Digital Commons Network^™

Resolution Of Physics And Deep Learning-Based Protein Engineering Filters: A Case Study With A Lipase For Industrial Substrate Hydrolysis, Spencer Gardiner, Peter Dollinger, Filip Kovacic, Jörge Pietruszka, Daniel Ess, Karl-Erich Jaeger, Gunnar F. Schröder, Dennis Della Corte

Faculty Publications

Computational enzyme design remains a powerful yet imperfect tool for optimizing biocatalysts, especially when targeting non-natural substrates. Using design tools we investigated Pseudomonas aeruginosa LipA, a lipase with a flexible lid domain crucial for substrate binding and turnover, aiming to enhance its hydrolysis of the industrially relevant substrate Roche ester. We generated an initial set of single-point mutations based on structural proximity to the active site and evaluated their effects using a computational pipeline integrating molecular dynamics (MD) simulations, density functional theory (DFT) calculations, and ensemble-based energy scoring. While we identified several active variants, attempts to rank them by activity …

Age-Related Change In Children’S Physical Activity And Sedentary Time: The International Children’S Accelerometry Database (Icad), Andrew J. Atkin, Lauren B. Sherar, Ulf Ekelund, Bjorge H. Hansen, Lars Bo Andersen, Sigmund Anderssen, Susi Kriemler, Soyang Kwon, Peter L. Kristensen, Niels Wedderopp, Kate Northstone, Russell Jago, Russell R. Pate Ph.D., Jardena J. Puder, Jo Salmon, Luis B. Sardinha, Esther M.F. Van Sluijs

Faculty Publications

Background

Many young people fail to achieve the minimum recommended amount of physical activity to benefit their health. Understanding the nature of age-related changes in behaviour and how this varies for population sub-groups is informative for intervention design. The aim of this study was to describe age-related changes in physical activity and sedentary time and examine variability in patterns of change across demographic sub-groups.

Methods

Data are from 13 studies in the International Children’s Accelerometry Database (ICAD), all of which provided ≥2 waves of waist-worn accelerometer data. Annual change in sedentary time, light intensity physical activity (LPA) and moderate to …

Physical Function And Pain As Predictors Of Movement Behaviors In Adults With Arthritis, Scott Jamieson, Sarah Wilcox Phd, Chih-Hsiang Yang Ph.D., Ye Sil Kim Phd, Christine Pellegrini Ph.D.

Faculty Publications

Purpose

Design

Setting

Subjects

Measures

Analysis …

Event-Based Sensor Noise Modeling For Space-Based Space Domain Awareness, Rachel Oliver, Brian Mcreynolds, Dmitry Savransky

Faculty Publications

Building off the foundation of a physics-based end-to-end model for event-based vision sensors (EVS) observing resident space objects (RSOs), we apply new techniques to model realistic low-light sensor noise. While previous approaches simulate memorized current leakage and apply temporal noise models, our methods improve on these approaches and additionally account for current-following noise as an event source. These improvements are key components for accurate event-generating simulators which can advise requirements and concepts of operations for dedicated event-based Space Domain Awareness (SDA) architectures. The EVS pixel’s independent and asynchronous recording of changes in photocurrent produces data with high temporal resolution and …

A C++ Library For Turbulent Mixing Simulation Using Hierarchical Parcel Swapping (Hips), Masoomeh Behrang, Tommy Starick, Heiko Schmidt, David O. Lignell

Faculty Publications

Turbulence models are crucial for simulating flows at all scales, capturing both large-scale structures and small-scale mixing. Software libraries that implement such models should support modular integration, customization, and scalability across different simulation frameworks. This paper presents Hierarchical Parcel Swapping (HiPS), a C++ library documented with Doxygen and available on GitHub. HiPS supports both mixing and reactions and can be used as a standalone model or as a subgrid model in CFD simulations. The code includes examples for users to run it as a standalone model. Additionally, considerations for using it as a subgrid model are provided.

