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At least 181 records · Page 10

MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes

While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.

59 BASIC BIOLOGICAL SCIENCES

Two-Level Sketching Alternating Anderson Acceleration for Complex Physics Applications

We present a novel two-level sketching extension of the Alternating Anderson–Picard (AAP) method for accelerating fixed-point iterations in challenging single- and multiphysics simulations governed by discretized PDEs. Our approach combines a static, physics-based projection that reduces the least-squares (LS) problem to the most informative field (e.g., via Schur-complement insight) with a dynamic, algebraic sketching stage driven by a backward stability analysis under Lipschitz continuity. We introduce inexpensive estimators for stability thresholds and cache-aware randomized selection strategies to balance computational cost against memory access overhead. The resulting algorithm solves reduced LS systems in place, minimizes memory footprints, and seamlessly alternates between low-cost Picard updates and Anderson mixing. Implemented in Julia, our two-level sketching AAP achieves up to 50% time-to-solution reductions compared to standard Anderson acceleration—without degrading convergence rates—on benchmark problems including Stokes, 𝑝-Laplacian, bidomain, and Navier–Stokes formulations at varying problem sizes. These results demonstrate the method’s robustness, scalability, and potential for integration into high-performance scientific computing frameworks. Our implementation is available open source in the AAP.jl library.

Barnafi, Nicolas [University of Chile, Santiago]

Phlex: Parallel, Hierarchical, and Layered EXecution of data-processing algorithms

Phlex is a computing framework supporting the parallel, hierarchical, and layered execution of data-processing algorithms. It is based on the functional-programming paradigm, thus guaranteeing thread-safety when invoking user-defined pure functions. Phlex allows users to specify arbitrary graph-based hierarchies of data organization, enabling more flexible processing of data as required by the constraints of the program.

Knoepfel, KyleJ. [Fermi National Accelerator Labor

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

Beam loss modeling and mitigation due to intra-beam stripping

Intra-Beam Stripping (IBS) is a critical beam loss mechanism in high-intensity H- linacs and presents a significant limitation to increasing beam power. This work presents a computational framework to evaluate and mitigate IBS-induced beam loss along the Spallation Neutron Source (SNS) LINAC. Our calculation is based on an analytic theory and involves evaluation of a 9D integral using the Monte-Carlo technique. We first benchmarked our calculations against simplified, analytically solvable cases. We then applied our algorithm to Gaussian bunches with a known probability density function (PDF). We next expanded our algorithm to arbitrary bunch distributions using the Neural Spline Flow (NSF) models trained on PyORBIT tracking data. In the future, we plan to validate our algorithm experimentally and apply it to design IBS mitigation strategies.

Nln, Shivam [ORNL]

Application of quantitative risk assessment to address stakeholder questions in geologic carbon storage

Ambitious international greenhouse gas emissions reduction targets demand a rapid transformation to a low-carbon economy. This transformation includes the accelerated adoption of carbon dioxide (CO2) capture and storage (CCS) technology. However, as with any large-scale engineering enterprise, the widespread commercial-scale deployment of geologic carbon storage (GCS) raises important questions about technology and cost-effectiveness, safety, environmental risk, and long-term liability. Effectively assessing and managing risks and liability associated with GCS projects is a key technical need throughout the project life cycle-from site selection and permitting to monitoring design, operational risk management, and post-operational site closure. This presentation highlights recent advancements in tools for quantitative risk assessment, being developed by the National Risk Assessment Partnership (NRAP). NRAP is a multi-year, multinational laboratory research collaboration sponsored by the U.S. Department of Energy's Office of Fossil Energy and Carbon Management. Our focus will be on these tools' applications in addressing critical stakeholder questions related to supporting permitting to ensure secure and environmentally protective storage; designing effective and efficient monitoring plans; evaluating the effectiveness of remedial actions and risk management alternatives; and informing liability assessment and investment decisions. This paper will detail the key functionality of NRAP’s Open-Source Integrated Assessment Model (NRAP-Open-IAM), a computational framework for assessing leakage risk and containment assurance. This model features streamlined workflows for calculating leakage risk profiles, delineating risk-based area of review, and assessing contingency plans and post-injection site care requirements. ORION is an open-source, observation-based ensemble forecasting toolkit to help operators assess the seismic hazard at a carbon storage site. The State of Stress Analysis Tool (SOSAT), designed to assess subsurface stress conditions and evaluate geomechanical risk resulting from CO2 injection in an area of interest will also be presented. We will also introduce a prototype model to evaluate storage project costs and liability associated with risk management. The Technoeconomic and Liability Evaluation for Storage (TALES) model uses results from forecasts of leakage and induced seismicity risk to estimate the lifecycle cost of managing risk. Finally, a preliminary example of how the NRAP Risk-based Adaptive Monitoring Plan (RAMP) tool can be used to design efficient and effective site monitoring plans and estimate the detectability of fluid leakage will be provided. The relevance of these tools for addressing key stakeholder questions amidst uncertainty will be emphasized.

