University of Tennessee Institute of Agriculture
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From Equilibrium to Non-equilibrium: Multiscale Modeling of Nucleoid Compaction and Separation in Escherichia coli
No full textThe organization and spatial localization of bacterial chromosomes is fundamental to cellular function, requiring DNA molecules with contour lengths of millimeters to not only compact into cells just micrometers in size, but also to separate properly during cell division — all without the membrane-bound organelles found in eukaryotes. This thesis investigates the physical mechanisms governing nucleoid compaction and separation in Escherichia coli through three complementary approaches that bridge equilibrium thermodynamics and out-of-equilibrium cellular processes.
We first develop a comprehensive free energy model to quantify the contributions of different macromolecular crowders to nucleoid compaction. We find that while polyribosomes initiate phase separation between the nucleoid and cytoplasm, cytosolic proteins primarily control the homeostatic nucleoid size, with protein concentration fluctuations near physiological levels capable of inducing rapid changes in nucleoid volume.
Next, we extend this framework to an one-dimensional reaction-diffusion model incorporating transcription, translation, and mRNA degradation to capture the spatiotemporal dynamics of DNA and ribosomes during the cell cycle. The model demonstrates that active polysome production within the nucleoid creates an instability that drives nucleoid splitting into two distinct lobes, with the accumulation of polysomes at mid-cell providing a mechanism for chromosome separation consistent with experimental observations.
To address limitations of continuum models, we implement molecular dynamics simulations in LAMMPS with explicit central dogma reactions, maintaining DNA chain connectivity and three-dimensional geometry. These simulations reveal that transcriptional activity expands the nucleoid proportionally to active RNA polymerase numbers, and that active processes are essential for complete chromosome separation. Without them, sister chromosomes remain in contact despite entropic forces. The results from the simulations also exhibits large stochastic fluctuations, which is absent in the previous one-dimensional reaction-diffusion model.
Collectively, the integration of equilibrium thermodynamics, reaction-diffusion dynamics, and molecular simulations provides a multi-scale framework demonstrating how active cellular processes couple with physical forces to organize genetic material. Our findings have implications for understanding the evolution of cellular organization of bacteria and the development of antibiotics targeting chromosome dynamics. The methodologies developed here — from analytical free energy models to large-scale molecular simulations — offer tools for investigating similar organizational principles in other cellular systems lacking membrane-bound compartments
Colloidal Mobility in Contaminated Subsurface Systems: Linking Biological and Chemical Processes
No full textThis dissertation investigates how colloids mediate contaminant mobility and microbial community structure in the chemically extreme groundwater of the ENIGMA Field Research Center (eFRC) at the Y-12 National Security Complex. Integrating directional hydrology, conservative tracer tests, ion and metal chemistry, colloid statistics, transmission electron microscopy (TEM), and genome-resolved multi-omics, the work links pore-scale interactions to ecosystem-scale trends and advances colloid transport from idealized theory to field conditions. Electron microscopy revealed ultra-small cells attached to sediment, providing the first direct evidence of such microbial interactions at the eFRC site. A synthesis of colloid transport models (colloid filtration theory, DLVO, and pore-to-continuum-scale approaches) shows why dissolved-phase frameworks fail under nitrate-rich, metal-loaded conditions and motivates empirical tests in this setting. Field analyses demonstrate that hydrologic variability and steep geochemical gradients jointly structure colloid dynamics: shallow intervals exhibit diffuse orientations, whereas deeper zones show stable, aligned transport vectors (Watson-Williams: 26 and 28 vertical and 35 and 36 lateral contrasts significant, p\u3c 0.05). Bromide behaved conservatively in lab and field, confirming clear picture of advective pathways. Ion data revealed strong nitrate enrichment in upper wells and covariation among sulfate, chloride, and nitrate, consistent with redox stratification and mixed sources. The deep zones paired chemical extremes with intermittently connected flow. Colloid distributions were highly structured (pairwise Kolmogorov-Smirnov D≈0.27-0.46 at L8, all p\u3c 0.001), with L8 well emerging as a chemically forced, high-mobility, uranium-maximum spot. L7 well was intermediate, and upper and medium wells formed a more stable cluster. Transmission Electron Microscopy images were grouped as abiotic, biotic, and mixed colloids (mineral fragments, EPS-rich aggregates, ultra-small