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Science & Technology Review December 2025 - Optimizing Future Design

At Lawrence Livermore National Laboratory, we focus on science and technology research to ensure our nation’s security. We also apply that expertise to solve other important national problems in energy, bioscience, and the environment. Science & Technology Review is published eight times a year to communicate, to a broad audience, the Laboratory’s scientific and technological accomplishments in fulfilling its primary missions. The publication’s goal is to help readers understand these accomplishments and appreciate their value to the individual citizen, the nation, and the world.

36 MATERIALS SCIENCE↗

Assessment of the Loss of Vacuum on the Local Metal Temperature in the TEX Experiment Assembly

A four-part assessment using analytical methods and semi-analytical simulation tools finds that the maximum temperature variation in the highly enriched uranium (HEU) Jemima plate assembly is less than ten Kelvin (< 10 K) in an abrupt loss of vacuum scenario. The temperature variation in the metals is likely to be one to four Kelvin (1 K – 4 K) based on the most realistic conditions in the assessment. The four assessment parts include: (1) the peak gas temperature bound for the initial influx of the ambient air; (2) the high-heat transfer limit during the high-speed forced convection period in an insulated HEU plate; (3) the high-heat transfer limit during the high-speed forced convection period with aluminum spacers; and (4) the longer-time thermal equilibration period between the air and metal stack. The four-part assessment serves as conservative upper bound on the temperature variation in the metal stack and remains well below the 40 Kelvin limit where the temperature-induced stresses could lead to permanent, plastic deformation.

42 ENGINEERING↗

MCNP6 Monte Carlo Code Optimization [Slides]

The MCNP6.1 Monte Carlo code, released in 2013, offers many features not available in previous versions, but runs 20-30% slower for most problems and 2-5x slower for some problems. The MCNP 2020 initiative was established in mid-2013 to address code performance and other issues, with 3 basic components: (1) Improve MCNP performance, with the specific goal of achieving a 2x performance gain within 2 years; (2) Upgrade the core MCNP software and algorithms in an evolutionary fashion, with the goal of achieving more agile and sustainable code; (3) Prepare for future exascale systems that will include massive parallelism and limited memory per core, with the goal of providing flexible and adaptable coding for possible exascale systems. This talk reviews the initial performance improvements to MCNP6.1 that have been incorporated into the 2014 update, MCNP6.1.1. The performance improvements to date have included both classic code optimizations and algorithm improvements. Testing on a variety of problems has demonstrated that the performance improvements were effective, yielding speedups by factors of 1.2x - 4x compared to MCNP6.1, depending on the type of problem. For criticality problems, MCNP6.1.1 runs 1.5x - 1.7x faster than MCNP6.1. Much more work is planned for improving MCNP6 performance, structure, and algorithms.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

Background: MicroRNAs (miRNAs) are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species. Given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput (HTP) miRNA data in an increasing number of model species. The Bioinformatics Resource Manager (BRM) v2.3 is a software environment for data management, mining, integration and functional annotation of HTP biological data. In this study, we report recent updates to BRM for miRNA data analysis and cross-species comparisons across datasets. Results: BRM v2.3 has the capability to query predicted miRNA targets from multiple databases, retrieve potential regulatory miRNAs for known genes, integrate experimentally derived miRNA and mRNA datasets, perform ortholog mapping across species, and retrieve annotation and cross-reference identifiers for an expanded number of species. Here we use BRM to show that developmental exposure of zebrafish to 30 uM nicotine from 6–48 hours post fertilization (hpf) results in behavioral hyperactivity in larval zebrafish and alteration of putative miRNA gene targets in whole embryos at developmental stages that encompass early neurogenesis. We show typical workflows for using BRM to integrate experimental zebrafish miRNA and mRNA microarray datasets with example retrievals for zebrafish, including pathway annotation and mapping to human ortholog. Functional analysis of differentially regulated (p<0.05) gene targets in BRM indicates that nicotine exposure disrupts genes involved in neurogenesis, possibly through misregulation of nicotine-sensitive miRNAs. Conclusions: BRM provides the ability to mine complex data for identification of candidate miRNAs or pathways that drive phenotypic outcome and, therefore, is a useful hypothesis generation tool for systems biology. The miRNA workflow in BRM allows for efficient processing of multiple miRNA and mRNA datasets in a single software environment with the added capability to interact with public data sources and visual analytic tools for HTP data analysis at a systems level. BRM is developed using Java™ and other open-source technologies for free distribution (http://www.sysbio.org/dataresources/brm.stm).

