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At least 1,225 records · Page 68

Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers

Chronic infection with hepatitis B virus (HBV) is caused by the persistence of closed circular DNA (cccDNA) in the nucleus of infected hepatocytes. Despite available therapeutic anti-HBV agents, eliminating the cccDNA remains challenging. Thus, quantifying and understanding the dynamics of cccDNA are essential for developing effective treatment strategies and new drugs. However, such study requires repeated liver biopsy to measure the intrahepatic cccDNA, which is basically not accepted because liver biopsy is potentially morbid and not common during hepatitis B treatment. We here aimed to develop a noninvasive method for quantifying cccDNA in the liver using surrogate markers in peripheral blood. We constructed a multiscale mathematical model that explicitly incorporates both intracellular and intercellular HBV infection processes. The model, based on age-structured partial differential equations, integrates experimental data from in vitro and in vivo investigations. By applying this model, we roughly predicted the amount and dynamics of intrahepatic cccDNA within a certain range using specific viral markers in serum samples, including HBV DNA, HBsAg, HBeAg, and HBcrAg. Our study represents a significant step towards advancing the understanding of chronic HBV infection. The noninvasive quantification of cccDNA using our proposed method holds promise for improving clinical analyses and treatment strategies. By comprehensively describing the interactions of all components involved in HBV infection, our multiscale mathematical model provides a valuable framework for further research and the development of targeted interventions.

59 BASIC BIOLOGICAL SCIENCES↗

Hyporheic hydraulic geometry: Conceptualizing relationships among hyporheic exchange, storage, and water age

Hyporheic exchange is now widely acknowledged as a key driver of ecosystem processes in many streams. Yet stream ecologists have been slow to adopt nuanced hydrologic frameworks developed and applied by engineers and hydrologists to describe the relationship between water storage, water age, and water balance in finite hydrosystems such as hyporheic zones. Here, in the context of hyporheic hydrology, we summarize a well-established mathematical framework useful for describing hyporheic hydrology, while also applying the framework heuristically to visualize the relationships between water age, rates of hyporheic exchange, and water volume within hyporheic zones. Building on this heuristic application, we discuss how improved accuracy in the conceptualization of hyporheic exchange can yield a deeper understanding of the role of the hyporheic zone in stream ecosystems. Although the equations presented here have been well-described for decades, our aim is to make the mathematical basis as accessible as possible and to encourage broader understanding among aquatic ecologists of the implications of tailed age distributions commonly observed in water discharged from and stored within hyporheic zones. Our quantitative description of “hyporheic hydraulic geometry,” associated visualizations, and discussion offer a nuanced and realistic understanding of hyporheic hydrology to aid in considering hyporheic exchange in the context of river and stream ecosystem science and management.

54 ENVIRONMENTAL SCIENCES↗

Experimental Observations of the Topology of Convolutional Neural Network Activations

Topological data analysis (TDA) is a branch of computational mathematics, bridging algebraic topology and data science, that provides compact, noise-robust representations of complex structures. Deep neural networks (DNNs) learn millions of parameters associated with a series of transformations defined by the model architecture resulting in high-dimensional, difficult to interpret internal representations of input data. As DNNs become more ubiquitous across multiple sectors of our society, there is increasing recognition that mathematical methods are needed to aid analysts, researchers, and practitioners in understanding and interpreting how these models' internal representations relate to the final classification. In this paper we apply cutting edge techniques from TDA with the goal of gaining insight towards interpretability of convolutional neural networks used for image classification. We use two common TDA approaches to explore several methods for modeling hidden layer activations as high-dimensional point clouds, and provide experimental evidence that these point clouds capture valuable structural information about the model's process. First, we demonstrate that a distance metric based on persistent homology can be used to quantify meaningful differences between layers and discuss these distances in the broader context of existing representational similarity metrics for neural network interpretability. Second, we show that a mapper graph can provide semantic insight as to how these models organize hierarchical class knowledge at each layer. These observations demonstrate that TDA is a useful tool to help deep learning practitioners unlock the hidden structures of their models.