Magnetic Nanoparticles Tethered With Zn–Dpa For The Removal Of Bacteria From Red Blood Cell Suspension, Tochukwu P. Okonkwo, Rajendra P. Gautam, Jacob B. Limburg, Breckin L. Forstrom, Bowen J. Houser, Aaron Rappleyea, Tyler P. Green, Joseph P. Talley, Alexander D. Daum, Stacey J. Smith, Karine Chesnel, William G. Pitt, Roger G. Harrison

Faculty Publications

Bacterial infections continue to drive the need for more effective and rapid methods for bacterial analysis. To address this, magnetic nanoparticles (MNPs) have emerged as promising tools, especially when their surfaces are modified with bacteria binders. The bis-zinc–dipicolylamine (Zn–DPA) complex is known for its broad affinity to bacteria. We have synthesized MNPs via a thermal decomposition method, encapsulated them in silica, modified their surface with Zn–DPA, and tested their ability to remove bacteria. The MNPs retain their superparamagnetic properties and crystallite structure after being encapsulated. The MNPs coated with silica and Zn–DPA effectively bind and remove both Gram-positive and Gram-negative …

Time Series Changes Of Surficial Sediments On Eastern Ship Shoal, Louisiana Shelf, Adam Gartelman, Kehui Xu, Brian J. Roberts, David Samuel Johnson, Madison Liotta

Faculty Publications

Ship Shoal, a large transgressive sand body on the Louisiana continental shelf, is a critical sediment source for coastal restoration. This study evaluates spatial and temporal variability in sediment grain size, percents organic matter (%OM), and carbonate (%CO3) across the shoal crest (REF), Caminada Dredge Pit (CAM), and Terrebonne Dredge Pit (TER). Sediment samples were collected between 2020 and 2022 using box cores and analyzed for grain size, %OM, and %CO3, with temporal and spatial patterns assessed through statistical comparisons, correlation analyses, and random forest regression models. Results show that dredged areas act as sinks for fine-grained, organic-rich sediments, with …

A Comparison Of Characteristics Of Infilling Sediments In Three Mud-Capped Dredge Pits On The Louisiana Continental Shelf, Wenqiang Zhang, Kehui Xu, Chaochen Jia, Adam Gartelman, Omar Alawneh, Navid Jafari, Colin Herke, Madison Liotta, Samuel J. Bentley

Faculty Publications

Due to high sedimentation rate up to ~1 m/year, mud-capped dredge pits (MCDP) are often considered natural laboratories for studying sedimentary processes, slope stability and the impacts of dredging activities on marine environments. Although many studies have been performed on the Louisiana shelf, there is a lack of high spatial resolution research covering the eastern, central and western Louisiana shelf to comprehensively investigate sediment infilling. Eighteen vibracores were collected from the Peveto Channel dredge pit (PC), Raccoon Island dredge pit (RI) and Sandy Point dredge pit (SP), and more than 1300 samples were analyzed to study the spatial variation in …

A Test Of The Abundant-Center Hypothesis For Stream Fishes, Matthew L.W. Zink, Brandon K. Peoples, Julian D. Olden, Lily M. Thompson, William K. Annis, Stephen R. Midway

Faculty Publications

The abundant-center hypothesis (ACH) provides a conceptual model for predicting range-wide distributions of species abundance, suggesting that abundance peaks in the center of the geographic range and declines towards range edges. Empirical studies testing the ACH and its subsequent derivations predominantly occurred in terrestrial systems and reported mixed support. Moreover, none of these models consider the possibility of multiple geographic areas of elevated abundance (which we refer to as ‘abundant cores'). Naturally dispersal limited species may exhibit multiple abundant cores, requiring refinement of the ACH. We used fish species abundances from 29 206 community monitoring surveys and weighted geospatial kernel …

Recovery Of The X-Ray Polarisation Of Swift J1727.8-1613 After The Soft-To-Hard Spectral Transition (Corrigendum) (Astronomy And Astrophysics (2024) 686 (L12) Doi: 10.1051/0004-6361/202450566), J. Podgorný, J. Svoboda, M. Dovčiak, A. Veledina, J. Poutanen, P. Kaaret, S. Bianchi, A. Ingram, F. Capitanio, S. R. Datta, E. Egron, H. Krawczynski, G. Matt, F. Muleri, P. O. Petrucci, T. D. Russell, J. F. Steiner, N. Bollemeijer, M. Brigitte, N. Castro Segura, R. Emami, J. A. García, K. Hu, M. N. Iacolina, V. Kravtsov, L. Marra, G. Mastroserio, T. Muñoz-Darias, E. Nathan, M. Negro, A. Ratheesh, N. Rodriguez Cavero, R. Taverna

Faculty Publications

(Figure presented) In Fig. 4, the X-ray hardness value for observation 8 was plotted using a count-based ratio instead of the energy-flux-based ratio used for other points in the figure. The correction of the position of this point in Fig. 4 does not affect any other figures, results, or conclusions in the paper.