59 BASIC BIOLOGICAL SCIENCES↗

Optimal structure and parameter learning of Ising models

Reconstruction of the structure and parameters of an Ising model from binary samples is a problem of practical importance in a variety of disciplines, ranging from statistical physics and computational biology to image processing and machine learning. The focus of the research community shifted toward developing universal reconstruction algorithms that are both computationally efficient and require the minimal amount of expensive data. Here, we introduce a new method, interaction screening, which accurately estimates model parameters using local optimization problems. The algorithm provably achieves perfect graph structure recovery with an information-theoretically optimal number of samples, notably in the low-temperature regime, which is known to be the hardest for learning. Here, the efficacy of interaction screening is assessed through extensive numerical tests on synthetic Ising models of various topologies with different types of interactions, as well as on real data produced by a D-Wave quantum computer. Finally, this study shows that the interaction screening method is an exact, tractable, and optimal technique that universally solves the inverse Ising problem.

97 MATHEMATICS AND COMPUTING↗

Idaho National Laboratory CY 2024 National Emission Standards for Hazardous Air Pollutants Analysis, Methodology, and Results for Radionuclides

This report documents the methodology and results for calculating the effective dose equivalent (EDE) to the maximally exposed individual (MEI) from atmospheric radionuclide emissions from Idaho National Laboratory (INL) sources in Calendar Year (CY) 2024. The calculations were performed in accordance with requirements in Code of Federal Regulations (CFR), Title 40, “Protection of the Environment,” Part 61, “National Emission Standards for Hazardous Air Pollutants (NESHAPs),” Subpart H, “National Emission Standards for Emissions of Radionuclides Other than Radon from Department of Energy Facilities” (40 CFR 61, Subpart H). UDFs were calculated using the computer model CAP88-PC for unit (1 Ci/yr) emission rates at INL Site facilities and INL in-town (Idaho Falls) facilities and stored in Microsoft Access databases. The UDFs—in this case, mrem/Ci—were then combined with radionuclide-specific release (emission) rates for each facility-specific source to compute doses at predetermined public receptor locations, including the MEI locations. This report contains the dose results and a description of the methodology and tools used to compute the doses.

07 - ISOTOPES AND RADIATION SOURCES↗

Language model-accelerated deep symbolic optimization

Symbolic optimization methods have been used to solve varied challenging and relevant problems such as symbolic regression and neural architecture search. However, the current state of the art typically learns each problem from scratch and is unable to leverage pre-existing knowledge and datasets that are available for many applications. Here, inspired by the similarity between sequence representations learned in natural language processing and the formulation of symbolic optimization as a discrete sequence optimization problem, we propose language model-accelerated deep symbolic optimization (LA-DSO), a method that leverages language models to learn symbolic optimization solutions more efficiently. We demonstrate LA-DSO in two tasks: symbolic regression, which allows us to perform extensive experimentation due to its low computation requirements, and computational antibody optimization, which shows that our proposal accelerates learning in challenging real-world problems.

97 MATHEMATICS AND COMPUTING↗

Towards Use of Mixed Precision in ECP Math Libraries [Exascale Computing Project]

The use of multiple types of precision in mathematical software has the potential to increase its performance on new heterogeneous architectures. The xSDK project focuses both on the investigation and development of multiprecision algorithms as well as their inclusion into xSDK member libraries. This report summarizes current efforts on including and/or using mixed precision capabilities in the math libraries Ginkgo, heFFTe, hypre, MAGMA, PETSc/TAO, SLATE, SuperLU, and Trilinos, including KokkosKernels. It contains both numerical results from libraries that already provide mixed precision capabilities, as well as descriptions of the strategies to incorporate multiprecision into established libraries.

97 MATHEMATICS AND COMPUTING↗

Intrusive Uncertainty Quantification and Optimal Experiment Design in the Open-Source Pyomo Ecosystem

This contribution describes ParmEst and Pyomo.DoE, two pillars of the open-source Python-based Pyomo ecosystem for computational optimization with (partial differential) algebraic equation mathematical models. Specifically, ParmEst facilitates intrusive frequentist parameter estimation (PE) and uncertainty quantification (UQ) through built-in features, such as covariance matrix estimation, bootstrapping, and likelihood ratio tests. Complementary, Pyomo.DoE enables optimal experiment design by maximizing various metrics of the Fisher information matrix, such as A-optimality (trace), D-optimality (determinant), E-optimality (minimum eigenvalue), and ME-optimality (condition number). ParmEst and Pyomo.DoE can solve high-dimensional optimization problems by leveraging the model structure and exact derivative information. Finally, we will discuss future opportunities to integrate PE and UQ capabilities with optimization under uncertainty, including robust optimization with non-convex models via PyROS.