cells, viruses, vesicles) and documented well-specific viral attachment states (χ2=14.26, df=3, p=0.0026). Microbial communities differed strongly among wells (PERMANOVA pseudo-F=9.74, p=0.001) and tracked geochemistry (Mantel r=0.628, p=0.001). At the same time, colloids contributed an independent, geochemistry-controlled signal (partial Mantel r≈0.143, p=0.005). Genome-resolved results demonstrate abundant mobile genetic elements and Caudoviricetes-dominated viromes, recurrent functional groupings (transporter-CRISPR, energy-nucleotide), and a predictive metals panel (W, Zr, B, Cd, Mg, Mn, U). The dominance of Rhodanobacter denitrificans spp. under high nitrate, low pH conditions suggest niche-specific adaptations that reduce microbial diversity. Overall, the findings support a unified framework: geochemical filtering sets community and metabolic structure; hydrologic coupling and colloids redistribute cells, viruses, plasmids, and metals; genomic plasticity consolidates successful adaptations. The work establishes the first metagenomic and viromic baseline for Subsurface Observatory (SSO) wells Saturated Zone 2 (SZ2) and offers a transferable framework for forecasting contaminant mobility and microbial resilience at nuclear legacy sites
Receptor Tyrosine Kinase-like Orphan Receptors: Elucidating receptor self-assembly in a native-like membrane environment at single molecule resolution
No full textInteractions between membrane proteins and their surrounding environment are essential to the maintenance, survival, and modulation of cellular behavior. Receptor tyrosine kinases are membrane proteins that undergo activation through protein-protein oligomerization that modulates these behaviors highlighting the importance of understanding the formation and function of these complexes. Thus, the development of techniques that allow us to dive deeper into these interactions will provide crucial insight into the inner workings of cellular networks. In this work, we present “SiMPull-POP,” a single-molecule pulldown-photobleaching method that utilizes a co-polymer compared to traditional detergent methodologies to solubilize membrane proteins within nanoparticles that contain endogenous lipids (Chapter II). This co-capturing allows for the study of proteins in a more native-like environment. In the work presented here, we validated SiMPull-POP using a known inducible-dimer system and then applied this method to study the self-assembly of the RTK EphA2 in response to ligand stimulation and membrane modification. Next, we investigated the ROR RTK family where the mechanism and modulation of their oligomerization is still not well understood. This RTK family is comprised of ROR1 and ROR2 that are key regulators of embryogenesis, aiding in the development of bone, muscle, and neural tissues. To provide insight into the assembly mechanism of this RTK family we quantified the self-assembly of ROR2 (Chapter III) and ROR1 (Chapter II) using SiMPull-POP. Elucidating that the self-assembly of ROR1 is promoted by cholesterol in the membrane while ROR2 self-assembly is modulated by calcium. In conclusion, the work presented here contributes a quantitative method to monitor protein interactions that has both confirmed and provided new insights into the self-assembly of membrane proteins
Advancing Crash Investigation with Connected and Automated Vehicle Data: Insights from a Survey of Law Enforcement
No full textSome of the 6 million plus police-reported crashes in the US require detailed investigations. As connected and automated vehicles (CAVs) gain popularity and are also involved in crashes, new data from CAVs can be used to improve the accuracy of crash investigations. In addition to information from Event Data Recorders, CAV data on vehicle trajectories and pre-crash conditions can enhance the understanding of causation factors. This study investigates how CAV data can advance crash investigations by answering research questions about what pertinent information is lacking in crash investigations and how law enforcement can use CAV data. This study addresses these questions by performing a survey of 61 law enforcement officials working in crash investigations in the state of Tennessee. The survey included respondents’ vehicle crash investigation experience, training exposure, and familiarity with automated vehicle technologies. The survey showed that respondents have previous experience working with video camera footage in crash investigations, and responses indicate that camera footage would provide the most helpful new information when investigating a crash. The survey also revealed law enforcement officials’ moderate familiarity with lidar and low familiarity with millimeter-wave radar and ultrasound sensors. Survey respondents also indicated that data such as vehicle trajectories made available through automated vehicle sensors would be useful during crash investigations. The survey revealed a need for standardization in CAV data retrieval and training processes. It resulted in a list of pertinent training topics for law enforcement that prioritizes a thorough understanding of CAV technology and data retrieval processes