topological data analysis, deep learning↗

Development and Evaluation of Distributed Energy Resource Device Models: Electric Vehicles, Electric Water Heaters, and Commercial Refrigeration Systems

In order to validate distributed energy resource (DER) models operated with grid services in the GMLC 1.4.2 team’s February (GMLC 2019a) and July (GMLC 2019b) reports, a test and measurement program using actual DER devices was conducted by national laboratories for three devices: (1) electric vehicles (EVs), (2) water heaters, and (3) commercial refrigeration. Test procedures were developed and carried out to identify the mathematical models and their parameters that describe the operational function, characterize the physics, and obey transient response of the devices. This report focuses on the experimental results obtained to develop and verify simulations of three specific EV models. This section summarizes elements of the mathematical model and shows the necessity data collected from the EVs while charging and discharging (driving). In the course of the study, we found it necessary to make some modifications to the model to deal with observed transient behavior. Section 1.2 details the model assumptions and equations, Section 1.3 provides details of the EVs tested, Section 1.4 outlines the test procedures developed for the projects, and Section 1.5 presents the experimental results obtained for the three different EVs tested and how these results compare to the models running the same test profiles.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Calculation of the First Moment of Energy Using D-T Reactivity Formalisms Under the Maxwell-Boltzmann Distribution (Pt. 1)

Nuclear fusion science is an example of a scientific field with a rich history of expert involvement and scientific publications, which together, form an expert-knowledge base. One example of this history is the utilization of published reaction rates from a variety of authors. Investigators for Deuterium-Tritium (D-T) ion fusion can choose from using frequently cited methods: the Bosch and Hale reactivity, thermonuclear reaction rates from Caughlan and Fowler, and the reactivity evaluation from Miley, Towner & Ivich which forms the basis of the Naval Research Lab (NRL) formulary. There are other choices available. Each of the reactivity formulations considered here, are based upon the Maxwell- Boltzmann velocity distribution for D-T fusion ion reactants. Numerical methods for computer codes simulating hot, energetic plasmas, include tabulations of the reactivity, and the first moment of energy. The purpose of this study is to answer the question: what is the first moment of energy, and how has it been formulated? This report is part of a series of reports by the authors on D-T fusion-reaction formalism. The present focus is on defining the mathematical relationship of the first moment of D-T fusion ion kinetic energy, $\langle$E$\rangle$, with the fusion crosssection, fusion reactivity and its derivative with respect to ion-temperature. Three variants of the first moment $\langle$E$\rangle$ are analytically developed and explored: 1) constant cross-section, 2) a normalized first moment, and 3) a particular function of the first moment. Much of the mathematical development is relegated to the Appendices, for a concise presentation of topics and results. A research component of this discussion is our comparison of some of the reactivity and its derivative results between evaluations (1) versus (2) and (3), which the authors have not found in any other publication to date. This investigation is useful for validation, verification (V&V) and uncertainty quantification (UQ) as it compares the work of several authors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Accelerometer Modeling in the State-Space

Generically, accelerometers are sensors that measure the accelerating force applied to an object. Their operation is based on a simple mechanical system and D’Alembert’s force principle along with Newton’s laws of motion. This device is typically mounted to the body of the test object under investigation that is subjected to an accelerating force. The displacement of the seismic or “proof” mass due to the acceleration is sensed by an embedded component from which the acceleration is determined. Interestingly enough, the resulting the resulting mathematical relations governing the dynamical motion is based on the underlying physics, sensor materials, geometry and fabrication. Mathematically, the various designs satisfy the underlying Newtonian equations of motion, but their type and performance differ significantly.