decision support

Arctic Critical Infrastructure: Assessing and Predicting the Risk to Critical Permafrost Infrastructure from Climate Change: A New Thermomechanical Approach

This study presents the development of a computational framework designed to predict the interaction between permafrost and infrastructure, addressing potential failure modes and mitigation strategies in the context of climate change. The framework, rooted in advanced modeling and simulation (mod/sim) techniques, integrates thermomechanical coupling to account for the complex interplay between heat flow, ice content, and mechanical behavior in permafrost. Existing models fail to fully capture these dynamics, particularly as they relate to the effects of ice saturation on structural integrity. Our innovative Arctic Coastal Erosion (ACE) framework fills this gap by coupling thermal and mechanical models to accurately simulate subsidence and deformation in permafrost environments. We applied the ACE framework to a representative runway, demonstrating its capability to predict settlement due to rising temperatures and subsequent permafrost thaw. This proof-of-concept showcases the potential of the framework to evaluate risks to Arctic infrastructure, which supports over four million people and 70% of existing permafrost-based structures. By simulating various infrastructure types and environmental conditions, our research offers insights into failure mechanisms and evaluates structural solutions to mitigate risk. The anticipated deliverables, including a prototype runway exemplar, position this project as a critical advancement in permafrost infrastructure modeling, with applications in national security and resilience planning.

54 ENVIRONMENTAL SCIENCES

Unifying Quantum Materials Modeling and Experiments: The Role of Machine Learning Interatomic Potentials

Computational experiments have emerged as a powerful complement to traditional experiments in the design of new materials. The development of machine learning (ML) and deep learning techniques, combined with database construction and data mining, has significantly enhanced traditional quantum mechanical methods. This synergy enables the rapid development of structure-property relationships. In this talk, I will discuss our recent efforts in applying Machine Learning Interatomic Potentials (MLIAPs) to accelerate materials modeling across various material classes and challenging applications where traditional methods fall short. First, I will highlight the success of MLIAPs in accurately modeling the melting behavior of complex materials. Our results demonstrate high fidelity with experimental observations and also with calculated reference melting temperatures. In the second application, I will discuss how MLIAPs are trained and applied to elucidate the interplay between segregation tendencies and surface reconstructions in CuNi alloys under oxidizing conditions. A key factor in the success of these MLIAP applications is the design of minimalistic yet flexible datasets along with a computational framework for training MLIAPs.

Saidi, Wissam

Advanced Modeling and Process-Materials Co-Optimization Strategies for Swing Adsorption Based Gas Separations

This project devised a computational framework for simultaneously co-optimizing pressure swing adsorption process designs along with the sorbent materials (specifically, metal-organic frameworks) to be employed in the associated packed bed columns. The materials optimization aspect involved search over a design space that can describe the material’s molecular structure, while the process optimization aspect considered various process degrees of freedom for steps arising in various cycle configurations. This framework was demonstrated on the separation of nitrogen and carbon dioxide, which arises ubiquitously in a multitude of post-combustion carbon capture and “blue” hydrogen production applications. Our results led to metal-organic framework molecular descriptor choices that are predicted to outperform standard structures used in practice, providing guidance for future metal-organic framework synthesis efforts.

