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At least 55 records · Page 3

Machine learning models for segmentation and classification of cyanobacterial cells

Abstract Timelapse microscopy has recently been employed to study the metabolism and physiology of cyanobacteria at the single-cell level. However, the identification of individual cells in brightfield images remains a significant challenge. Traditional intensity-based segmentation algorithms perform poorly when identifying individual cells in dense colonies due to a lack of contrast between neighboring cells. Here, we describe a newly developed software package called Cypose which uses machine learning (ML) models to solve two specific tasks: segmentation of individual cyanobacterial cells, and classification of cellular phenotypes. The segmentation models are based on the Cellpose framework, while classification is performed using a convolutional neural network named Cyclass. To our knowledge, these are the first developed ML-based models for cyanobacteria segmentation and classification. When compared to other methods, our segmentation models showed improved performance and were able to segment cells with varied morphological phenotypes, as well as differentiate between live and lysed cells. We also found that our models were robust to imaging artifacts, such as dust and cell debris. Additionally, the classification model was able to identify different cellular phenotypes using only images as input. Together, these models improve cell segmentation accuracy and enable high-throughput analysis of dense cyanobacterial colonies and filamentous cyanobacteria.

Huffine, Clair A.

A Microservices Architecture Toolkit for Interconnected Science Ecosystems

Microservices architecture is a promising approach for developing reusable scientific workflow capabilities for inte- grating diverse resources, such as experimental and observational instruments and advanced computational and data management systems, across many distributed organizations and facilities. In this paper, we describe how the INTERSECT Open Architec- ture leverages federated systems of microservices to construct interconnected science ecosystems, review how the INTERSECT software development kit eases microservice capability develop- ment, and demonstrate the use of such capabilities for deploying an example multi-facility INTERSECT ecosystem.

Brim, Michael

HP-FLEX MPC v0.1.0

HP-FLEX MPC is control software developed by Lawrence Berkeley National Laboratory with support from the California Energy Commission (CEC) through EPIC-19-301. HP-FLEX aims to provide load flexibility for heat pumps (HPs) in response to dynamic grid signals (including Time-of-Use, Dynamic Pricing, and Critical Peak Pricing) while maintaining thermostat temperatures within user-specified bounds. The software includes a system-identification module, which models the dynamics of the building envelope with thermostat data, and a control module based on a model predictive controller (MPC) to make optimal decisions. HP-FLEX receives forecasts of outdoor air temperature, solar irradiation, and internal gain (if available), as well as trajectories of energy price, temperature lower and upper bounds over a prediction horizon. It then optimizes heating and cooling capacities to minimize energy cost and peak power (with a user-defined weight on peak power) over the prediction horizon, while maintaining room air temperature within the temperature constraints, and outputs the optimal thermostat setpoints.

Kim, Donghun

CI-MOR Final Report: Analysis and Validation of Critical Infrastructure Models using Model Order Reduction

This report summarizes the research and capabilities developed as part of the project “Analysis and Validation of Critical Infrastructure Models using Model Order Reduction” (CI-MOR) LDRD project. CI-MOR research enables the solution of large, complex optimization models that naturally arise in national security challenges involving critical infrastructures. Specifically, CI-MOR researchers developed methods to (1) rigorously approximate complex, nonlinear optimization formulations, (2) identify alternative near-optimal solutions, (3) accelerate optimization workflows used for complex applications, and (4) rigorously integrate domain knowledge in stochastic-process models. This report provides an overview of the research done in CI-MOR, and we describe application exemplars used to illustrate CI-MOR capabilities. Furthermore, we describe the software developed by CI-MOR that researchers can leverage to analyze new applications.

97 MATHEMATICS AND COMPUTING

Development of POTATO for 2S Module Grading for the CMS Phase-2 Outer Tracker Upgrade

Due to the High Luminosity-Large Hadron Collider (HL-LHC) upgrade, several detectors of the Compact Muon Solenoid (CMS) will need to be replaced, specifically the new Outer Tracker (OT) that will be assembled with 13,200 silicon modules. The OT is composed of two types of modules; the PS (pixel-strip) and the 2S (strip-strip) modules. With a large influx of production of modules, extensive testing is required to ensure quality of the modules. This research introduces POTATO (Phase-II Outer Tracker Analyzer of Test Outputs), a specialized software developed in C++ to analyze, grade, and store results in a centralized database. Module data will be collected from various international production facilities. The implementation of POTATO will facilitate with selecting the best performing modules for the Outer Tracker upgrade. This research is focused on the implementation of the analysis of 2S Module results within POTATO.

