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DOE OSTI2020

Continuous and discrete modeling of HIV-1 decline on therapy

Mathematical models have shed light on the dynamics of HIV- 1 infection in vivo. In this paper, we generalize continuous mathematical models of drug therapy for HIV-1 by Perelson et al. (Science 271:1582–1586, 1996) and Perelson and Nelson (SIAM Rev 41:3–44, 1999) on time scales, i.e., a nonempty closed subset of real numbers in order to derive new discrete models that predict the total concentration of plasma virus as a function of time. Here, one of our main goals is to compare discrete mathematical models with the continuous model in Perelson et al. (1996) where HIV infected patients were given protease inhibitors and sampled frequently thereafter. For the comparison, we use experimental data collected in Perelson et al. (1996) and estimate the parameters such as the virion clearance rate and the rate of loss of infected cells by fitting the total concentration of plasma virus to this data set. Our results show that discrete systems describe the best fit. In the previous models of this study, the efficacy of protease inhibitor is assumed to be perfect. Motivated by Perelson and Nelson (1999), we end the paper with a mathematical model of imperfect protease inhibitor and reverse transcriptase (RT) inhibitor combination therapy of HIV-1 infection on time scales with its stability analysis.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Comparison of steady-state analytical wake models implemented in wind farm analysis software

A common set of mathematical wind turbine wake models are implemented in a few, well-adopted computational tools for wind farm wake modelling. Although the referenced mathematical formulations are common, implementation details may lead to differences in results. This study presents a systematic comparison of the implementation of mathematical wake models in open source, Python-based wind turbine wake modelling software, and a set of the models are directly compared. Despite aligning only the mathematical model parameters and retaining the default computational model parameters, good agreement is found across most of the model implementations, and additional agreement is expected upon further parameters alignment.

17 WIND ENERGY↗

DOE OSTI2025

Reliable and Efficient Machine Learning (Final Technical Report)

Modern scientific experiments generate massive amounts of data at a pace much faster than humans can manually analyze. While machine learning has revolutionized commercial data analysis (such as recommending movies or recognizing faces), applying these tools to complex scientific discovery is challenging because scientific answers must be precise, interpretable, and adhere to physical laws. The research under this project aims to develop new mathematical tools and computer algorithms specifically designed for scientific applications. Major progress has been made in automatically cleaning and deconstructing messy experimental data, analyzing the visual information of physical phenomena, determining the underlying physical variables, and providing rig orous mathematical analysis of interesting algorithms and concepts widely used in machine learning. This project addressed the critical gap between our ability to generate massive scientific data and our ability to extract interpretable information from it. We established mathematical foundations for Scientific Machine Learning (SciML) aimed at effective data analytics and automated discovery. Our work focused on three core objectives: (1) developing reliable feature extraction methods for dynamic high-dimensional data, (2) establishing mathematical foundations for discovering dynamics via neural networks, and (3) creating rigorous optimization techniques for these models. Key outcomes come from two fronts. On the practical side, they include the development of algorithms that significantly enhance the extraction of signals from field data, as well as the capability to handle situations that exhibit smooth variations or physical stretching due to temperature changes. They also include the creation of an automated framework for discovering fundamental state variables from raw experimental data, demonstrating the ability to identify intrinsic physical dimensions without prior knowledge of the governing laws. On the theoretical front, the research results in theoretical advances in Optimal Transport, a widely used notion in SciML, specifically regarding functions with fixed-size nodal sets, provide sharp bounds relevant to uncertainty quantification. Meanwhile, the outcomes also include the establishment of convergence theories for nonlocal gradient descent methods, enabling robust optimization with noisy data in high-dimensional settings commonly encountered in scientific modeling. The project also helps creating opportunities to train the next generation of researchers, equipping them with the necessary technical skills for today’s workplace and preparing them for future advances.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Overcoming the Challenges to Enhancing Experimental Plant Biology With Computational Modeling