Sub-Gev Dark Matter And Mev Gamma-Ray Detection With Cosi, Yu Watanabe, Shigeki Matsumoto, Christopher M. Karwin, Tom Melia, Michela Negro, Thomas Siegert, Yuki Watanabe, Hiroki Yoneda, Tadayuki Takahashi

Faculty Publications

Sub-GeV dark matter (DM) has been attracting more attention due to the negative results searching for traditional weakly interacting massive particles (WIMPs). Such particles are expected to produce gamma rays from annihilation in the MeV energy region. Advancements in technology have opened up possibilities to precisely detect MeV gamma rays, leading to the upcoming space-based mission of the Compton Spectrometer and Imager (COSI). We comprehensively and quantitatively study the phenomenology of sub-GeV DM to determine if the COSI observations will probe their viable model parameter regions. We first construct models to describe sub-GeV DM based on the minimality and renormalizability …

Phase-Amplitude Separation Of Wave Function As Local Gauge Transformation, A. R.P. Rau

Faculty Publications

A quantum-mechanical wave function is complex, but all observations are real, expressible through expectation values and transition matrix elements that involve the wave functions. It can be useful to separate at the outset the amplitude and phase as real quantities that together carry the same information that is contained in the complex wave function. Two main avenues for doing so go way back in the history of the subject and have been used both for scattering and bound states. A connection is made here to gauge transformations of electrodynamics where the advent of quantum mechanics and later quantum field theory …

Root Exudates: The Rhizospheric Frontier For Advancing Sustainable Plant Protection, Muhammad Rahil Afzal, Misbah Naz, Youbo Yu, Lisha Yan, Peiyi Wang, Janaki Mohotti, Gefei Hao, Jing-Jiang Zhou, Zhou Chen, Libo Zhang, Qian Wang

Faculty Publications

Root exudates (REs), a diverse array of bioactive metabolites secreted by plant roots in response to environmental stimuli, serve as key mediators of rhizosphere ecology and plant defense responses, offering a promising avenue for sustainable pest management and eco-friendly plant protection. While earlier reviews primarily focus on root exudates in the context of general rhizosphere dynamics and plant-microbial interactions, critical knowledge gaps persist in REs-plant-pest tripartite interactions, the mechanistic basis of REs-mediated plant defense, and their practical integration with integrated pest management (IPM) frameworks. This review provides a synthesis of the latest literature on the biochemical diversity and functions of …

Effect Of Short-Chain Polymer Binders On The Mechanical And Electrochemical Performance Of Silicon Anodes, Fei Sun, L. Zurita-Garcia, Dean R. Wheeler

Faculty Publications

Polymer binders are crucial components in providing both mechanical support and chemical stability to the structure of porous Li-ion electrodes. Particularly in silicon anodes, the active material undergoes substantial volume expansion of up to 275%. Due to the mechanical constraint of the current collector, these silicon materials tend to expand in the normal direction while exhibiting substantial particle rearrangement and plastic deformation. Conventional rigid binders such as polyacrylic acid (PAA) and polyimide (PI), while providing satisfactory initial capacity, do not eliminate diminished long-term performance. Our research attempts to develop binder formulations that can accommodate sufficient flexibility for the substantial volume …

Categorial Declinations & Democracy, Brenner M. Fissell

Faculty Publications

The most contentious action taken by reform prosecutors has been the issuance of categorical declination policies. Opponents decry this as bureaucratic nullification of democratically enacted offenses, while the prosecutors themselves counter that they are responding to the will of their local electorate. Democracy claims, it appears, have taken center stage in this debate, and they are deployed by both sides. How should we think about democracy and categorical declinations? The most comprehensive scholarly work on this subject is a 2021 article by Professor Kerrel Murray. In this essay, I hope to continue the work begun by Murray, offering additional insights …