42 ENGINEERING↗

Entanglement in Gravity and Quantum Field Theory (Final Report)

It is becoming increasingly clear that ideas from quantum information theory, particularly the notion of quantum entanglement, play a fundamental role in some of the deepest aspects of our modern theories of quantum fields and gravity. The aim of this research was to explore the role that quantum entanglement plays in quantum field theories and in the nature of space-time and gravity. Building on a variety of earlier results obtained in these regards at the University of Illinois, we explored the constraints on the dynamical content of quantum field theories that follow from their entanglement properties. Topological field theories are important examples of particularly simple quantum field theories whose patterns of entanglement make connections between high energy physics, condensed matter physics and mathematics. These theories are directly relevant to low energy properties of certain materials. The study of such theories allowed us to investigate ideas that are relevant to quantum information research, such as new notions of entanglement between multiple parties and the quantum properties of interfaces between different phases of such materials. In addition, we employed new results in mathematics which strengthen monotonicity constraints on relative entropy to study their ramifications in quantum field theories, and we used quantum information methods to study the emergence of quantum gravity and string theory in holographic quantum field theories.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Multi-shock design tools in double shell models

The essence of the project was to implement a program in python that demonstrated certain models put forth by fusion physicists. Across the time spent at Los Alamos National Laboratory, much was spent programming. Though fundamentally programmatical in nature, the task contained considerable difficulty hid within mathematically deriving and manipulating the models while maintaining data discretization. The result of solving these complications gave invaluable experience in applied mathematics. The final product, a piece of lengthy code, ended up having the full range of desired capabilities, with plans for more. Given the laser power history from a pulse shot on NIF, Omega, or any other Inertial Confinement Fusion facility, the code maps the terrain of radiation temperature inside the hohlraum throughout the period of the shot. Additionally, shock wave convergence prediction was implemented as additional capability. As the name of the project suggests, this tool acts as a compass of direction for researchers designing laser power profiles. Further development of this tool will undoubtedly assist in the research conducted on single and double-shell indirect ICF, consequently expanding the capabilities of operating stewardship over the national nuclear stockpile.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Further development of finite-temperature density functional theory (Technical Report on FG02-08ER46496)

The final year of funding was spent supporting research into extending conditional probability theory to generate the thermal dependence of PBE. The necessary background work led to a paper being published on the uniform electron gas (Dennis Perchak, Ryan J. McCarty, and Kieron Burke, Phys. Rev. B 105, 165143 (2022).). The graduate student John Kozlowski also contributed to a mathematical paper about DFT (Steven Crisostomo, Ryan Pederson, John Kozlowski, Bhupalee Kalita, Antonio C. Cancio, Kiril Datchev, Adam Wasserman, Suhwan Song, and Kieron Burke, Letters in Mathematical Physics 113, 42 (2023).).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

New perspectives on QFT and gravity from quantum entanglement

The work accomplished by the PI as part of this award included studying the fundamental as- pects of quantum field theory (QFT) and the nature of space-time and gravity via the patterns of quantum entanglement present in these theories. By following these patterns the PI attacked basic questions on the nature of quantum gravity and found new constraints on the dynamical content of QFT. These topics find a natural home within the holographic dualiy, a deep mathemat- ical correspondence discovered in string theory where a gravitational system can be described by a quantum system without gravity. By studying the spatial distribution of quantum correlation, or entanglement, in various quantum systems the PI managed to directly observe the holographic emergence of quantum gravity within this mathematical framework. The PI also characterized the space-time structure that emerges via the duality. In achieving these aims the project shed light on the thermodynamic nature of gravity and had considerable impact on understanding of the uni- fication of gravity with quantum mechanics. Additionally, this work shed light on the structure of quantum entanglement in QFT and in so doing used powerful constraints satisfied by entanglement and it’s generalizations to place bounds on the basic data of the QFT. The project also related these bounds to causality constraints and quantum energy conditions in field theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