Klupshas, Anna

Development of POTATO for 2S Module Grading for the CMS Phase-2 Outer Tracker Upgrade

Due to the High Luminosity-Large Hadron Collider (HL-LHC) upgrade, several detectors of the Compact Muon Solenoid (CMS) will need to be upgraded, specifically the new Outer Tracker detector that will be composed of 13,200 silicon modules. The Outer Tracker features two types of modules; the PS (pixel-strip) and the 2S (strip-strip) modules. With a large influx of production of modules, extensive testing is required to ensure they fulfill the performance requirements. This research introduces POTATO (Phase-II Outer Tracker Analyzer of Test Outputs), a specialized software developed in C++ to analyze, grade, and store results in a centralized database since module data will be collected from various international production facilities. The implementation of POTATO will facilitate the selection of the best performing modules for the Outer Tracker upgrade. This paper is focused on the implementation of the analysis of 2S Module results within POTATO.

43 PARTICLE ACCELERATORS

Digitizing Today’s Buildings in the Real World: Lessons from Field Demonstrations

Digital twins, created by generating a virtual replica of a building, enable safe evaluation of operational scenarios and applications like fault detection and diagnosis and advanced controls. However, a prerequisite is the creation of a machine-readable digital representation of a building, currently hindered by fragmented information scattered across mechanical drawings, point lists, and natural language sequences. As a result, digital twin development remains labor-intensive, error-prone, and difficult to validate. To address these challenges, two efforts from ASHRAE aim to support the digitalization of buildings. ASHRAE s223 establishes a semantic model of buildings, representing system components, configuration, and data sources. ASHRAE s231 defines a vendor-neutral programming language for expressing their control logic. As the industry evaluates implementing them in their products, understanding the challenges that vendors and implementers may face is crucial. In this paper, we present findings and lessons learned from field demonstrations in five buildings that implemented control applications using ASHRAE s223 and s231. The demonstrations highlight how semantic modeling and formalized control descriptions can significantly reduce software development time, manual point mapping, and hard-coding. Beyond time efficiency, they enable reliable automation by minimizing human interpretation and providing a means for consistency across projects. We describe the processes and best practices for model creation and model usage, from translating heterogeneous building documentation into semantic representations to implementing control logic in real-world systems. Finally, we discuss the challenges that persist, including integration with legacy software environments, gaps in interoperability, and the level of expertise still required to effectively leverage semantic models.

Prakash, Anand Krishnan

Graph-Based Modeling for the Detection and Tracking of Sarin-Surrogate-Induced Neurotoxicity Using a Human-Relevant, In-Vitro Brain Model

Organophosphorus (OP) nerve agents are a chemical threat to the United States, to the civilian population (e.g., pesticides) and historically weaponized (e.g., sarin) as chemical warfare agents. The unprecedented, accelerated process from “bench-to-bedside” during the SARSCov2 pandemic has made it clear that technology and tools need to be readily available for immediate response. Advances in human organ tissue mimetic systems are a promising technology to evaluate the human-relevant response in vitro for basic and applied research and drug screening. In particular, current brain microphysiological systems (MPS) have the capability to monitor and detect changes in engineered human neural circuit activity. However, current data analytics approaches for these systems lack the granularity to functionally detect and distinguish the different mechanisms that occur in the brain following neurotoxicity, injury, and disease. The goal of this project was to advance the computational analytical capabilities of the brain MPS to detect functional changes in neural circuit structure at different stages of Sarin surrogate-induced neurotoxicity. We developed graph-based models to (1) identify the composition of the neural circuit structure; (2) detect and monitor how this structure changes following sarin-induced neurotoxicity; and (3) evaluate the analytical pipeline using known/promising oxime reactivators. Through experiments on the bMPS where in vitro neuronal cultures were exposed to a sarin surrogate, we demonstrated the capabilities of our computational pipeline to identify different responses in the functional networks of brain cells exposed to low and high concentrations of the nerve agent. We identified a biphasic response of human neural network activity following exposure to a sarin-surrogate that had not been reported in the literature before. The graph-based models and software developed in this project can be used for future studies that leverage the brain MPS technology, such as treatment efficacy assessment.

