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At least 1,531 records · Page 85

Three phase spectral interferometry for recording high dynamic range optical waveforms with <1 ps resolution over >2 ns records applied to closed-loop pulse shaping

Herein we demonstrate, to our knowledge, a novel spectral interferometry technique that simultaneously captures three spectral interferograms of a signal waveform with a reference pulse. The measured performance is robust to nonidealities and ambient drifts by implementing a precisely calibrated 3 × 3 polarization maintaining (PM) splitter that provides three phase shift differences nominally spaced 120° apart. The system can achieve long record length by implementing three, high resolution, virtually imaged phase array (VIPA) spectrometers. Here, we experimentally implement this technique and demonstrate the measurement of waveforms with >2ns of record while maintaining <1ps resolution.

42 ENGINEERING↗

Entanglement-based quantum digital signatures over a deployed campus network

The quantum digital signature protocol offers a replacement for most aspects of public-key digital signatures ubiquitous in today’s digital world. A major advantage of a quantum-digital-signatures protocol is that it can have information-theoretic security, whereas public-key cryptography cannot. Here we demonstrate and characterize hardware to implement entanglement-based quantum digital signatures over our campus network. Over 25 hours, we collect measurements on our campus network, where we measure sufficiently low quantum bit error rates (<5% in most cases) which in principle enable quantum digital signatures at over 50 km as shown through rigorous simulation accompanied by a noise model developed specifically for our implementation. These results show quantum digital signatures can be successfully employed over deployed fiber. Moreover, our reported method provides great flexibility in the number of users, but with reduced entanglement rate per user. Finally, while the current implementation of our entanglement-based approach has a low signature rate, feasible upgrades would significantly increase the signature rate.

97 MATHEMATICS AND COMPUTING↗

Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor

Protein-protein interaction networks are one of the most effective representations of cellular behavior. In order to build these models, high-throughput techniques are required. Next-generation interaction screening (NGIS) protocols that combine yeast two-hybrid (Y2H) with deep sequencing are promising approaches to generate interactome networks in any organism. However, challenges remain to mining reliable information from these screens and thus, limit its broader implementation. Here, we present a computational framework, designated Y2H-SCORES, for analyzing high-throughput Y2H screens. Y2H-SCORES considers key aspects of NGIS experimental design and important characteristics of the resulting data that distinguish it from RNA-seq expression datasets. Three quantitative ranking scores were implemented to identify interacting partners, comprising: 1) significant enrichment under selection for positive interactions, 2) degree of interaction specificity among multi-bait comparisons, and 3) selection of in-frame interactors. Using simulation and an empirical dataset, we provide a quantitative assessment to predict interacting partners under a wide range of experimental scenarios, facilitating independent confirmation by one-to-one bait-prey tests. Simulation of Y2H-NGIS enabled us to identify conditions that maximize detection of true interactors, which can be achieved with protocols such as prey library normalization, maintenance of larger culture volumes and replication of experimental treatments. Y2H-SCORES can be implemented in different yeast-based interaction screenings, with an equivalent or superior performance than existing methods. Proof-of-concept was demonstrated by discovery and validation of novel interactions between the barley nucleotide-binding leucine-rich repeat (NLR) immune receptor MLA6, and fourteen proteins, including those that function in signaling, transcriptional regulation, and intracellular trafficking.

59 BASIC BIOLOGICAL SCIENCES↗

Gate-based quantum computing for protein design

Protein design is a technique to engineer proteins by permuting amino acids in the sequence to obtain novel functionalities. However, exploring all possible combinations of amino acids is generally impossible due to the exponential growth of possibilities with the number of designable sites. The present work introduces circuits implementing a pure quantum approach, Grover’s algorithm, to solve protein design problems. Our algorithms can adjust to implement any custom pair-wise energy tables and protein structure models. Moreover, the algorithm’s oracle is designed to consist of only adder functions. Quantum computer simulators validate the practicality of our circuits, containing up to 234 qubits. However, a smaller circuit is implemented on real quantum devices. Our results show that using iterations, the circuits find the correct results among all N possibilities, providing the expected quadratic speed up of Grover’s algorithm over classical methods (i.e.,).