Exact And Approximate Conformal Inference For Multi-Output Regression, Chancellor Johnstone, Eugene Ndiaye

Faculty Publications

It is common in machine learning to estimate a response y given covariate information x . However, these predictions alone do not quantify any uncertainty associated with said predictions. One way to overcome this deficiency is with conformal inference methods, which construct a set containing the unobserved response with a prescribed probability. Unfortunately, even with a one-dimensional response, conformal inference is computationally expensive despite recent encouraging advances. In this paper, we explore multi-output regression, delivering exact derivations of conformal inference p-values when the predictive model can be described as a linear function of y . Additionally, we introduce a multivariate …

Wind Turbine Rotor Design Using High-Fidelity Aerostructural Optimization, Marco Mangano, Sicheng He, Yingqian Liao, Denis-Gabriel Caprace, Andrew Ning, Joaquim R. R. A. Martins

Faculty Publications

Large wind turbines yield more energy but demand careful aeroelastic blade design. Coupled multiphysics design strategies can reduce wind energy costs exploiting fluid-structure interactions. This work presents the first high-fidelity aerostructural optimization study of a large wind turbine rotor.We use blade-resolved fluid dynamics and structural solvers in a monolithic gradient-based optimization framework to explore steady-state torque and blade mass trade-offs. The coupled-adjoint approach computes gradients efficiently, enabling the optimization of over 100 structural and geometric parameters simultaneously. Our optimization study modifies a DTU 10 MW benchmark with a simplified structure and isotropic material properties. The tightly coupled optimizations increase torque …

Comparative Analysis Of Different Magnetic Anomaly Datasets Using Navigation Performance With Flight Test Data, Aaron P. Nielsen, Brandon M. Blakely, Patrick Duff

Faculty Publications

Magnetic Anomaly Navigation (MagNav) is a map-based method of navigation which relies on accurately obtaining the anomaly field to a high level of precision to achieve good navigation results. This requires utilizing high quality sensors, accurately modeling disturbance fields from the aircraft & other sources, and creating high-fidelity maps. Aeromagnetic survey data or marine track survey data must be processed into a product that can be used as a reference for a magnetic navigator and a variety of techniques can be utilized for this processing. The data collection for different survey types reflects choices typically made to study the underlying …

I Do, And I Will: Effectual Religiosity May Strengthen The Triad Chord Of Commitment For Women Of Faith, Tamara M. Chamberlain, Loren Marks, David C. Dollahite, Ashley Lebaron-Black, Elizabeth Kay Madsen, Christina N. Cooper

Faculty Publications

Although religiosity is commonly linked to marital satisfaction in sociological research, few studies have examined how it strengthens marital commitment among women of faith. This study explored the perspectives of religious, heterosexual married women using interviews in the United States from 196 highly religious couples with successful marriages. Three core themes emerged: (1) personal commitment—including the decision to marry, religious beliefs and practices, and the need for effort and sacrifice; (2) moral commitment—highlighting sexual relations before marriage, promises made before God, family, and friends, and views on fidelity and divorce; and (3) structural commitment— emphasizing the role of a religious …

Surprisingly Robust Photochemistry In Subarctic Particles During Winter: Evidence From Photooxidants, Laura M. D. Heinlein, Junwei He, Michael Oluwatoyin Sunday, Fangzhou Guo, James Campbell, Allison Moon, Sukriti Kapur, Ting Fang, Kasey Edwards, Meeta Cesler-Maloney, Alyssa J. Burns, Jack E. Dibb, William Simpson, Manabu Shiraiwa, Becky Alexander, Jingqiu Mao, James H. Flynn Iii, Jochen Stutz, Cort Anastasio

Faculty Publications

Subarctic cities notoriously experience severe winter pollution episodes with fine particle (PM2.5) concentrations above 35 µg m−3, the US Environmental Protection Agency (EPA) 24 h standard. While winter sources of primary particles in Fairbanks, Alaska, have been studied, the chemistry driving secondary particle formation is elusive. Biomass burning is a major source of wintertime primary particles, making the PM2.5 rich in light-absorbing brown carbon (BrC). When BrC absorbs sunlight, it produces photooxidants – reactive species potentially important for secondary sulfate and secondary organic aerosol formation – yet photooxidant measurements in high-latitude PM2.5 remain scarce. During the winter of 2022 Alaskan …