59 BASIC BIOLOGICAL SCIENCES

Benchmark for two-dimensional large scale coherent structures in partially magnetized E × B plasmas—community collaboration & lessons learned

Low-temperature plasmas (LTPs) are essential to both fundamental scientific research and critical industrial applications. As in many areas of science, numerical simulations have become a vital tool for uncovering new physical phenomena and guiding technological development. Code benchmarking remains crucial for verifying implementations and evaluating performance. This work continues the Landmark benchmark initiative, a series specifically designed to support the verification of LTP codes. In this study, seventeen simulation codes from a collaborative community of nineteen international institutions modeled a partially magnetized E × B Penning discharge. The emergence of large scale coherent structures, or rotating plasma spokes, endows this configuration with an enormous range of time scales, making it particularly challenging to simulate. The codes showed excellent agreement on the rotation frequency of the spoke as well as key plasma properties, including time-averaged ion density, plasma potential, and electron temperature profiles. Achieving this level of agreement came with challenges, and we share lessons learned on how to conduct future benchmarking campaigns. Comparing code implementations, computational hardware, and simulation runtimes also revealed interesting trends, which are summarized with the aim of guiding future plasma simulation software development.

benchmarking

Visualization at exascale: Making it all work with VTK-m

The VTK-m software library enables scientific visualization on exascale-class supercomputers. Exascale machines are particularly challenging for software development in part because they use GPU accelerators to provide the vast majority of their computational throughput. Algorithmic designs for GPUs and GPU-centric computing often deviate from those that worked well on previous generations of high-performance computers that relied on traditional CPUs. Fortunately, VTK-m provides scientific visualization algorithms for GPUs and other accelerators. VTK-m also provides a framework that simplifies the implementation of new algorithms and adds a porting layer to work across multiple processor types. This paper describes the main challenges encountered when making scientific visualization available at exascale. Here, we document the surprises and obstacles faced when moving from pre-exascale platforms to the final exascale designs and the performance on those systems including scaling studies on Frontier, an exascale machine with over 37,000 AMD GPUs. We also report on the integration of VTK-m with other exascale software technologies. Finally, we show how VTK-m helps scientific discovery for applications such as fusion and particle acceleration that leverage an exascale supercomputer.

97 MATHEMATICS AND COMPUTING

The Short-Baseline Near Detector at Fermilab: Input to the European Strategy for Particle Physics 2026 Update

SBND is a 112 ton liquid argon time projection chamber (LArTPC) neutrino detector located 110 meters from the Booster Neutrino Beam (BNB) target at Fermilab. Its main goals include searches for eV-scale sterile neutrinos as part of the Short-Baseline Neutrino (SBN) program, other searches for physics beyond the Standard Model, and precision studies of neutrino-argon interactions. In addition, SBND is providing a platform for LArTPC neutrino detector technology development and is an excellent training ground for the international group of scientists and engineers working towards the upcoming flagship Deep Underground Neutrino Experiment (DUNE). SBND began operation in July 2024, and started collecting stable neutrino beam data in December 2024 with an unprecedented rate of ~7,000 neutrino events per day. During its currently approved operation plans (2024-2027), SBND is expected to accumulate nearly 10 million neutrino interactions. The near detector dataset will be instrumental in testing the sterile neutrino hypothesis with unprecedented sensitivity in SBN and in probing signals of beyond the Standard Model physics. It will also be used to significantly advance our understanding of the physics of neutrino-argon interactions ahead of DUNE. After the planned accelerator restart at Fermilab (2029+), opportunities are being explored to operate SBND in antineutrino mode in order to address the scarcity of antineutrino-argon scattering data, or in a dedicated beam-dump mode to significantly enhance sensitivity to searches for new physics. SBND is an international effort, with approximately 40% of institutions from Europe, contributing to detector construction, commissioning, software development, and data analysis. Continued European involvement and leadership are essential during SBND's operations and analysis phase for both the success of SBND, SBN and its role leading up to DUNE.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Alquimia v1.0: a generic interface to biogeochemical codes – a tool for interoperable development, prototyping and benchmarking for multiphysics simulators