The study of complex biological systems necessitates computational modeling approaches that are currently underutilized in plant biology. Many plant biologists have trouble identifying or adopting modeling methods to their research, particularly mechanistic mathematical modeling. Here we address challenges that limit the use of computational modeling methods, particularly mechanistic mathematical modeling. We divide computational modeling techniques into either pattern models (e.g., bioinformatics, machine learning, or morphology) or mechanistic mathematical models (e.g., biochemical reactions, biophysics, or population models), which both contribute to plant biology research at different scales to answer different research questions. We present arguments and recommendations for the increased adoption of modeling by plant biologists interested in incorporating more modeling into their research programs. As some researchers find math and quantitative methods to be an obstacle to modeling, we provide suggestions for easy-to-use tools for non-specialists and for collaboration with specialists. This may especially be the case for mechanistic mathematical modeling, and we spend some extra time discussing this. Through a more thorough appreciation and awareness of the power of different kinds of modeling in plant biology, we hope to facilitate interdisciplinary, transformative research.

58 GEOSCIENCES↗

DOE OSTI2026

Regional Earthquake Ground Motion Simulations for Southern California With EQSIM: Insights From the 2008 Chino Hills, 2024 Highland Park, and 2021 Carson Earthquakes

This study presents physics-based, 3D simulations using the EQSIM framework for several earthquakes in the Los Angeles region. The primary objective was to assess the ability of deterministic physics-based ground motion simulations to reproduce the observed motions from historical events. The selected events included the mathematical equation M w 5.4 2008 Chino Hills, the mathematical equation M w 4.4 2024 Highland Park, and the mathematical equation M w 4.3 2021 Carson events. The simulated motions were evaluated by comparing the recorded and simulated seismograms, as well as the Fourier amplitude spectra, across multiple seismic stations. The SCEC 3D velocity model, CVM-S4.26.M01, was used to represent the regional geology, and ground motion simulations were carried out with a resolution of up to 5 Hz. The results indicate that the simulated motions captured the recorded motions up to approximately 4 Hz. While careful iterations regarding source parameters and corner frequencies were required, and, for the case of the Highland Park event, some of the near-source stations had relatively low accuracy, the present study established a positive step toward the utilization of physics-based simulations in practical applications. The computational efficiencies exhibited by EQSIM, especially on GPU clusters, further supported this assertion, as wall-clock times of simulations involving more than 10 billion grid points were as low as mathematical equation minutes. This permits ensemble simulations for a considered scenario event so that modeling uncertainties (e.g., source and geology) can be bracketed.

EQSIM↗

DOE OSTI2021

Elucidating Cycling Rate-Dependent Electrochemical Strains in Sodium Iron Phosphate Cathodes for Na-ion Batteries

Battery electrodes materials undergo significant mechanical instabilities which affects their longevity and exert rate-limitations during the cycling process. In this study, we investigate the rate-dependent mechanical response of sodium iron phosphate (NaFePO4, NFP) cathodes during Na intercalation via galvanostatic cycling at different rates by employing digital image correlation, electrochemical methods, and mathematical model. The mechanical behaviour of the electrode shows strong dependance on the applied scan rate. At slower rates, electrode shows asymmetrical strain generation between anodic and cathodic cycles, which is attributed to the formation of cathode-electrolyte interface layers. The electrode undergoes smaller strain generation when cycled at slower rates when the same amount of Na ions is removed or inserted into the electrode. A mathematical model was developed to predict strain evolution in the composite electrode as well as the concentration profile of the Na ions in the electrode particles. Rate-dependent and time dependent factors on the strain generation in the electrode are attributed to the capacity-dependent intercalation strains, rate-dependent mismatch strains, and time-dependent irreversible strains. The combination of in situ strain measurements with the analytical model provided new insight into the electrochemically induced mechanical deformations in Na-ion cathode electrodes.