MODELING AND METHOD FOR OPTICAL PERFORMANCE OF A RECEIVER COATING AND ITS DEGRADATION DUE TO OPERATION

The optical properties of the coating used on a concentrated solar power (CSP)’s receiver directly impact the performance of the power plant. Receiver coatings are designed to absorb as much heat as possible and transfer it to the circulating fluid. Over time, the absorptivity of the receiver coating degrades due to environmental and operational conditions. This project aims to (1) create a test apparatus that allows coatings to undergo accelerated lifetime testing under conditions that mimic what the coating will experience on-tower; and (2) develop a mathematical model that based on the test data predicts absorptivity over time. To create the mathematical model, samples of BrightSource Energy’s Gen1 and Gen2 coatings were tested first looking at individual failure modes (such as high temperature cycling) and then for combined failure modes in the newly developed apparatus. In addition to taking optical measurements, the samples were destroyed to allow for metalogical evaluation to understand what was happening on a microscopic level. Pre-existing models from the literature that describe accelerated testing as well as individual phenomena observed in the coating were then combined to create the model. Additionally, the Gen2 and Gen3 coatings are being testing at the Plataforma Solar de Almería (PSA) facility in Almeria, Spain to confirm that the apparatus test results are similar to those received on-sun. (PSA’s facility closely mimics on-tower conditions). The goal is to enable industry players to test coatings using the new apparatus, gather absorptivity measurements (without needing to destroy samples), and input the information into the model to determine how the coating will perform over time, thus allowing the optical performance of coatings to be compared even before they are used on-tower. The model will be publicly available by the end of the project (currently projected as December 2024).

14 SOLAR ENERGY↗

Alternative Conceptual Models of the Subsurface at the Hanford Site

This report describes the use of a multipoint geostatistics (MPS) framework with multiple data types for developing alternative conceptual-mathematical models of the subsurface at the Hanford Site. Developing multiple conceptual-mathematical models of the site is important for assessing potential uncertainties related to the features, events, and processes that control the subsurface flow of groundwater and the transport of contaminants of concern (COCs). Evaluating the effects of these uncertainties can result in better site characterization, monitoring, and remedial decisions.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Precision Computations in Strongly Coupled Conformal Field Theories (Final Technical Report)

Conformal Field Theories (CFTs) are quantum field theories that are invariant under the conformal symmetry group (which includes translations and rotations, but also local rescalings of spacetime). They are building blocks of general quantum field theories, and appear in many areas of physics, including statistical physics, condensed matter physics, particle physics, and quantum gravity. Because of their extra symmetries, the mathematical structure of CFTs is tightly constrained, and this leads to the idea of the ``conformal bootstrap," which is to use these mathematical structures to constrain, and in some cases determine, CFT observables. A new numerical implementation of the conformal bootstrap idea appeared in 2008 with the work of Rattazzi, Rychkov, Tonni, and Vichi. Their observation was that certain bootstrap constraints (conformal symmetry and unitarity) could be combined to yield a convex optimization problem that constraints CFT data. By solving this convex optimization problem on a computer, one could obtain bounds on observables like critical exponents and operator product expansion (OPE) coefficients. Over the course of this award, the PI has improved numerical bootstrap techniques by optimizing known algorithms and finding new ones for performing the required convex optimization computations. The PI has applied these techniques to compute high-precision observables in several important strongly-coupled systems. The PI has also explored both analytical and numerical bootstrap methods for constraining the space of low energy effective field theories of quantum gravity, and developed new analytical techniques for CFT and QFT more broadly.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Non-invertible Symmetries and their Applications (Final Report)

Symmetries have long been a staple of theoretical physics. Recent developments have led to extensions of the notion of symmetry to so-called generalized symmetries, a particularly interesting class of which are non-invertible symmetries. Whereas traditional symmetries form a group—a mathematical structure capturing the intuition that the composition of two symmetry transformations is another symmetry transformation, and that every symmetry transformation can be undone by an inverse transformation—non-invertible symmetries have the interesting property that they do not form a group. The current award was used to pursue the study of non-invertible symmetries, focusing on both their mathematical framework and physical applications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Developing ML/AI Methods for High-Throughput Characterization of Multiple-Sensor Streams of Tokamak Dynamics for High-Speed Control (Final Report)

This project evaluated and developed new mathematical and algorithmic techniques capable of handling (in real-time) the growing amounts of data generated by modern fusion research. While existing numerical linear algebra (NLA) methods provide the backbone to classical data analysis and algorithms, these methods fundamentally do not port to distributed architectures nor do they allow low-latency data reduction for control. Motivated by the needs for modern fusion reactors, this project explored and implemented new numerical methods to characterize plasma dynamics, respond in real-time to discharge evolution, and to process massive-scale data accurately and rapidly more fully. This project links expertise in multiple-sensor diagnostics of tokamak plasma dynamics from Columbia University’s Plasma Physics Laboratory with expertise in massive-scale data reduction and extreme data control algorithms at Columbia University’s Data Science Institute. This interdisciplinary project (i) applied machine learning methods, (ii) implemented a properly-trained neural-network for very fast processing of high-speed plasma videography, and (ii) developed the applied mathematical methods, based on randomized-NLA (rNLA) routines, for data analysis, reduction, and real-time control. The Columbia University High Beta Tokamak-Extended Pulse (HBT-EP) facility provided data to test new algorithms and partnership with Columbia University's Data Sciences Institute evaluated the broader use of new algorithms for many challenging control applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Manipulation of Geographic Information in Global Seismology