Alquimia v1.0 is a generic interface to geochemical solvers that facilitates development of multiphysics simulators by enabling code coupling, prototyping and benchmarking. The interface enforces the function arguments and their types for setting up, solving, serving up output data and carrying out other common auxiliary tasks while providing a set of structures for data transfer between the multiphysics code driving the simulation and the geochemical solver. Alquimia relies on a single-cell approach that permits operator splitting coupling and parallel computation. We describe the implementation in Alquimia of two widely used open-source codes that perform geochemical calculations: PFLOTRAN and CrunchFlow. We then exemplify its use for the implementation and simulation of reactive transport in porous media by two open-source flow and transport simulators: Amanzi and ParFlow. We also demonstrate its use for the simulation of coupled processes in novel multiphysics applications including the effect of multiphase flow on reaction rates at the pore scale with OpenFOAM, the role of complex biogeochemical processes in land surface models such as the E3SM Land Model (ELM) and the impact of surface–subsurface hydrological interactions on hydrogeochemical export from watersheds with the Advanced Terrestrial Simulator (ATS). These applications make it apparent that the availability of a well-defined yet flexible interface has the potential to improve the software development workflow, freeing up resources to focus on advances in process models and mechanistic understanding of coupled problems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Supporting ARPA-E Power Grid Optimization (Final Report)

Pacific Northwest National Laboratory (PNNL), Arizona State University (ASU), Georgia Institute of Technology (Georgia Tech), Los Alamos National Laboratory (LANL), National Renewable Energy Laboratory (NREL), Texas A&M University (TAMU), The University of Texas at Austin (UT), and the University of Wisconsin-Madison (UW-M) supported the ARPA-E Grid Optimization (GO) Competition by providing a common problem formulation, data format, datasets, evaluation mechanism, scoring, rules, and results that resulted in the awarding of $\$9.24$ million dollars to teams from academia, industry, and national labs for solving three sets of increasingly difficult non-linear, security- constrained AC Optimal Powerflow (AC-OPF) optimization problems in order to increase the efficiency of the US Electric Grid. It is estimated that a 1% increase in efficiency can save $\$1$ billion. Current industry practices typically use a linear DC model (DC-OPF) in order solve the OPF problem within the time constraints of the operation schedule. The GO Competition challenges the best power engineers, mathematicians, and computer scientists to make possible operational decisions based on accurate physical models. To accomplish this, the GO Competition created a series of Challenges and funded teams to produce the best solver. Challenge 1 was to solve the security constrained Alternating Current Optimal Power Flow (ACOPF) problem. Challenge 2 extended that to by adding adjustable transformer tap ratios, phase shifting transformers, switchable shunts, price-responsive demand, ramp rate constrained generators and loads, and fast-start unit commitment (UC). Furthermore, Challenge 2 was a maximization problem while Challenge 1 was a minimization problem. While Challenge 3 was being developed, the entrants were invited to find better solutions to the Challenge 2 synthetic datasets with no restrictions on time, hardware, or algorithms. The Challenge 2 solutions turned out to be very good. Challenge 3 expanded the Challenge 2 problem further by using multiperiod dynamic markets, including advisory models for extreme weather events, day-ahead markets, and the real-time markets with an extended look-ahead. These problems included active bid-in demand and topology optimization. Together the Challenges used nearly 30 million CPU hours. Since each team was working on the same problem, using the same data, and running on the same hardware, fair comparisons could be drawn as to the best solver. The datasets were varied enough, however, that the best solver for one dataset was not necessarily the best at another, so cumulative scores were used. The process was managed by the PNNL maintained website https://GOCompetition.energy.gov, where Entrants could find information about the problem, the data, the rules, submit their solver for evaluation, and see the scores of all the competing teams on a Leaderboard. Interest was world-wide but only American teams were eligible for prizes. The Competition has produced 34 journal articles 115 papers and been cited over 500 times in the literature, including 12 dissertations (4 from foreign countries; Columbia (2), Germany, and Italy) and 3 from the DOE ExaScale project. Software developed by Pearl Street Technologies for Challenges 1 and 2 is now deployed by Southwest Power Pool (SPP) and Midcontinent Independent Service Operator (MISO). Other teams have received inquiries from venture capitalists. Google DeepMind has thanked the Competition for making the datasets developed for the Competition public. They are using it to train machine learning models. The larger datasets have billions of unknowns to be solved for, but only a small percent matter in the final solution. Knowing what unknowns are important can dramatically speedup the solution.