Computational Detection Of Articulation Transients In Clarinet Performance, Whitney L. Coyle, Max Griffin, Makayle S. Kellison

Faculty Publications

Accurate measurement of note-to-note transitions is essential for analyzing articulation in clarinet performance. Traditional methods rely on either subjective amplitude thresholds—such as the time between 5% and 95% RMS levels—or direct measurement of tongue-reed contact time using reed-mounted sensors. These approaches are limited by their dependence on user-defined parameters or invasive hardware. This study proposes a computational alternative: ΔT, a curvature-based metric defined as the time interval between surrounding minima in the second derivative of the mouthpiece pressure envelope. Using data from a sensor-equipped mouthpiece (SEM), we compare ΔT to both threshold-based timing (T_t) …

Feasibility Evaluation Of Secure Offline Large Language Models With Retrieval-Augmented Generation For Cpu-Only Inference, Erick Tyndall, Torrey J. Wagner, Colleen Gayheart, Alexandre Some, Brent T. Langhals

Faculty Publications

Recent advances in large language models and retrieval-augmented generation, a method that enhances language models by integrating retrieved external documents, have created opportunities to deploy AI in secure, offline environments. This study explores the feasibility of using locally hosted, open-weight large language models with integrated retrieval-augmented generation capabilities on CPU-only hardware for tasks such as question answering and summarization. The evaluation reflects typical constraints in environments like government offices, where internet access and GPU acceleration may be restricted. Four models were tested using LocalGPT, a privacy-focused retrieval-augmented generation framework, on two consumer-grade systems: a laptop and a workstation. A technical …

The Complexity Of Promoting Physical Activity In English State Primary Schools: An In-Depth Qualitative Analysis Of The Role Of Social Context, Robert Walker, Danielle House, Alice Porter, Ruth Salway, Simona Kent-Saisch, Michael Beets Ph.D., David Revalds Lubans, Frank De Vocht, Russell Jago

Faculty Publications

Background

Primary schools present an opportunity to equitably promote physical activity. To date, school-based interventions have had limited success. Contextual differences between schools could be a key factor that contributes to this lack of impact. However, the elements that constitute a school’s social context (i.e. the organisational, political, cultural, and sociodemographic characteristics) and how they might impact on primary school physical activity are unclear. The aims of this study were to conduct an in-depth qualitative analysis of state primary school social context related to physical activity and, using this analysis, provide recommendations for policy and practice.

Methods

We conducted one-to-one …

Impact Of Retrieval Augmented Generation And Large Language Model Complexity On Undergraduate Exams Created And Taken By Ai Agents, Erick S. Tyndall, Colleen Gayheart, Alexandre Some, Joseph Genz, Torrey J. Wagner, Brent T. Langhals

Faculty Publications

The capabilities of large language models (LLMs) have advanced to the point where entire textbooks can be queried using retrieval-augmented generation (RAG), enabling AI to integrate external, up-to-date information into its responses. This study evaluates the ability of two OpenAI models, GPT-3.5 Turbo and GPT-4 Turbo, to create and answer exam questions based on an undergraduate textbook. 14 exams were created with four true-false, four multiple-choice, and two short-answer questions derived from an open-source Pacific Studies textbook. Model performance was evaluated with and without access to the source material using text-similarity metrics such as ROUGE-1, cosine similarity, and word embeddings. …

Decreasing Foraminiferal Flux In Response To Ongoing Climate Change In The Santa Barbara Basin, California, Emily Harvard, Katherine Cherry, Claudia R. Benitez-Nelson, Eric Tappa, Catherine V. Davis

Faculty Publications

The rapid response of foraminiferal assemblages to changing climate makes their shells an invaluable geological record of the past. However, the time frame over which foraminifera respond to climatic signals and the specific drivers influencing assemblage composition and abundance remain obscure. We focus on the impact of ongoing, anthropogenic climate change on planktic foraminifera in the California Current ecosystem, which would appear as a nearly instantaneous event in the sediment record. The Santa Barbara Basin sediment trap, located off the coast of California, USA since 1993, provides a record of more than 30 years of particulate and foraminiferal flux in …