Geographic data, such as seismic event locations, station locations, etc., are generally given in geographic latitude Φ ’, longitude θ , and depth below sea level, ζ , using the WGS84 ellipsoid as a reference. In software systems that use this type of geographic data, it is necessary to manipulate the data mathematically in order to perform such tasks as finding the angular distance or azimuth from one point to another, to find an array of points along a great circle, to rotate a point about a pole of rotation, to move a point some angular distance in a specified direction, to find the intersections of two great circles or to find the intersections of a great circle and a small circle. In this paper, equations are presented that convert geographic locations first to geocentric coordinates and then to Earth-centered Cartesian coordinates where many mathematical manipulations can be performed conveniently and efficiently.

58 GEOSCIENCES↗

Explainable and Differentiable Reinforcement Learning for Multi-objective Optimization in Particle Accelerators

Operating particle accelerators involves optimizing multiple goals simultaneously, which can be challenging due to trade-offs among objectives. While evolutionary algorithms like the genetic algorithm (GA) have been used for various Multi-Objective Optimization (MOO) tasks, they are not inherently suited for complex control problems. This talk highlights two variations of Reinforcement Learning (RL) for concurrently optimizing heat load and trip rates at the Continuous Electron Beam Accelerator Facility (CEBAF). The problem involves strict constraints on individual states, actions, and overall energy requirements of the beam. First, this talk highlights how differentiability can be harnessed through a Deep Differentiable Reinforcement Learning (DDRL) approach to address MOO issues within particle accelerators. We examine the DDRL method alongside Model Free Reinforcement Learning (MFRL), GA, and Bayesian Optimization (BO). The performance of these methods is assessed by generating a Pareto-front for two objectives. Our findings indicate that DDRL excels in handling high-dimensional problems more effectively than MFRL, BO, and GA. Next, we will show integration of explainable physics-based constraints into RL algorithms to enhance trans- parency and trust in decision-making processes by enabling users to verify that agents adhere to established physical principles. This surrogate function can be modeled using neural networks or sparse dictionary mod- els. By examining the mathematical form of the learned constraint function, we are able to confirm the agent has learned to use the established physics of each environment provided but the surrogate model. In addi- tion, we find that the introduction of a mathematical functional dictionary based surrogate model enables our reinforcement learning algorithms to reliably converge for difficult high-dimensional accelerator controls environments.

Rajput, Kishansingh [Thomas Jefferson National Acc↗

SUSY 2025 at UC Santa Cruz (Final Technical Report)

The 32nd International Conference on Supersymmetry and the Unification of Fundamental Interactions (SUSY 2025) took place from August 18--23, 2025. During the week preceding the SUSY 2025 conference, the associated pre-SUSY school took place from August 11--15, 2025. Both events were organized and hosted by the Santa Cruz Institute for Particle Physics at the University of California, Santa Cruz. The SUSY 2025 conference brought together theorists and experimentalists specializing in particle physics, astroparticle physics, cosmology, mathematical physics, and string theory to discuss recent developments in these areas, with a focus on theoretical aspects and experimental searches associated with phenomena that lie beyond the Standard Model of particle physics and the standard mathematical framework of modern cosmology. The pre-SUSY school provided advanced pedagogical lectures for graduate students and early-career postdoctoral researchers on many of the foundational topics that were subsequently addressed in the main SUSY 2025 conference that followed. DOE support helped increase accessibility for early-career scientists by covering conference support costs that enabled free participation in the pre-SUSY school and substantially reduced registration fees for students attending the conference.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