Ozdogru, Bertan↗

DOE OSTI2026

NLML: A Deep Neural Network Emulator for the Exact Nonlinear Interactions in a Wind Wave Model

Nonlinear wave interactions describe the resonant energy transfer between wave components, playing a fundamental role in the evolution of ocean wave spectra. Nonlinear wave interactions significantly influence wave growth and development, making them essential for accurate wave modeling. However, resolving the full six-dimensional Boltzmann integral of the exact nonlinear wave interactions (Webb-Resio-Tracy method, WRT) is computationally expensive, limiting its application in real-time operational wave forecasting and for research purposes. Current approximations, such as the Discrete Interaction Approximation (DIA), prioritize computational speed over accuracy, resulting in significant errors in wave mean parameters. Here, we introduce NLML, a machine learning (ML) emulator designed to approximate the exact nonlinear wave interactions within WAVEWATCH III (WW3), with the goal of achieving the accuracy of WRT while maintaining the stability and computational speed of DIA. By leveraging GPU capabilities such as half precision inference, we achieved substantial speedups, up to 136x mathematical equation faster than the WRT and only a modest 1.04x mathematical equation slowdown relative to DIA, while achieving 2x mathematical equation the accuracy of DIA in global wave spectral energy and mean wave parameters, with up to 7x mathematical equation higher accuracy in some regions. Unlike previous ML approaches, NLML maintained inherent stability throughout model integration in a standalone, year-long WW3 simulation, without requiring additional constraints. Our new ML parameterization bridges the gap between accuracy and efficiency, offering a promising alternative for improving wave modeling in operational settings and research purposes.

16 TIDAL AND WAVE POWER↗

DOE OSTI2019

The Bloch equation for spin dynamics in electron storage rings: Computational and theoretical aspects

In this paper, we describe our work on spin polarization in high-energy electron storage rings which we base on the Full Bloch equation (FBE) for the polarization density and which aims towards the [Formula: see text] option of the proposed Future Circular Collider (FCC-ee) and the proposed Circular Electron Positron Collider (CEPC). The FBE takes into account non spin-flip and spin-flip effects due to synchrotron radiation including the spin-diffusion effects and the Sokolov–Ternov effect with its Baier–Katkov generalization as well as the kinetic-polarization effect. This mathematical model is an alternative to the standard mathematical model based on the Derbenev–Kondratenko formulas. For our numerical and analytical studies of the FBE, we develop an approximation to the latter to obtain an effective FBE. This is accomplished by finding a third mathematical model based on a system of stochastic differential equations (SDEs) underlying the FBE and by approximating that system via the method of averaging from perturbative ODE theory. We also give an overview of our algorithm for numerically integrating the effective FBE. This discretizes the phase space using spectral methods and discretizes time via the additive Runge–Kutta (ARK) method which is a high-order semi-implicit method. We also discuss the relevance of the third mathematical model for spin tracking.

Physics↗

DOE OSTI2020

Method for enhancing a computer to estimate an uncertainty of an onset of a signal of interest in time-series noisy data

A computer-implemented method of enhancing a computer to estimate an uncertainty of an onset of a signal of interest in time-series noisy data. A first mathematical model of first time series data that contains only noise is calculated. A second mathematical model of second time series data that contains the noise and an onset of a signal of interest in the second time series data is calculated. A difference is evaluated between a first combination, being the first mathematical model and the second mathematical model, and a second combination, being the first time series data and the second time series data, wherein evaluating is performed using a generalized entropy metric. A specific time when an onset of the signal of interest occurs is estimated from the difference. An “a posteriori” distribution is derived for an uncertainty of the specific time at which the onset occurs.