20 FOSSIL-FUELED POWER PLANTS

Radiation damage effects in beryllium for next generation neutrino beam targetry (Final Technical Report)

Current and future high-power accelerators put severe requirements on materials used for target and beam windows and target facilities have been recognized as a critical challenge in development of future particle accelerators. In accelerators, window and target materials are exposed to extreme conditions, which include bombardment with very high energy protons (1- 100 GeV) and thermomechanical shock waves. Radiation can cause direct damage in the material, and it leads to production of transmutation products (especially helium), both phenomena having a potential adverse effect on the stability and durability of the target/window material. At high enough temperatures, He can aggregate to form gas bubbles, which in turn cause significant dimensional changes (swelling), enable easy crack propagation, and eventually cause failure by fracture. On the other hand, if the temperature is too low, radiation damage accumulates in the form of internal defects (e.g., dislocations), leading to hardening and a decreased ductility of the material. In this project, we will focus on beryllium since it is considered to be one of the candidate materials for beam windows and targets in the next-generation proton accelerators, e.g., the Long Baseline Neutrino Facility (LBNF). Radiation effects in Be have been studied in the context of nuclear fusion reactor applications. However, key differences exist between reactor and accelerator conditions, including neutron vs. proton irradiation, continuous vs. pulsed beam flux, much higher energies of bombarding particles in accelerators, and higher operating temperatures for typical reactors. For example, the impact of beam pulsing on the radiation damage and the He bubble kinetics is largely unknown. While results obtained on Be from fusion research might not be directly transferrable to understanding target materials, there is an opportunity to bring state-of-the-art tools from materials research in nuclear reactors to aid design of target and beam window materials in high-power accelerators. To this end, the overarching goal of this project are to develop an experimentally-validated computational framework capable of predicting radiation damage evolution in beryllium relevant to beam window and target conditions, focusing on He bubble formation and growth as a function of irradiation temperature. Our model will be based on the cluster dynamics formalism, where size distribution of defects and He bubbles is simulated as a function of time, temperature, and radiation dose. Parameters for the model will be taken from published experiments and from high-fidelity atomistic simulations proposed in this project. In addition, we will carry out a series of targeted ex-situ and in-situ dual-beam experiments using low-energy protons to provide critical data for validation of the model on the effects of radiation on He clustering, He bubble distribution, and dislocation loop density/size in proton irradiated Be.

36 MATERIALS SCIENCE

Probing Condensed-Phase Structure and Dynamics in Hierarchical Zeolites and Nanosheets for Catalytic Upgradation of Biomass (Final Report)

Understanding complex reaction pathways in systems governed by multi-scale collective interactions across time and length scales remains a central scientific challenge. This project was guided by the hypothesis that the interplay among oligomers, solvents, and active sites can be tuned by a suitable choice of solvation environment and pore architecture in solid-acid catalysts to direct chemical transformations relevant to biomass conversion. Zeolites and zeolite nanosheets were used as model platforms, allowing for the interaction of macromolecules with the surface of the zeolite nanosheets and with smaller pores that host catalytically active sites. To investigate these coupled phenomena, we employ a multi-scale computational framework that integrates molecular-level descriptions with advanced sampling approaches to capture key physical and chemical interactions. Our work through this project improved fundamental understanding of how reactants and solid-acid catalysts interact in solvent-rich environments, thereby enabling the rational design of catalytic systems that upgrade biomass with enhanced selectivity and energy efficiency. In addition, the project developed advanced sampling methodologies critical for disentangling complex, reactive processes in multi-component catalytic environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Advanced Modeling of Beam Physics and Performance Optimization for Nuclear Physics Colliders

High energy colliders provide a critical tool in nuclear physics study by probing the fundamental structure and dynamics of matter. To maximize the potential of scientific discovery in nuclear physics study, it is important to optimize the parameters of these colliders to attain the best performance. The performance of a collider is typically measured by its integrated luminosity of colliding beams since the probability of a new event is proportional to the integrated luminosity. However, the achievable luminosity is limited by the electromagnetic interactions (beam-beam effects) of two colliding beams at higher energy, and the interplay between the space-charge effects and the beam-beam effects at lower energy. To achieve the best performance of a collider means to attain the highest luminosity of the collider with optimized collider parameters. Optimizing the collider’s machine parameters is both computationally and experimentally expensive. A fast and robust computational framework including beam-beam and space-charge effects will be critical to attaining the best performance of the collider. In this project, we will study the beam dynamics challenges, specifically the interplay of the space-charge and the beam-beam effects, and the machine tuning models for maximizing the performance of RHIC experiments. We will develop an advanced modeling framework based on first-principles physical simulations, lattice models and the state-of-the-art machine learning methods and apply this framework to performance improvement of the RHIC in operation. We will build data manipulation packages to connect the simulation data and the experimental data with the framework, develop a self-consistent hybrid model of space-charge and beam-beam effects, study underlying physics mechanisms, build surrogate models using the labeled data, integrate the models into the advanced modeling framework, and apply the framework to RHIC luminosity (STAR and sPHENIX) optimization. The success of this project would substantially improve the performance of existing and future colliders and increase the opportunity for scientific discovery.