24 POWER TRANSMISSION AND DISTRIBUTION

CG-Kit: Code Generation Toolkit for performant and maintainable variants of source code applied to Flash-X hydrodynamics simulations

CG-Kit is a new Code Generation tool-Kit that we have developed as a part of the solution for portability and maintainability for multiphysics computing applications. The development of CG-Kit is rooted in the urgent need created by the shifting landscape of high-performance computing platforms and the algorithmic complexities of a particular large-scale multiphysics application: Flash-X. To efficiently use computing resources on a heterogeneous node, an application must have a map of computation to resources and a mechanism to move the data and computation to the resources according to the map. Most existing performance portability solutions are focussed on abstracting the expression of computations so that a unified source code can be specialized to run on different resources. However, such an approach is insufficient for a code like Flash-X, which has a multitude of code components that can be assembled in various permutations and combinations to form different instances of applications. Similar challenges apply to any code that has composability, where a single specified way of apportioning work among devices may not be optimal. Additionally, use cases arise where the optimal control flow of computation may differ for different devices while the underlying numerics remain identical. This combination leads to unique challenges including handling an existing large code base in Fortran and/or C/C++, subdivision of code into a great variety of units supporting a wide range of physics and numerical methods, different parallelization techniques for distributed and shared memory systems and accelerator devices, and heterogeneity of computing platforms requiring coexisting variants of parallel algorithms. All of these challenges demand that scientific software developers apply existing knowledge about domain applications, algorithms, and computing platforms to determine custom abstractions and granularity for code generation. There is a critical lack of tools to tackle those problems. CG-Kit is designed to fill this gap by providing a user with the ability to express their desired control flow and computation-to-resource map in the form a pseudocode-like recipe. It consists of standalone tools that can be combined into highly specific and, we argue, highly effective portability and maintainability toolchains. Here we present the design of our new tools: parametrized source trees, control flow graphs, and recipes. The tools are implemented in Python. They are agnostic to the programming language of the source code targeted for code generation. In conclusion, we demonstrate the capabilities of the toolkit with two examples, first, multithreaded variants of the basic AXPY operation, and second, variants of parallel algorithms within a hydrodynamics solver, called Spark, from Flash-X that operates on block-structured adaptive meshes.

Algorithmic portability

Quantitative insights for diagnosing performance bottlenecks in lithium–sulfur batteries

Lithium–sulfur (Li–S) batteries hold significant promise for electric vehicles and aviation due to their high energy density and cost-effectiveness. However, understanding the root causes of performance degradation remains a formidable challenge, as the interplay of multiple factors obscures key failure mechanisms. A major limitation has been the inability to quantify soluble sulfur species within practical detection limits accurately and to correlate electrochemical processes with associated physical inventory changes. Here, we introduce the high-performance liquid chromatography-ultraviolet spectroscopy and gas chromatography sequential characterization (HUGS) toolkit, capable of precisely quantifying seven distinct sulfur and polysulfide species at concentrations as low as 40 ppb. HUGS has been successfully applied to practical coin and pouch cells without requiring cell modification. Furthermore, our self-developed software, Dr HUGS, enhanced the data analysis speed by over 30 times, enabling multi-source data integration and delivering comprehensive analysis results within minutes. Using HUGS, we identify significant capacity losses from inactive lithium and sulfur during initial cycles and sulfide-rich solid–electrolyte interphase (SEI) formation on the anode during later cycles. Notably, our findings reveal that soluble polysulfides have minimal contributions to capacity loss, challenging long-standing assumptions. Moreover, HUGS demonstrates that constant-pressure setups in Li–S pouch cells improve compositional uniformity compared to constant-gap configurations. For sulfurized polyacrylonitrile (SPAN) cathodes, unique issues such as non-sulfide SEI formation and lithium pulverization are observed, which can be mitigated through localized high-concentration electrolytes to enhance lithium inventory retention. By enabling precise quantification of critical inventory components, HUGS provides transformative insights into failure mechanisms across various electrolytes and cathode chemistries, guiding rational design strategies for next-generation energy storage systems.