97 MATHEMATICS AND COMPUTING↗

Numerical analysis of a thermal contact problem with adhesion

In this paper, we study a class of dynamic thermal problems involving a frictional normal compliance adhesive contact model and a non-clamped condition for visco-elastic materials. The variational formulation of the problem leads to a general system defined by a second-order quasi-variational evolution inequality on the displacement field coupled with the two first-order evolution equations describing the evolution of the temperature and adhesion. We establish an existence and uniqueness result of the solution on displacement, temperature and adhesion. Then we provide a fully discrete numerical scheme of approximation and derive an error estimate. Finally, various numerical computations are included.

97 MATHEMATICS AND COMPUTING↗

Exploring adverse drug events at the class level

Background: While the association between a drug and an adverse event (ADE) is generally detected at the level of individual drugs, ADEs are often discussed at the class level, i.e., at the level of pharmacologic classes (e.g., in drug labels). We propose two approaches, one visual and one computational, to exploring the contribution of individual drugs to the class signal. Methods: Having established a dataset of ADEs from MEDLINE, we aggregate drugs into ATC classes and ADEs into high-level MeSH terms. We compute statistical associations between drugs and ADEs at the drug level and at the class level. Finally, we visualize the signals at increasing levels of resolution using heat maps. We also automate the exploration of drug-ADE associations at the class level using clustering techniques. Results: Using our visual approach, we were able to uncover known associations, e.g., between fluoroquinolones and tendon injuries, and between statins and rhabdomyolysis. Using our computational approach, we systematically analyzed 488 associations between a drug class and an ADE. Conclusions: The findings gained from our exploratory techniques should be of interest to the curators of ADE repositories and drug safety professionals. Our approach can be applied to different drug-ADE datasets, using different drug classification systems and different signal detection algorithms.

59 BASIC BIOLOGICAL SCIENCES↗

A survey of numerical linear algebra methods utilizing mixed-precision arithmetic

The efficient utilization of mixed-precision numerical linear algebra algorithms can offer attractive acceleration to scientific computing applications. Especially with the hardware integration of low-precision special-function units designed for machine learning applications, the traditional numerical algorithms community urgently needs to reconsider the floating point formats used in the distinct operations to efficiently leverage the available compute power. In this study, we provide a comprehensive survey of mixed-precision numerical linear algebra routines, including the underlying concepts, theoretical background, and experimental results for both dense and sparse linear algebra problems.

97 MATHEMATICS AND COMPUTING↗

Los Alamos National Laboratory Computational Physics Summer Student Workshop (Final Report)

The numerical solution of highly compressible, multi-material flows is an ongoing research area. These types of flows can be solved with a Lagrangian type mesh which moves with the material in a simulation to allow precise material interface tracking. Currently, researchers at Los Alamos National Laboratory and elsewhere are investigating cell-centered Lagrangian algorithms with the aim of producing methods that have second-order accuracy, preserve symmetry, and do not generate spurious vorticity. The new cell-centered algorithms solve a Riemann-like problem at the vertex of a cell. Professor Phil Roe at the University of Michigan has proposed a new structure for Lagrangian hydrodynamic algorithms that does not rely on the solution of the Riemann problem. The new approach utilizes Flux Corrected Transport (FCT) and it implements a form of vorticity control. The first step in the development of this method has been to construct an algorithm that solves the acoustic equations on an Eulerian mesh. The algorithm, which builds on the work of Morton and Roe, calculates fluxes at cell vertices, attains second-order accuracy using FCT, and has the special property of preserving vorticity. Results are presented that confirm the second order accuracy of the scheme and the vorticity preserving properties. The results are compared to the output produced by a MUSCL-Hancock algorithm. Some discussion of limiting methods for the FCT algorithm is also given.

42 ENGINEERING↗

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

Sustaining a robust metabolic network requires a balanced and fully functioning proteome. In addition to amino acids, many enzymes require cofactors (coenzymes and engrafted prosthetic groups) to function properly. Extensively validated resource allocation models, such as genome-scale models of metabolism and gene expression (ME-models), have the ability to compute an optimal proteome composition underlying a metabolic phenotype, including the provision of all required cofactors. Here we apply the ME-model for Escherichia coli K-12 MG1655 to computationally examine how environmental conditions change the proteome and its accompanying cofactor usage. We found that: (1) The cofactor requirements computed by the ME-model mostly agree with the standard biomass objective function used in models of metabolism alone (M-models); (2) ME-model computations reveal non-intuitive variability in cofactor use under different growth conditions; (3) An analysis of ME-model predicted protein use in aerobic and anaerobic conditions suggests an enrichment in the use of peroxyl scavenging acids in the proteins used to sustain aerobic growth; (4) The ME-model could describe how limitation in key protein components affect the metabolic state of E . coli . Genome-scale models have thus reached a level of sophistication where they reveal intricate properties of functional proteomes and how they support different E . coli lifestyles.