43 PARTICLE ACCELERATORS

Computational materials reliability assessment of hydrogen fueled gas turbine power generation engines

The use of blended fuel sources in land based gas turbine engines drives variations in the resulting operational profile (temperatures and pressures) which can impact engine reliability. Furthermore, variability in the manufacture of components affects the resulting microstructure which directly impacts material performance and reliability. Currently, data-driven models are typically used for maintaining and inspecting fleets of engines. Without explicitly capturing material and operational sources of variability conservatism must be used in developing component-level reliability models. Therefore, there exists an opportunity to use information from materials-scale physics models to better inform reliability modeling and reduce conservatism; the impact is more cost-efficient operation and maintenance of current and future fleets. Specifically, this work establishes a computational framework for evaluating the probabilistic high temperature creep performance of hot-section Ni-based superalloys where uncertainty comes from both microstructural and operational variability. A novel high-fidelity physics model which phenomenologically captures grain-boundary sensitive phenomena has been established. A probabilistic calibration procedure was used to calibrate the model and capture uncertainty in the parameterized model coefficients. A design of experiments methodology was established for identifying informative microstructural digital representations for suitable for forward model evaluation. Results show that training a machine-learning surrogate using this design criteria outperforms random selection of microstructural representations. Finally, two surrogate models were developed: (1) a deterministic surrogate model which predicts the local field response given microstructure, constitutive model parameters, and operating conditions (stress, temperature) and (2) a probabilistic model, where uncertainty comes from constitutive law uncertainty, built using denoising diffusion probabilistic models which samples responses given (1) microstructure and (2) operating conditions. These surrogate models enable partner Siemens Energy to rapidly perform UQ analysis specific to creep deformation across a range of microstructures and operating conditions. The impact is that these ML and physics codes can be used to establish more advanced reliability models for the inspection, servicing, and maintenance of land based gas turbine engines.

36 MATERIALS SCIENCE

SynthEsizing Novel H2 Sensors for Operational Resilience in Pipeline Infrastructure (SENSOR)

A flexible and extensible computational framework acts as a black-box materials discovery engine, capable of screening, predicting, and designing advanced materials with minimal manual intervention was developed. While developed for hydrogen sensing, the approach can be readily adapted to other materials challenges, offering a powerful tool for data-driven materials innovation.

08 HYDROGEN

Collaborative: Fundamental studies of how water influences the synthesis and behavior of zeolite catalysts for reactions in the circular carbon economy (Final Technical Report)

This project established a computational framework to predict and interpret how synthesis conditions control active site location in MFI zeolites and how those site distributions influence catalytic reactivity. The Hibbitts Group led the theoretical effort, applying periodic DFT calculations to quantify (i) SDA–framework–heteroatom interactions during crystallization and (ii) the energetics and mechanisms of arene methylation reactions within distinct MFI environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Thermal Reservoir Networks for Modularly Expandable Thermal Microgrids

