalysis Interim (ERA-Interim), and the free-running WACCM (Whole Atmosphere Community Climate Model). The diurnal variation of stratospheric ozone results from photochemical and dynamical processes depending on altitude, latitude, and season. MACC reanalysis and WACCM use similar chemistry modules and calculate a similar diurnal cycle in ozone when it is caused by a photochemical variation. The results of the two model systems are confirmed by observations of the Superconducting Submillimeter-Wave Limb-Emission Sounder (SMILES) experiment and three selected sites of the …

The Zorich Transform And Generalizing Koenigs Linearization Theorem To Quasiregular Maps, Jacob A. Pratscher

Graduate Research Theses & Dissertations

This dissertation investigates the role that a new tool called the Zorich transform plays in quasiregular dynamics as a generalization of the logarithmic transform in complex dynamics. In particular we use the Zorich transform to construct analogues of the logarithmic spiral maps and interpolation between radial stretch maps. These constructions are then used to completely classify the orbit space of a quasiregular map. Also, conditions are given in which a quasiregular map $f:D\to\R^n$, where $D\subset\R^n$ is a domain, that is quasiconformal in a neighborhood of a geometrically attracting fixed point can be conjugated by a quasiconformal map to the asymptotic …

¹² C(E,E'Pn) Measurements Of Short Range Correlations In The Tensor-To-Scalar Interaction Transition Region, I. Korover, J. R. Pybus, A. Schmidt, F. Hauenstein, M. Duer, L. B. Weinstein, M. J. Amaryan, D. Bullumulla, M. Hattawy, X. Zheng, Et Al., The Clas Collaboration

Physics Faculty Publications

High-momentum configurations of nucleon pairs at short-distance are probed using measurements of the ¹²C(e,'p) and ¹²C (e,e'pN) reactions (where N is either n or p), at high Q² and 𝒙_B > 1.1. The data span a missing-momentum range of 300-1000 MeV/c and are predominantly sensitive to the transition region of the strong nuclear interaction from a tensor to scalar interaction. The data are well reproduced by theoretical calculations using the generalized contact formalism with both chiral and phenomenological nucleon-nucleon (NN) interaction models. This agreement suggests that the measured high missing-momentum protons up to 1000 MeV/c predominantly …

Quantifying Confinement Of Chain Dynamics For Chains Tethered To Self-Assembling Crystalline Nanodomains Using Neutron Spin Echo Spectroscopy, Logan Benninghoff

Williams Honors College, Honors Research Projects

Polyisobutylene (PIB) rubbers can be reinforced with crystalline β-alanine nanodomains. Progress has been made in understanding the morphology of the nanodomains, but the dynamics of the PIB molecule chains attached to the surface of the nanodomains and in the matrix are not well understood. It is possible to observe the motion of these PIB chains using Neutron Spin Echo (NSE) experiments, since the experimental technique can give data for smaller timescales. Data collection for reinforced rubber samples has already been performed, but the data still need to be analyzed. For my honors project I will be comparing the data to …

Composite Network Of Actin And Microtubule Filaments, Self-Organization And Steady-State Dynamics, Leila Farhadi

Doctoral Dissertations

Actin and microtubule filaments, with their auxiliary proteins, enable the cytoskeleton to perform vital processes in the cell by tuning the organizational, mechanical properties and dynamics of the network. Despite their critical importance and interactions in cells, we are only beginning to uncover information about the composite network. Here, I use florescence microscopy to explore the role of filaments characteristics, interactions and activities in the self-organization and steady-state dynamics of the composite network of filaments. First, I discuss active self-organization of semiflexible actin and rigid microtubule filaments in the 2D composite network while myosin II and kinesin-1 motor proteins propel …