59 BASIC BIOLOGICAL SCIENCES↗

COVID-19-associated school closures and related efforts to sustain education and subsidized meal programs, United States, February 18-June 30, 2020

Pre-emptive school closures are frontline community mitigation measures recommended by the US Centers for Disease Control and Prevention (CDC) for implementation during severe pandemics. This study describes the spatiotemporal patterns of publicly announced school closures implemented in response to the coronavirus disease 2019 (COVID-19) pandemic and assesses how public K-12 districts adjusted their methods of education delivery and provision of subsidized meals. During February 18–June 30, 2020, we used daily systematic media searches to identify publicly announced COVID-19–related school closures lasting ≥1 day in the United States (US). We also collected statewide school closure policies from state government websites. Data on distance learning and subsidized meal programs were collected from a stratified sample of 600 school districts. The first COVID-19–associated school closure occurred on February 27, 2020 in Washington state. By March 30, 2020, all but one US public school districts were closed, representing the first-ever nearly synchronous nationwide closure of public K-12 schools in the US. Approximately 100,000 public schools were closed for ≥8 weeks because of COVID-19, affecting >50 million K-12 students. Of 600 districts sampled, the vast majority offered distance learning (91.0%) and continued provision of subsidized meal programs (78.8%) during the closures. Despite the sudden and prolonged nature of COVID-19–associated school closures, schools demonstrated flexibility by implementing distance learning and alternate methods to continue subsidized meal programs.

60 APPLIED LIFE SCIENCES↗

Data and scripts associated with a manuscript modeling microbial regulation of priming effects

This data package is associated with the publication “Modeling Microbial Regulatory Feedback in Organic Matter Decomposition Identifies Copiotrophic Traits as Key Drivers of Positive Priming” published as a preprint on BioRXiv by Ahamed et al. (2026); https://doi.org/10.1101/2024.08.11.607483. The package contains MATLAB scripts and saved simulation outputs used to implement a cybernetic model of microbial regulation during complex organic matter (OM) decomposition governing priming effects. It includes models of (i) single microbial functional groups (copiotrophic or oligotrophic degraders) and (ii) binary consortia composed of degraders and non-degraders with contrasting or common growth traits. Simulation results were generated using Monte Carlo analyses, with randomized key model parameters across a range of environmental mixing fractions of complex and labile OM. The dataset was created to provide a transparent and reusable computational framework for systematically exploring how microbial growth traits, metabolic regulation, and community composition influence OM decomposition dynamics and priming effects. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes the variable definitions. This package includes: (1) annotated MATLAB code implementing the system of ordinary differential equations and cybernetic control laws; (2) saved output files containing data (e.g., biomass, substrates, enzyme levels, priming metrics); and (3) scripts for processing saved outputs and regenerating figures. Specifically, the data package contains three main MATLAB scripts: runPrimingModel.m, runPlotData.m, and runPlotSuppFigS1.m, along with this readme and supporting documentation. Users should begin with runPrimingModel.m, which contains the annotated code implementing the system of ordinary differential equations and cybernetic control laws. This script runs the Monte Carlo simulations of microbial OM decomposition and allows users to modify microbial trait definitions, adjust parameter distributions, or define new community configurations. Simulation outputs are automatically saved as .mat files in the folder named SavedData, which stores all pre-generated results included in this package. The second script, runPlotData.m, reads files from the SavedData folder and processes them to regenerate the figures presented in the manuscript. The third script, runPlotSuppFigS1.m, specifically generates Figure S1 in the Supplementary Material of the manuscript. The package also includes the aforementioned files in non-proprietary .txt format. If users intend to use them, they should first save the files in their respective .m or .mat formats prior to execution in MATLAB.