Exploring Pedestrian Safety on Interstates with Bayesian and Machine Learning Models
No full textDespite being prohibited from walking on freeways per federal laws, 14 to 17% of all pedestrian crashes in the United States happen on the interstates. Examining these crashes within the context of the safe systems approach is essential with an emphasis on the mitigation of safety risks for all road users. This study investigates the correlates of pedestrian crash injury severity on interstates in North Carolina, focusing on pedestrian actions, roadway conditions, and the type of vehicles involved in the crashes. The study utilizes police-reported pedestrian crash data from 2007 to 2022, coded by the Pedestrian and Bicycle Crash Analysis Tool (PBCAT) which provides unique and comprehensive crash descriptors. The analysis considers 882 pedestrian crash observations on freeways. The dependent variable, pedestrian injury severity, is categorized into distinct binary outcomes, fatal and severe injuries versus minor injuries. The study applies frequentist and Bayesian binary logit models with various prior specifications, along with a robust machine learning algorithm Random Forest for their ability to provide reliable estimates even with a limited sample size. The results show that pedestrian crashes are more predominant in rural (47%) than urban freeways (40%) in North Carolina. Key findings indicate that pedestrians crossing the roadway, crashes on dark unlit roads, and crashes involving pedestrian alcohol impairment are associated with a higher risk of severe injuries to pedestrians. The study findings highlight the need for faster roadside assistance to stranded pedestrians, stringent penalties for alcohol impairment, and the implementation of physical barriers preventing pedestrian access on freeways
ADDRESSING DATA DEFICIENCIES: LICHENS OF THE PALOUSE PRAIRIE (U.S.) AND THE POTENTIAL OF LARGE LANGUAGE MODELS FOR GEOCODING
No full textData deficiency remains a conservation barrier for many organismal groups, with declines in biodiversity and ecosystem health predicted to continue. The historical focus toward groups generally considered to be more charismatic has ultimately led to a lack of data available for assessing extinction risk in lesser-known taxa, and we lack baseline taxonomic knowledge across many ecosystems. Fungi are just one example of an understudied speciose group that has more recently been gaining conservation attention. While efforts to digitize natural history collections continue to increase our overall understanding of biodiversity, this cannot directly address underlying sampling biases that skew organismal representation across physical collections. Additionally, many digitized collections accessed for conservation-related research are skeletal records that do not include latitude and longitude values to reflect where the specimen was collected from. To address some of these gaps in baseline taxonomic knowledge and physical collections holdings, 360 unidentified lichen specimens from an incomplete biodiversity inventory of Washington’s Palouse Prairie were identified to species. Digitized herbarium records were also analyzed to compare against current identifications., as well as to synthesize historical information for Palouse lichens into a referenceable document. The digitization of newly identified collections and submission to multiple herbaria increases the representation of dryland ecosystems in the northwestern U.S. and provides data for use in both local and state conservation efforts. To contribute to resolving gaps in digital collections, the capabilities of Large Language Models (LLMs) in geocoding from locality strings held in digital occurrence data were tested to gain insight on the potential use of such tools to help with georeferencing tasks. It was found for the current combination of prompts and LLMs that model selection greatly influenced the accuracy of an LLM to choose coordinates based on 500 GBIF locality strings, but that the specific prompt given made no difference. It was additionally found that when asked to perform this geocoding task when disconnected from the internet, the chain-of-reasoning reflected actions that would not be possible without an internet connection. Overall, this works adds to ongoing efforts that address data deficiencies related to natural history collections and our knowledge of biodiversity
Assessment of secondary aqueous processes in sulfate formation on Earth and Mars using geochemical and orbital methods