The Department of Defense (DoD) faces the substantial challenge of cost-effectively retrofitting one to two installations per month, each comprising approximately 1,000 buildings, to improve resilience, reduce energy consumption, and enhance energy supply security. Achieving these objectives requires optimal system selection and effective risk mitigation during system integration. To address this need, we introduce Platform-Based Design (PBD), a structured, hierarchical methodology adapted from other industrial sectors to the domain of energy system retrofits. We demonstrate the effectiveness of PBD through a techno-economic feasibility study comparing geothermal-coupled thermal energy networks (TENs) with conventional energy systems for heating, cooling, and powering 17 buildings at Joint Base Andrews (JBA) in Maryland. Our analysis illustrates that the PBD approach enables rigorous, data-driven, sequential decision making, resulting in a family of Pareto-optimal systems, among which the TEN emerged as the most promising solution. The selected TEN design integrates geothermal borefields, heat recovery heat pumps, photovoltaic (PV) arrays, and battery storage. Compared to the baseline system – gas heating combined with air-source chillers – the proposed TEN reduces annual imported energy by 74% and peak electricity demand by 45%, achieves a levelized cost of energy of $\$0.210$/kWh, and substantially enhances resilience. Life-cycle costs increase by approximately 6%, and initial investment costs are about 2.5 times higher than the baseline. However, if central plant infrastructure, district loops, and utility-scale PV and battery systems are privately funded and operated, the initial investment would fall below the baseline system cost. Critical to achieving these significant performance improvements were detailed nonlinear dynamic simulations coupling geothermal heat transfer, energy system operation, and realistic feedback control logic. These simulations identified essential design modifications and control strategy refinements that substantially reduced energy use, peak demand, and compressor shortcycling, thereby improving durability and reliability—issues that would have been significantly more expensive to resolve during operation. Additionally, the verification step highlighted sensitivities to key design parameters that could reduce initial investment by approximately $\$2$ million and reduce annual life-cycle costs more than $\$300,000$. We recommend adopting the PBD methodology for future feasibility studies and TEN pilot projects to gain valuable operational experience. Furthermore, we recommend that DoD invest in transferring and scaling the PBD methodology to other installations. This entails developing standardized computational frameworks and component libraries as well as training industry in conducting PBD. Such investments would enable rapid, robust, reliable, and cost-effective retrofits, supporting DoD’s ambitious energy system modernization goals.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI

Towards verifiable cancer digital twins: tissue level modeling protocol for precision medicine

Cancer exhibits substantial heterogeneity, manifesting as distinct morphological and molecular variations across tumors, which frequently undermines the efficacy of conventional oncological treatments. Developments in multiomics and sequencing technologies have paved the way for unraveling this heterogeneity. Nevertheless, the complexity of the data gathered from these methods cannot be fully interpreted through multimodal data analysis alone. Mathematical modeling plays a crucial role in delineating the underlying mechanisms to explain sources of heterogeneity using patient-specific data. Intra-tumoral diversity necessitates the development of precision oncology therapies utilizing multiphysics, multiscale mathematical models for cancer. This review discusses recent advancements in computational methodologies for precision oncology, highlighting the potential of cancer digital twins to enhance patient-specific decision-making in clinical settings. We review computational efforts in building patient-informed cellular and tissue-level models for cancer and propose a computational framework that utilizes agent-based modeling as an effective conduit to integrate cancer systems models that encode signaling at the cellular scale with digital twin models that predict tissue-level response in a tumor microenvironment customized to patient information. Furthermore, we discuss machine learning approaches to building surrogates for these complex mathematical models. These surrogates can potentially be used to conduct sensitivity analysis, verification, validation, and uncertainty quantification, which is especially important for tumor studies due to their dynamic nature.

60 APPLIED LIFE SCIENCES

Comparative Analysis via CFD Simulation on the Impact of Graphite Anode Morphologies on the Discharge of a Lithium-Ion Battery

The morphology of electrode materials plays a crucial role in determining the performance of lithium-ion batteries. Traditional computational models often simplify graphite flakes as uniformly sized spheres, which limits their predictive accuracy. In this study, we present a computational workflow that overcomes these limitations by incorporating a more realistic representation of graphite morphologies. This workflow is designed to be flexible and reproducible, enabling efficient evaluation of electrochemical performance across diverse material structures. By exploring different graphite morphologies, our approach accelerates the optimization of material preparation techniques and processing conditions. Our findings reveal that incorporating greater morphological complexity leads to significant deviations from classical model predictions. Instead, our refined model offers a more accurate representation of battery discharge behavior, closely aligning with experimental data. This improvement underscores the importance of detailed morphological descriptions in advancing battery design and performance assessments. To promote accessibility and reproducibility, we provide the developed code for seamless integration with the COMSOL API, allowing researchers to implement and adapt it easily. This computational framework serves as a valuable tool for investigating the impact of graphite morphology on battery performance, bridging the gap between theoretical modeling and experimental validation to enhance lithium-ion battery technology.

25 ENERGY STORAGE