Biomass concentration↗

Improved measurements of nonlinear integrable optics at IOTA

Nonlinear integrable optics (NIO) are a promising novel approach at improving the stability of high intensity beams. Implementations of NIO based on specialized magnetic elements are being tested at the Integrable Optics Test Accelerator (IOTA) at Fermilab. One method of verifying proper implementation of these solutions is by measuring the analytic invariants predicted by theory. The initial measurements of nonlinear invariants were performed during IOTA run in 2019/20, however the covid-19 pandemic prevented the full-scale experimental program from being completed. Several important improvements were implemented in IOTA for the 2022/23 run, including the operation at higher beam energy of 150 MeV, improved optics control, and chromaticity correction. This report presents on the improved calibrations of the NIO for nonlinear invariant measurements.

43 PARTICLE ACCELERATORS↗

RegularizedOptimization.jl: A Julia framework for regularized and nonsmooth optimization

RegularizedOptimization.jl is a Julia package that implements families of quadratic regularization and trust-region methods for solving the nonsmooth optimization problem $^{\textrm{minimize}}_{𝑥∈ℝ^𝑛}$ 𝑓(𝑥) + ℎ(𝑥) subject to 𝑐(𝑥) = 0, (1) where 𝑓 ∶ ℝ 𝑛 → ℝ and 𝑐 ∶ ℝ 𝑛 → ℝ 𝑚 are continuously differentiable, and ℎ ∶ ℝ 𝑛 → ℝ∪{+∞} is lower semi-continuous. The nonsmooth objective ℎ can be a regularizer, such as a sparsity inducing penalty, model simple constraints, such as 𝑥 belonging to a simple convex set, or can be a combination of both. All 𝑓, ℎ, and 𝑐 can be nonconvex. RegularizedOptimization.jl provides a modular and extensible framework for solving (1), and developing novel solvers. Currently, the following solvers are implemented: • Trust-region solvers TR and TRDH (Aravkin et al., 2022; Leconte & Orban, 2025) • Quadratic regularization solvers R2, R2DH and R2N (Aravkin et al., 2022; Diouane, Habiboullah, et al., 2024) • Levenberg-Marquardt solvers LM and LMTR (Aravkin et al., 2024) used when 𝑓 is a least-squares residual. • Augmented Lagrangian solver AL (De Marchi et al., 2023). All solvers rely on first derivatives of 𝑓 and 𝑐, and optionally on their second derivatives in the form of Hessian-vector products. If second derivatives are not available, quasi-Newton approximations can be used. In addition, the proximal mapping of the nonsmooth part ℎ, or adequate models thereof, must be evaluated. At each iteration, a step is computed by solving a subproblem of the form (1) inexactly, in which 𝑓, ℎ, and 𝑐 are replaced with appropriate models around the current iterate. The solvers R2, R2DH, and TRDH are particularly well suited to solve the subproblems, though they are general enough to solve (1). All solvers are allocation-free, so re-solves incur no additional allocations. To illustrate our claim of extensibility, a first version of the AL solver was implemented by an external contributor. Furthermore, a nonsmooth penalty approach, described in Diouane, Gollier, et al. (2024), is currently being developed, that relies on the library to efficiently solve the subproblems.

Gollier, Maxence [Polytechnique Montréal, QC (Cana↗

SmoQyDEAC.jl: A differential evolution package for the analytic continuation of imaginary time correlation functions

We introduce the SmoQyDEAC.jl package, a Julia implementation of the Differential Evolution Analytic Continuation (DEAC) algorithm [N. S. Nichols et al., Phys. Rev. E 106, 025312 (2022)] for analytically continuing noisy imaginary time correlation functions to the real frequency axis. Our implementation supports fermionic and bosonic correlation functions on either the imaginary time or Matsubara frequency axes, and treatment of the covariance error in the input data. This paper presents an overview of the DEAC algorithm and the features implemented in the SmoQyDEAC.jl package. It also provides detailed benchmarks of the package's output against the popular maximum entropy and stochastic analytic continuation methods.