No full textOn Earth, low temperature aqueous processes and chemical weathering of sulfur (S)-rich bedrock often lead to abundant formation of secondary calcium (Ca) and magnesium (Mg)-sulfate minerals, particularly in dry climates. In Gale crater on Mars, secondary Ca- and Mg-sulfates have been observed by the Curiosity rover in veins and sediment cement throughout the central mound called Aeolis Mons (informally named Mount Sharp), but the sulfate source(s) and climate conditions during their formation are poorly understood. Therefore, we investigated the formation of secondary sulfate minerals in an analog environment of the Rio Puerco watershed located in northwestern New Mexico using sulfur, oxygen, and hydrogen isotope compositions. The obtained isotope results suggest that weathering (oxidation) of bedrock sulfide minerals is the main sulfate source for precipitation of sulfate minerals in veins and cement. These formation processes are controlled by multiple events of infiltration and top-down movement of meteoric water occurring in a semi-arid climate and often exhibit distinctive surface expressions of the bright-toned sulfate-rich salt accumulations on the exhumed surfaces at outcrop scale. The latter shows similarities with some of the sulfate occurrences detected by Curiosity in halo-like features and on eroded bedding planes of Aeolis Mons. Comparisons of aerial imagery, mineralogy, and climate data suggest that these surface accumulations of secondary salts result from post-lithification fluid flows involving multiple cycles of redissolution and reprecipitation of already existing sulfate salts in the surficial deposits. Further analyses of orbital hyperspectral and imagery data of hydrated Mg-sulfate minerals from Aeolis Mons in Gale imply they are often bright-toned and present on hillslopes, at local topographic lows, and crossing morphological boundaries. Overall, this suggests that the widespread and abundant presence of secondary Mg-sulfates in the sedimentary strata of Aeolis Mons reflects multiple processes of water-rock interactions that took place during diagenesis and subsequent fluid flows
An Intelligent Multi-Agent System for Enhanced Dementia Care: Integrating Computer Vision, Adaptive Learning, and Caregiver Guidance
No full textDementia poses a significant global health challenge, yet existing technology-assisted care systems often fail to adapt to the complex and evolving behaviors of patients, leading to inefficient monitoring and increased caregiver burden. This thesis addresses the critical shortcomings of current patient monitoring systems, which typically rely on static or random search strategies when patients wander, resulting in dangerous delays in detection and compromising patient safety.
To overcome these limitations, this work presents a novel intelligent multi-agent system that integrates adaptive spatial-temporal learning, computer vision, loop prevention mechanisms, and comprehensive biometric simulation within a realistic behavioral framework. The system employs an algorithm that dynamically learns individual patient movement patterns to build a probabilistic model of their location, which in turn guides an intelligent system for proactive and efficient care. A key innovation is the integration of a synthetic biometric monitoring system that generates realistic vital signs, including heart rate, HRV, and SpO2 to model stress responses, simulate medical emergencies, and objectively measure the physiological impact of care interventions. This allows for the data-driven adaptation of care strategies, which are tested and refined within a sophisticated multi-agent simulation featuring patient agents with realistic cognitive decline and caregiver agents employing evidence-based intervention techniques. The system incorporates an adaptive loop prevention framework that detects and breaks repetitive interaction patterns, utilizing confidence scoring to prioritize effective interventions while avoiding counterproductive cycles.
Through extensive simulation-based experiments, the system demonstrated a 40--60\% reduction in average patient detection time compared to baseline methods. The biometric-guided approach increased care intervention success rates from a baseline of 38\% to 55\% and achieved 94\% sensitivity in detecting simulated medical emergencies. The loop prevention system successfully identified and mitigated repetitive interaction patterns, preventing escalation of patient agitation. This research contributes a comprehensive, adaptive, and empirically validated framework that enhances patient safety, reduces caregiver burden, and shifts the paradigm from reactive monitoring to proactive, personalized, and physiologically-informed dementia care
Out of the Ground (Into the Sky)
No full textOut of the Ground (Into the Sky) is written for clarinetist, with computer processing in combination with fixed audio. It is a multilayered performance project, that aims to memorialize a loved one. The performance (by both clarinetist, and the computer) is nuanced and visceral. This is intended to be a memorable concert piece
Tape Piece
No full textTape Piece is part of a series of single-sound-source daydream pieces, where a solitary object or family of objects is repurposed to create an otherworldly soundscape. This work uses tape--masking, scotch, aluminum, packing, and duct--sometimes recognizable, and sometimes heavily processed. The familiar is juxtaposed with the fresh, and what starts out with unrolling and tearing quickly unravels as sounds evocative of gunfire, of bombs and explosions, and of Geiger counters suggesting the downfall of civilization. New creatures emerge throughout, each trying to find their place in a world that has come unglued