Stracuzzi, David John↗

DOE OSTI2023

Convergence analysis of single rate and multirate fixed stress split iterative coupling schemes in heterogeneous poroelastic media

Recently, the accurate modeling of flow–structure interactions has gained more attention and importance for both petroleum and environmental engineering applications. Of particular interest is the coupling between subsurface flow and reservoir geomechanics. Different single rate and multirate iterative and explicit coupling schemes have been proposed and analyzed in the past. In addition, Banach fixed point contraction results were obtained for iterative coupling schemes, and conditionally stable results were obtained for explicit coupling schemes. In this work, we will consider the mathematical analysis of the single rate and multirate fixed stress split iterative coupling schemes for spatially heterogeneous poroelastic media. We will re–establish the contractivity for both schemes in the localized case, and we will show that heterogeneities come at the expense of imposing more restricted conditions on the number of fine flow time steps that can be taken within one coarse mechanics time step in the multirate case. Our mathematical analysis is supplemented by numerical simulations validating our derived upper bounds. Finally, to the best of our knowledge, this is the first rigorous mathematical analysis of the multirate fixed–stress split iterative coupling scheme in heterogeneous poroelastic media.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Structural conserved moiety splitting of a stoichiometric matrix

Characterising biochemical reaction network structure in mathematical terms enables the inference of functional biochemical consequences from network structure with existing mathematical techniques and spurs the development of new mathematics that exploits the peculiarities of biochemical network structure. The structure of a biochemical network may be specified by reaction stoichiometry, that is, the relative quantities of each molecule produced and consumed in each reaction of the network. A biochemical network may also be specified at a higher level of resolution in terms of the internal structure of each molecule and how molecular structures are transformed by each reaction in a network. The stoichiometry for a set of reactions can be compiled into a stoichiometric matrix N ϵ Z mxn where each row corresponds to a molecule and each column corresponds to a reaction. We demonstrate that a stoichiometric matrix may be split into the sum of m - rank(N) moiety transition matrices, each of which corresponds to a subnetwork accessible to a structurally identifiable conserved moiety. The existence of this moiety matrix splitting is a property that distinguishes a stoichiometric matrix from an arbitrary rectangular matrix.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Early Career Paths at Los Alamos National Laboratory

We represent a selection of early career staff at LANL with backgrounds in mathematics. There are many possible paths to a position at LANL. The lab has very active graduate research and postdoctoral programs, and it is not uncommon for graduate students to become postdocs, who can then be “converted” to staff. Conversion from being a postdoc is not the only route to a position at LANL, nor is it a guarantee, but most of us did postdocs here before becoming staff. Being a postdoc here also gives you an idea of whether you’d like living in northern New Mexico, a rugged, beautiful, and somewhat remote area. It is important to say here that citizenship is not a requirement for many of the positions at the lab. The lab historically and currently welcomes investigators from all over the world. LANL offers a broad spectrum of mathematical challenges that are largely problem driven. Particularly to those who feel that academic mathematics can be stove-piped, with a focus on deep but not necessarily broad expertise, the LANL environment gives the flexibility to move and grow in many different directions. The lab encourages a team-based approach to problems, which not only enhances the breadth of our approach to solving problems, but also gives team members access to new fields. From the outside (academia), however, it can be difficult to see how fields map between academia and the lab. This is one of the reasons that having interaction with the lab as a graduate student or postdoc can be helpful in understanding if the environment would be a good match for you. An important advantage of working at the lab is our high visibility both in academia, as well as in industry and the government. Because of its mission-driven projects, LANL, and more broadly the Department of Energy Laboratories, help set research directions that are picked up by researchers in academia. For this reason, many lab staff have worked at LANL for a number of years, then have transferred into academia after having set the agenda for their field of expertise. Below, we will share some of our experiences, opinions, and reflections in order to give the reader a feel for our own early career experiences.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Classifying photonic topology using the spectral localizer and numerical K -theory