97 MATHEMATICS AND COMPUTING↗

Codebase release r1.1 for SmoQyDEAC.jl

We introduce the SmoQyDEAC.jl package, a Julia implementation of the Differential Evolution Analytic Continuation (DEAC) algorithm [N. S. Nichols et al., Phys. Rev. E 106, 025312 (2022)] for analytically continuing noisy imaginary time correlation functions to the real frequency axis. Our implementation supports fermionic and bosonic correlation functions on either the imaginary time or Matsubara frequency axes, and treatment of the covariance error in the input data. This paper presents an overview of the DEAC algorithm and the features implemented in the SmoQyDEAC.jl package. It also provides detailed benchmarks of the package’s output against the popular maximum entropy and stochastic analytic continuation methods. The code for this package can be downloaded from our GitHub repository at https://github.com/SmoQySuite/SmoQyDEAC.jl or installed using the Julia package manager. The online documentation, including examples, can be accessed at https://smoqysuite.github.io/SmoQyDEAC.jl/stable/.

Neuhaus, James (ORCID:0000000169048510)↗

Adapting Existing Energy Planning, Simulation, and Operational Models for Resilience Analysis

Resilience is a topic receiving much attention in relation to energy systems, with particular attention being paid to the supply of electricity. As a result, research communities have proposed a plethora of candidate indicators and metrics for resilience, most of which remain immature at different scales and segments within the energy system. Given the complexity of resilience analyses and mitigation strategies, there is limited value in attempting to identify a single resilience metric, as no one metric can quantify resilience or its associated value for all stakeholders. Instead, a necessary focus of the research community should lie in implementing, testing, and validating resilience metrics and analysis approaches in energy sector models, which will be invaluable for informing resilience planning and investment decisions. Recognizing that implementing, testing, and validating resilience metrics are challenges that need to be addressed, the National Renewable Energy Laboratory (NREL) dedicated staff and time to researching how to effectively integrate resilience considerations into energy sector models and tools, as part of the Laboratory Directed Research and Development (LDRD) program. The overarching goal of the effort was to evaluate the data needs, methodologies, and outcomes - including consequences and/or changes in investment or operational decisions due to avoided consequences - based on resilience analysis in a range of existing tools. In particular, we selected five models originally built at NREL to explore non-resilience energy research questions to implement and exercise resilience metrics and analysis approaches.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Library of Advanced Materials for Engineering (LAM) 4.56

Accurate and efficient constitutive modeling remains a cornerstone issue for solid mechanics analysis. Over the years, the LAME advanced material model library has grown to address this challenge by implementing models capable of describing material systems spanning soft polymers to stiff ceramics including both isotropic and anisotropic responses. Inelastic behaviors including (visco)plasticity, damage, and fracture have all incorporated for use in various analyses. This multitude of options and flexibility, however, comes at the cost of many capabilities, features, and responses and the ensuing complexity in the resulting implementation. Therefore, to enhance confidence and enable the utilization of the LAME library in application, this effort seeks to document and verify the various models in the LAME library. Specifically, the broader strategy, organization, and interface of the library itself is first presented. The physical theory, numerical implementation, and user guide for a large set of models is then discussed. Importantly, a number of verification tests are performed with each model to not only have confidence in the model itself but also highlight some important response characteristics and features that may be of interest to end-users. Finally, in looking ahead to the future, approaches to add material models to this library and further expand the capabilities are presented.