25 ENERGY STORAGE

CI/CD Efforts for Validation, Verification and Benchmarking OpenMP Implementations

Software developers must adapt to keep up with the changing capabilities of platforms so that they can utilize the power of High-Performance Computers (HPC), including exascale systems. OpenMP, a directive-based parallel programming model, allows developers to include directives to existing C, C++, or Fortran code to allow node level parallelism without compromising performance. This paper describes our CI/CD efforts to provide easy evaluation of the support of OpenMP across different compilers using existing testsuites and benchmark suites on HPC platforms. Our main contributions include (1) the set of a Continuous Integration (CI) and Continuous Development (CD) workflow that captures bugs and provides faster feedback to compiler developers, (2) an evaluation of OpenMP (offloading) implementations supported by AMD, HPE, GNU, LLVM, and Intel, and (3) evaluation of the quality of compilers across different heterogeneous HPC platforms. With the comprehensive testing through the CI/CD workflow, we aim to provide a comprehensive understanding of the current state of OpenMP (offloading) support in different compilers and heterogeneous platforms consisting of CPUs and GPUs from NVIDIA, AMD, and Intel.

Jarmusch, Aaron

Nucleus++ : a new tool bridging AME and NUBASE for advancing nuclear data analysis

The newly developed software, Nucleus++ , is an advanced tool for displaying basic nuclear physics properties from NUBASE and integrating comprehensive mass information for each nuclide from Atomic Mass Evaluation. Additionally, it allows users to compare experimental nuclear masses with predictions from different mass models. Building on the success and learning experiences of its predecessor, Nucleus , this enhanced tool introduces improved functionality and compatibility. With its user-friendly interface, Nucleus++ was designed as a valuable tool for scholars and practitioners in the field of nuclear science. Finally, this article offers an in-depth description of Nucleus++ , highlighting its main features and anticipated impacts on nuclear science research.

AME

MARLOWE: An Untargeted Proteomics, Statistical Approach to Taxonomic Classification for Forensics

General proteomics research for fundamental science typically addresses laboratory- or patient-derived samples of known origin and composition. However, in a few research areas, such as environmental proteomics, clinical identification of infectious organisms, archeology, art/cultural history, and forensics, attributing the origin of a protein-containing sample to the organisms that produced it is a central focus. A small number of groups have approached this problem and developed software tools for taxonomic characterization and/or identification using bottom-up proteomics. Most such tools identify peptides via database search, and many rely on organism-specific peptides as markers. Our group recently introduced MARLOWE, a software tool for taxonomic characterization of unknown samples based on de novo peptide identification and signal-erosion-resistant strong peptides, which are shared peptides distributed in a taxonomy-dependent manner. In the current work, we further characterize the utility of MARLOWE using publicly available proteomics data from forensically-relevant samples. MARLOWE characterizes samples based on their protein profile, and returns ranked organism lists of potential contributors and taxonomic scores based on shared strong peptides between organisms. Overall, the correct characterization rate ranges between 44 and 100%, depending on the sample type and data acquisition parameters (with lower numbers associated with lower-quality data sets). MARLOWE demonstrates successful characterization of true contributors and close relatives, and provides sufficient specificity to distinguish certain microbial species. MARLOWE demonstrates its ability to provide insight into potential taxonomic sources for a wide range of sample types without prior assumptions about sample contents. As a result, this approach can find utility in forensic science and also broadly in bioanalytical applications that utilize proteomics approaches for taxonomic characterization.

Bacteria