59 BASIC BIOLOGICAL SCIENCES↗

Verification of 2-D Detonation Shock Dynamics in conjunction with Los Alamos Lagrangian hydrocode

As the latest version of the fast-tube Detonation Shock Dynamics (DSD) solver is linked with the Los Alamos Lagrangian hydrocode, verification problems from a 2006 DSD report (LA-14277) have been duplicated with some of the verification criteria changed to more quantitative ones. The observed error convergence is as good as or better than reported in, quite possibly due to the careful treatment of floating point numbers to ensure that their precision level is maintained throughout the code. This report duplicates the three sample verification problems in LA-14277 using the Los Alamos ASC Lagrangian hydrocode (FLAG), official release of 3.2 Alpha6 with a few modifications. This version of FLAG is linked with the latest fast-tube Detonation Shock Dynamics (DSD) version beta 2 solver released in 2011 as part of the LanlDSD software product. New verification criteria are used for the arcwave problem where two specific locations are chosen for burn arrival time comparison. For this report FLAG's internal driver code prepares the distance function ({Psi}) and material ID fields from its hydro setup, instead of the stand-alone driver that is being utilized by the other LANL hydrocodes currently interfaced to LanlDSD. As it is implemented in version 3.2 Alpha6, the {Psi} and material ID fields and other parameters are passed from FLAG to the DSD solver directly, and the burn table is directly passed back to FLAG as part of the calling arguments. The burn-front arrival time 'exact' solutions, mentioned in the sequel for the rate-stick and 'arc-wave' problems, are computed using a pair of special-purpose Fortran codes provided by Aslam. In each case an ansatz for the form of the solution is made in which the radius from the detonator center point is used as the independent space coordinate. This leads to a simplified, problem-specific, 1D form of the governing equation. This equation is solved using 2nd-order spatial differencing and the forward Euler method on a very fine temporal and geometric mesh. The boundary conditions are handled exactly at the correct location, with second order accuracy. Care has been taken to ensure that this solution is fully converged.

36 MATERIALS SCIENCE↗

Information Geometry of Quantum Resources

I review recent works showing that information geometry is a useful framework to characterize quantum coherence and entanglement. Quantum systems exhibit peculiar properties which cannot be justified by classical physics, e.g. quantum coherence and quantum correlations. Once confined to thought experiments, they are nowadays created and manipulated by exerting an exquisite experimental control of atoms, molecules and photons. It is important to identify and quantify such quantum features, as they are deemed to be key resources to achieve supraclassical performances in computation and communication protocols. The information geometry viewpoint elucidates the advantage provided by quantum superpositions in phase estimation. Furthermore, it enables to link measures of coherence and entanglement to observables, which can be evaluated in a laboratory by a limited number of measurements.

97 MATHEMATICS AND COMPUTING↗

Low-dissipation centred schemes for hyperbolic equations in conservative and non-conservative form

We propose a one-parameter family of low-dissipation centred numerical schemes for solving hyperbolic equations in conservative or non-conservative form, using finite volume or discontinuous Galerkin finite element methods. The new schemes spring out from the multi-dimensional FORCE method and are determined by a single parameter α ≥ 1. Given an increasing sequence of real numbers 1 ≤ α 1 < α 2 < . . . < α K , there corresponds a sequence of numerical schemes with stability restriction associated to a decreasing sequence of Courant numbers 1 > c 1 > c 2 > . . . > c K > 0 and a decreasing sequence of corresponding numerical viscosity functions d 1 > d 2 > . . . > d K . For a given Courant number c k ≤ 1 there is a real number α k > 0 and a corresponding stable scheme with minimal numerical viscosity d k . The proposed schemes suit very well the family of high-order discontinuous Galerkin finite element methods and the recently proposed class of ADER-TR schemes, whose orders of accuracy define decreasing sequences of Courant numbers, as the order of accuracy increases. The centred methods of this paper are stable in 2D and 3D in the frame of simultaneous updating formulae, unlike other centred methods, such as 1D FORCE, which are not. Furthermore, the schemes are highly accurate for slowly-moving waves, which is precisely the kind of waves that traditional centred methods smear disastrously. Additional features of the proposed schemes include ease of implementation and applicability to any hyperbolic system either in conservative or non-conservative form. Here, the proposed schemes are analysed and computationally assessed through a suite of test problems for a linear model system, for the Euler equations in one and two space dimensions, and for the Baer-Nunziato equations for compressible two-phase flow.

97 MATHEMATICS AND COMPUTING↗