36 MATERIALS SCIENCE↗

A Quantum Analog Coprocessor for Correlated Electron Systems Simulation

Analog quantum simulation is an approach for studying physical systems that might otherwise be computationally intractable to simulate on classical high-performance computing (HPC) systems. The key idea behind analog quantum simulation is the realization of a physical system with a low-energy effective Hamiltonian that is the same as the low-energy effective Hamiltonian of some target system to be studied. Purpose-built nanoelectronic devices are a natural candidate for implementing the analog quantum simulation of strongly correlated materials that are otherwise challenging to study using classical HPC systems. However, realizing devices that are sufficiently large to study the properties of a non-trivial material system (e.g., those described by a Fermi-Hubbard model) will eventually require the fabrication, control, and measurement of at least 0(10) quantum dots, or other engineered quantum impurities. As a step toward large-scale analog or digital quantum simulation platforms based on nanoelectronic devices, we propose a new approach to analog quantum simulation that makes use of the large Hilbert space dimension of the electronic baths that are used to adjust the occupancy of one or a few engineered quantum impurities. This approach to analog quantum simulation allows us to study a wide array of quantum impurity models. We can further augment the computational power of such an approach by combining it with a classical computer to facilitate dynamical mean-field theory (DMFT) calculations. DMFT replaces the solution of a lattice impurity problem with the solution of a family of localized impurity problems with bath couplings that are adjusted to satisfy a self-consistency condition between the two models. In DMFT, the computationally challenging task is the high-accuracy solution of an instance of a quantum impurity model that is determined self-consistently in coordination with a mean-field calculation. We propose using one or a few engineered quantum impurities with adjustable couplings to baths to realize an analog quantum coprocessor that effects the solution of such a model through measurements of a physical quantum impurity, operating in coordination with a classical computer to achieve a self-consistent solution to a DMFT calculation. We focus on implementation details relevant to a number of technologies for which Sandia has design, fabrication, and measurement expertise. The primary technical advances outlined in this report concern the development of a supporting modeling capability. As with all analog quantum simulation platforms, the successful design and operation of individual devices depends critically on one's ability to predict the effective low-energy Hamiltonian governing its dynamics Our project has made this possible and lays the foundation for future experimental implementations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Library of Advanced Materials for Engineering (LAMÉ) 4.58

Accurate and efficient constitutive modeling remains a cornerstone issue for solid mechanics analysis. Over the years, the LAMÉ advanced material model library has grown to address this challenge by implementing models capable of describing material systems spanning soft polymers to stiff ceramics including both isotropic and anisotropic responses. Inelastic behaviors including (visco)plasticity, damage, and fracture have all incorporated for use in various analyses. This multitude of options and flexibility, however, comes at the cost of many capabilities, features, and responses and the ensuing complexity in the resulting implementation. Therefore, to enhance confidence and enable the utilization of the LAMÉ library in application, this effort seeks to document and verify the various models in the LAMÉ library. Specifically, the broader strategy, organization, and interface of the library itself is first presented. The physical theory, numerical implementation, and user guide for a large set of models is then discussed. Importantly, a number of verification tests are performed with each model to not only have confidence in the model itself but also highlight some important response characteristics and features that may be of interest to end-users. Finally, in looking ahead to the future, approaches to add material models to this library and further expand the capabilities are presented.

36 MATERIALS SCIENCE↗

Guidance on Including Social, Organizational and Technical Influences in Nuclear Utility and Plant Modernization Plans

The objective of this report is to provide the nuclear power industry with guidance on including socio-technical issues in plans developed for current and future modernization efforts. Socio-technical issues of concern include social, organizational and related technical aspects of modernized systems. These can be addressed using a set of systematic analysis and design methods developed to address socio-technical issues of the sort facing the nuclear power industry. The next phase of this work will involve developing and implementing a modernization plan that includes socio-technical tools and methods identified and discussed in a report by Dainoff and colleagues (2020). The plan is expected to be developed and implemented in cooperation with a nuclear utility that has expressed interest in participating. The Dainoff et al report provides the foundation for the present effort and presents a methodological tool set for analyzing socio-technical issues applicable to many modernization efforts. The tools described by Dainoff et al are based on principles of human factors engineering, safety engineering, and systems engineering and are discussed within the specific context of nuclear utility modernization and transformation efforts. It is expected that the plan and the concepts described in the current report will be developed and implemented with a nuclear utility partner. The plan developed with the nuclear utility partner will have a substantially higher level of detail than the guidance provided in this report, particularly with regard to details of plan logistics, etc.