Recently, the spectral localizer framework has emerged as an efficient approach for classifying topology in photonic systems featuring local nonlinearities and radiative environments. In nonlinear systems, this framework provides rigorous definitions for concepts such as topological solitons and topological dynamics, where a system’s occupation induces a local change in its topology due to nonlinearity. For systems embedded in radiative environments that do not possess a shared bulk spectral gap, this framework enables the identification of local topology and shows that local topological protection is preserved despite the lack of a common gap. However, as the spectral localizer framework is rooted in the mathematics of C*-algebras, and not vector bundles, understanding and using this framework requires developing intuition for a somewhat different set of underlying concepts than those that appear in traditional approaches for classifying material topology. In this tutorial, we introduce the spectral localizer framework from a ground-up perspective and provide physically motivated arguments for understanding its local topological markers and associated local measure of topological protection. In doing so, we provide numerous examples of the framework’s application to a variety of topological classes, including crystalline and higher-order topology. We then show how Maxwell’s equations can be reformulated to be compatible with the spectral localizer framework, including the possibility of radiative boundary conditions. To aid in this introduction, we also provide a physics-oriented introduction to multi-operator pseudospectral methods and numerical K-theory, two mathematical concepts that form the foundation for the spectral localizer framework. Finally, we provide some mathematically oriented comments on the C*-algebraic origins of this framework, including a discussion of real C*-algebras and graded C*-algebras that are necessary for incorporating physical symmetries. Looking forward, we hope that this tutorial will serve as an approachable starting point for learning the foundations of the spectral localizer framework.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Verification of MOOSE/Bison's Heat Conduction Solver Using Combined Spatiotemporal Convergence Analysis

Bison is a computational physics code that uses the finite element method to model the thermo-mechanical response of nuclear fuel. Since Bison is used to inform high-consequence decisions, it is important that its computational results are reliable and predictive. One important step in assessing the reliability and predictive capabilities of a simulation tool is the verification process, which quantifies numerical errors in a discrete solution relative to the exact solution of the mathematical model. One step in the verification process—called code verification—ensures that the implemented numerical algorithm is a faithful representation of the underlying mathematical model, including partial differential or integral equations, initial and boundary conditions, and auxiliary relationships. In this paper, the code verification process is applied to spatiotemporal heat conduction problems in Bison. Simultaneous refinement of the discretization in space and time is employed to reveal any potential mistakes in the numerical algorithms for the interactions between the spatial and temporal components of the solution. For each verification problem, the correct spatial and temporal order of accuracy is demonstrated for both first- and second-order accurate finite elements and a variety of time-integration schemes. Furthermore, these results provide strong evidence that the Bison numerical algorithm for solving spatiotemporal problems reliably represents the underlying mathematical model in MOOSE. The selected test problems can also be used in other simulation tools that numerically solve for conduction or diffusion.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

TNet: A Model-Constrained Tikhonov Network Approach for Inverse Problems

Deep learning (DL), in particular deep neural networks, by default is purely data-driven and in general does not require physics. This is the strength of DL but also one of its key limitations when applied to science and engineering problems in which underlying physical properties—such as stability, conservation, and positivity—and accuracy are required. DL methods in their original forms are often not capable of respecting the underlying mathematical models or achieving desired accuracy even in big-data regimes. On the other hand, many data-driven science and engineering problems, such as inverse problems, typically have limited experimental or observational data, and DL would overfit the data in this case. Leveraging information encoded in the underlying mathematical models, we argue, not only compensates for missing information in low data regimes but also provides opportunities to equip DL methods with the underlying physics, hence promoting better generalization. This paper develops a model-constrained DL approach and its variant TNet—a Tikhonov neural network—which are capable of learning not only information hidden in the training data but also in the underlying mathematical models to solve inverse problems governed by partial differential equations in low data regimes. We provide the constructions and some theoretical results for the proposed approaches for both linear and nonlinear inverse problems. Since TNet is designed to learn inverse solutions with Tikhonov regularization, it is interpretable: in fact it recovers Tikhonov solutions for linear cases while potentially approximating Tikhonov solutions for nonlinear inverse problems. We also prove that data randomization can enhance not only the smoothness of the networks but also their generalizations. Comprehensive numerical results confirm the theoretical findings and show that with even as little as 1 training data sample for one-dimensional (1D) deconvolution, 5 for an inverse 2D heat conductivity problem, 100 for inverse initial conditions for a time-dependent 2D Burgers’s equation, and 50 for inverse initial conditions for 2D Navier–Stokes equations, TNet solutions can be as accurate as Tikhonov solutions while being several orders of magnitude faster. Furthermore, this is possible owing to the model-constrained term, replications, and randomization.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine

The advancements in next-generation sequencing have made it possible to effectively detect somatic mutations, which has led to the development of personalized neoantigen cancer vaccines that are tailored to the unique variants found in a patient’s cancer. These vaccines can provide significant clinical benefit by leveraging the patient’s immune response to eliminate malignant cells. However, determining the optimal vaccine dose for each patient is a challenge due to the heterogeneity of tumors. To address this challenge, we formulate a mathematical dose optimization problem based on a previous mathematical model that encompasses the immune response cascade produced by the vaccine in a patient. We propose an optimization approach to identify the optimal personalized vaccine doses, considering a fixed vaccination schedule, while simultaneously minimizing the overall number of tumor and activated T cells. To validate our approach, we perform in silico experiments on six real-world clinical trial patients with advanced melanoma. We compare the results of applying an optimal vaccine dose to those of a suboptimal dose (the dose used in the clinical trial and its deviations). Our simulations reveal that an optimal vaccine regimen of higher initial doses and lower final doses may lead to a reduction in tumor size for certain patients. Our mathematical dose optimization offers a promising approach to determining an optimal vaccine dose for each patient and improving clinical outcomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

ASCR@40: Highlights and Impacts of ASCR’s Programs

A report compiled by the ASCAC Subcommittee on the 40-year history of ASCR for the U.S. Department of Energy’s Office of Advanced Scientific Computing Research. The Office of Advanced Scientific Computing Research (ASCR) sits within the Office of Science in the Department of Energy (DOE). Per their web pages, “the mission of the ASCR program is to discover, develop, and deploy computational and networking capabilities to analyze, model, simulate, and predict complex phenomena important to the DOE.” This succinct statement encompasses a wide range of responsibilities for computing and networking facilities; for procuring, deploying, and operating high performance computing, networking, and storage resources; for basic research in mathematics and computer science; for developing and sustaining a large body of software; and for partnering with organizations across the Office of Science and beyond. While its mission statement may seem very contemporary, the roots of ASCR are quite deep—long predating the creation of DOE. Applied mathematics and advanced computing were both elements of the Theoretical Division of the Manhattan Project. In the early 1950s, the Manhattan Project scientist and mathematician John von Neumann, then a commissioner for the AEC (Atomic Energy Commission), advocated for the creation of a Mathematics program to support the continued development and applications of digital computing. Los Alamos National Laboratory (LANL) scientist John Pasta created such a program to fund researchers at universities and AEC laboratories. Under several organizational name changes, this program has persisted ever since, and would eventually grow to become ASCR.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

ASCR@40: Four Decades of Department of Energy Leadership in Advanced Scientific Computing Research

Throughout its long history, the Office of Advanced Scientific Computing Research (ASCR) has built the critical technologies to ensure U.S. leadership in energy science and national security. It has made its parent agency, the Department of Energy (DOE) and its Office of Science, the world’s recognized leader in computational science. ASCR’s stated mission is “to discover, develop, and deploy computational and networking capabilities to analyze, model, simulate, and predict complex phenomena important to the DOE.” To accomplish this goal, ASCR oversees a large complex of computing and networking facilities and is responsible for procuring, deploying and operating high-performance computing (HPC), networking and storage resources; conducting basic research in mathematics and computer science; developing and sustaining a large body of software; and collaborating with other Office of Science programs, academia and industry. ASCR’s computational science leadership has a long history, predating even DOE’s inception. Applied mathematics and advanced computing were both elements of the Manhattan Project’s Theoretical Division. In the 1950s, DOE’s predecessor, the Atomic Energy Commission, created a mathematics program to develop and apply digital computing by supporting researchers at universities and AEC laboratories. Several organizational and name changes later, this program would grow and become ASCR.

97 MATHEMATICS AND COMPUTING↗