Investigation Of A Stable And Saturated Reference Electrode Using Metal Chlorides And Oxides In Eutectic Licl-Kcl Molten Salts, Carlos Mejia, Devin Rappleye

Faculty Publications

Stable and reproducible reference electrodes (REs) are essential for electrochemical systems operating in high-temperature molten salts, where consistent control of potential is required. This study uses three different solutes to investigate the development and evaluation of REs in eutectic LiCl-KCl at 773 K. The solutes tested were NiCl2, AgCl, and NiO, each prepared at multiple concentrations to assess stability, reproducibility, and saturation. Electrochemical stability was measured over three days using chronopotentiometry (CP), followed by open circuit potential (OCP), with cyclic voltammetry (CV) also integrated to monitor changes in electrochemical behavior over time. The CP-OCP approach established a Li+/Li redox potential, …

Tort Liability For Failure To Age Gate: A Promising Regulatory Response To Digital Public Health Hazards, Matthew B. Lawrence, Brett Frischmann, Avi Sholkoff

Faculty Publications

Tort liability for failure to “age gate” is a promising legal response to the public health hazards of AI, social media, sports gambling, and other digital spaces. Tort liability for failure to “age gate” hinges liability for harms to minors on an app’s failure to take reasonable steps to prevent minors from gaining access or otherwise to apply appropriate governance rules, such as privacy-protective default settings or ensuring genuine parental consent. While no one legal response is a panacea, tort liability for failure to age gate carries several distinctive advantages that make it a particularly promising option at this stage …

Menopause-Related Changes In Sleep And The Associations With Cardiometabolic Health: A Narrative Review, Joshua R. Sparks, Xuewen Wang Ph.D., Faha

Faculty Publications

This narrative review examines the complex relationship between sleep changes during the menopausal transition and cardiometabolic risks. The most common complaint about sleep is increased awakenings during sleep. Other complaints include having trouble falling asleep, waking up too early, insufficient and non-restorative sleep, and overall poor quality. Sleep determined using objective methods also indicates that greater awakenings after sleep onset are associated with the period of menopausal transition. Polysomnography recordings suggest physiological hyperarousal during sleep. Changes in other sleep metrics, such as sleep latency and sleep duration, are less consistent, and some studies suggest they may not worsen during the …

The Impact Of Objective Urban Features On Perception Of Neighbourhood Environments, Jiuling Li, Mohammad Javad Koohsari, Jing Zhao, Andrew T. Kaczynski, Gavin R. Mccormack, Koichiro Oka, Tomoki Nakaya, Ryo Tanimoto, Reo Watanabe, Tomoya Hanibuchi

Faculty Publications

Perceptions of the neighbourhood environment can play an important role in promoting public health, yet modifying perceptions is challenging. Adjusting the built environment may be a pathway to influence perceptions. In addition to the physical environment, intrapersonal factors may shape perceptions. This study analysed data from several Japanese major cities to explore the association between objective and perceived neighbourhood environment attributes, stratified by age and gender. Perceived neighbourhood environment measures were adapted from established scales, while objective measures were derived from participants’ geographic address data. Multivariate linear regression was employed to assess these associations. All objective measures were positively associated …

“I Feel Like A Lot Of Times Women Are The Ones Who Are Problem-Solving For All The People That They Know”: The Gendered Impacts Of The Pandemic On Women In Alaska, Marya Rozanova-Smith, Andrey N. Petrov

Faculty Publications

The impacts of the COVID-19 pandemic and post-pandemic recovery in urban communities in the Arctic have been substantial, but their gendered aspects remain largely unknown. The goal of this study was to enhance the understanding of the gender-based impact on women in the urban areas of Alaska by exploring strengths and constraints to resilience in the social and economic domains of gender equality during and in the aftermath of the COVID-19 pandemic. Drawing on grounded theory methodology, this study is based on 29 in-depth, semi-structured interviews. The study methodology utilized a conceptual framework that integrated deficit-based and strength-based analytical perspectives. …