99 GENERAL AND MISCELLANEOUS↗

Noisy Intermediate-Scale Quantum Applications on a Pathfinder System

Work performed under this one-year LDRD was concerned with estimating resource requirements for small quantum test beds that are expected to be available in the near future. This work represents a preliminary demonstration of our ability to leverage quantum hardware for solving small quantum simulation problems in areas of interest to the DOE. The algorithms enabling such studies are hybrid quantum-classical variational algorithms, in particular the widely-used variational quantum eigensolver (VQE). Employing this hybrid algorithm, in which the quantum computer complements the classical one, we implemented an end-to-end application-level toolchain that allows the user to specify a molecule of interest and compute the ground state energy using the VQE approach. We found significant limitations attributable to the classical portion of the hybrid system, including a greater than greater-than-quartic power scaling of the classical memory requirements with the system size. Current VQE approaches would require an exascale machine for solving any molecule with size greater than 150 nuclei. Our findings include several improvements that we implemented into the VQE toolchain, including a new classical optimizer that is decades old but hadn't been considered before in the VQE ecosystem. Our findings suggest limitations to variational hybrid approaches to simulation that further motivate the need for a gate-based fault-tolerant quantum processor that can implement larger problems using the fully digital quantum phase estimation algorithm.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Xyce Parallel Electronic Simulator Users' Guide (Version 7.2)

This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandias needs, including some radiation-aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.

42 ENGINEERING↗

Multi-Model and Multi-Scale Global Sensitivity Analysis for Identifying Controlling Processes of Complex Systems

An environmental model consists of multiple process level sub-models, and each sub-model represents a process that is key to the operation of the simulated system. Global sensitivity analysis methods have been widely used to identify important processes for system model development and improvement. The existing methods of global sensitivity analysis only consider parametric uncertainty, and are not capable of handling model uncertainty caused by multiple process models that arise from competing hypotheses about one or more processes. To address this problem, this project develops a new method to probe model output sensitivity to competing process models by integrating model averaging methods with variance-based global sensitivity analysis to address uncertainty in process models and parameters. The new method yields three process sensitivity indices. The first one is called first-order process sensitivity index, and it is derived as a single summary measure of relative process importance. Evaluating the index is computationally expensive, because it relies in a Monte Carlo scheme that requires thousands and even millions of model executions. To reduce computational cost, this project develops a computationally efficient, quasi Monte Carlo method, and this method is presented in Chapter 2 of this report with and a numerical example for demonstration. The numerical example shows that the results of the quasi Monte Carlo method are substantially close to those of the full Monte Carlo method, but the computational cost of the quasi Monte Carlo method is only 0.7% of that of the full Monte Carlo method. The second index is called total-effect process sensitivity index, and it measures interactions between different processes. Therefore, this sensitivity index includes the first-order process sensitivity index, and can be used to identify influential processes. On the other hand, the total-effect process sensitivity index can also be used to screen non-influential processes. This is demonstrated by two numerical examples using the Sobol-G* functions and groundwater flow models that consider recharge process, geological process, and snowmelt process. The numerical examples shows that the total-effect process sensitivity index is more informative than the first-order process sensitivity. The derivation of the process sensitivity index and the numerical examples are discussed in Chapter 3. Chapter 4 presents two computationally efficient methods for screening non-influential processes to exclude them from further investigation. The two methods are the multi-model difference-based sensitivity (MMDS) analysis method, which can be implemented using the Latin Hypercube Sampling. The second one is the implementation of MMDS method using a binning method. The numerical example for the Sobol-G* function indicates the two methods are capable of identifying non-influential models, and the numerical examples for the groundwater flow and reactive transport show that the two methods are effective for groundwater problems. However, it should be noted that the two methods are numerical approximations, and they can only be used for screening non-influential processes, not for ranking importance of system processes. All the sensitivity analysis methods are implemented by developing python codes, and the codes are in a software called SAMMPY: a python package for process sensitivity analysis under multiple models. The SAMMPY design and structure are discussed in Chapter 5, and the package is released to the public for free download.

54 ENVIRONMENTAL SCIENCES↗