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DOE OSTI2025

A small number of point mutations confer formate tolerance in Shewanella oneidensis

ABSTRACT Microbial electrosynthesis (MES) is a sustainable approach to chemical production from CO 2 and clean electricity. However, limitations in electron transfer efficiency and gaps in understanding of electron transfer pathways in MES systems prevent full realization of this technology. Shewanella oneidensis could serve as an MES biocatalyst because it has a well-studied, efficient transmembrane electron transfer pathway. A key first step in MES in this organism could be CO 2 reduction to formate. However, we report that wild-type S. oneidensis does not tolerate high levels of formate. In this work, we created and characterized formate-tolerant strains of S. oneidensis for further engineering and future use in MES systems through adaptive laboratory evolution. Two different point mutations in a gene encoding a predicted sodium-dependent bicarbonate transporter and a DUF2721-containing protein separately confer formate tolerance to S. oneidensis . The mutations were further evaluated to understand their role in improving formate tolerance. We also show that the wild-type and mutant versions of the putative sodium-dependent bicarbonate transporter improve formate tolerance of Zymomonas mobilis , indicating the potential of transferring this formate tolerance phenotype to other organisms. IMPORTANCE Shewanella oneidensis is a bacterium with a well-studied, efficient extracellular electron transfer pathway. This capability could make this organism a suitable host for microbial electrosynthesis using CO 2 or formate as feedstocks. However, we report here that formate is toxic to S. oneidensis , limiting the potential for its use in these systems. In this work, we evolve several strains of S. oneidensis that have improved formate tolerance, and we investigate some mutations that confer this phenotype. The phenotype is confirmed to be attributed to several single point mutations by transferring the wild-type and mutant versions of each gene to the wild-type strain. Finally, the formate tolerance mechanism of one variant is studied using structural modeling and expression in another host. This study, therefore, presents a simple method for conferring formate tolerance to bacterial hosts.

Cross, Megan C. Gruenberg (ORCID:0000000291589900)↗

DOE OSTI2025

Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification

Accurate metagenomic classification relies on comprehensive, up-to-date, and validated reference databases. While the NCBI BLAST Nucleotide (nt) database, encompassing a vast collection of sequences from all domains of life, represents an invaluable resource, its massive size—currently exceeding 10 12 nucleotides—and exponential growth pose significant challenges for researchers seeking to maintain current nt-based indices for metagenomic classification. Recognizing that no current nt-based indices exist for the widely used Centrifuge classifier, and the last public version currently available was released in 2018, we addressed this critical gap by leveraging advanced high-performance computing resources. We present new Centrifuge-compatible nt databases, meticulously constructed using a novel pipeline incorporating different quality control measures, including reference decontamination and filtering. These measures demonstrably reduce spurious classifications, as shown through our reanalysis of published metagenomic data where Plasmodium annotations were dramatically reduced using our decontaminated database, highlighting how database quality can significantly impact research conclusions. Through temporal comparisons, we also reveal how our approach minimizes inconsistencies in taxonomic assignments stemming from asynchronous updates between public sequence and taxonomy databases. These discrepancies are particularly evident in taxa such as Listeria monocytogenes and Naegleria fowleri, where classification accuracy varied significantly across database versions. These new databases, made available as pre-built Centrifuge indexes, respond to the need for an open, robust, nt-based pipeline for taxonomic classification in metagenomics. Applications such as environmental metagenomics, forensics, and clinical metagenomics, which require comprehensive taxonomic coverage, will benefit from this resource. Our work highlights the importance of treating reference databases as dynamic entities, subject to ongoing quality control and validation akin to software development best practices. This approach is crucial for ensuring accuracy and reliability of metagenomic analysis, especially as databases continue to expand in size and complexity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Improving topological cluster reconstruction using calorimeter cell timing in ATLAS

Clusters of topologically connected calorimeter cells around cells with large absolute signal-to-noise ratio (topo-clusters) are the basis for calorimeter signal recon struction in the ATLAS experiment. Topological cell clus tering has proven performant in LHC Runs 1 and 2. It is, however, susceptible to out-of-time pile-up of signals from soft collisions outside the 25 ns proton-bunch-crossing window associated with the event’s hard collision. To reduce this effect, a calorimeter-cell timing criterion was added to the signal-to-noise ratio requirement in the clustering algorithm. Multiple versions of this criterion were tested by reconstructing hadronic signals in simulated events and Run 2 ATLAS data. The preferred version is found to reduce the out-of-time pile-up jet multiplicity by ~50% for jet p T ~ 20 GeV and by ~80% for jet p T ≳ 50 GeV, while not disrupting the reconstruction of hadronic signals of interest, and improving the jet energy resolution by up to 5% for 20 < p T < 30 GeV. Pile-up is also suppressed for other physics objects based on topo-clusters (electrons, photons, τ-leptons), reducing the overall event size on disk by about 6% in early Run 3 pile up conditions. Offline reconstruction for Run 3 includes the timing requirement.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Holographic map for cosmological horizons

Here, we propose a holographic map between Einstein gravity coupled to matter in a de Sitter background and large N quantum mechanics of a system of spins. Holography maps a spin model with a finite-dimensional Hilbert space defined on a version of the stretched horizon into bulk gravitational dynamics. The full Hamiltonian of the spin model contains a nonlocal piece which generates chaotic dynamics, widely conjectured to be a necessary part of quantum gravity, and a local piece which recovers the perturbative spectrum in the bulk.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Review of Particle Physics

The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 3,200 new measurements from 903 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Most of the 118 reviews are updated, including many that are heavily revised.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Virtual Time III, Part 2: Combining Conservative and Optimistic Synchronization

This is Part 2 of a trio of works intended to provide a unifying framework in which conservative and optimistic synchronization for parallel discrete event simulations can be freely and transparently combined in the same logical process on an event-by-event basis. Here, in this article, we continue the outline of an approach called Unified Virtual Time (UVT) that was introduced in Part 1, showing in detail via two extended examples how conservative synchronization can be refactored and combined with optimistic synchronization in the UVT framework. We describe UVT versions of both a basic time windowing algorithm called Unified Simple Time Windows and a refactored version of the Chandy-Misra-Bryant Null Message algorithm called Unified CMB.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Tensor Network Quantum Virtual Machine for Simulating Quantum Circuits at Exascale

The numerical simulation of quantum circuits is an indispensable tool for development, verification, and validation of hybrid quantum-classical algorithms intended for near-term quantum co-processors. The emergence of exascale high-performance computing (HPC) platforms presents new opportunities for pushing the boundaries of quantum circuit simulation. Here, we present a modernized version of the Tensor Network Quantum Virtual Machine (TNQVM) that serves as the quantum circuit simulation backend in the eXtreme-scale ACCelerator (XACC) framework. The new version is based on the scalable tensor network processing library ExaTN (Exascale Tensor Networks). It provides multiple configurable quantum circuit simulators that perform either an exact quantum circuit simulation via the full tensor network contraction or an approximate simulation via a suitably chosen tensor factorization scheme. Upon necessity, stochastic noise modeling from real quantum processors is incorporated into the simulations by modeling quantum channels with Kraus tensors. By combining the portable XACC quantum programming frontend and the scalable ExaTN numerical processing backend, we introduce an end-to-end virtual quantum development environment that can scale from laptops to future exascale platforms. We report initial benchmarks of our framework, which include a demonstration of the distributed execution, incorporation of quantum decoherence models, and simulation of the random quantum circuits used for the certification of quantum supremacy on Google’s Sycamore superconducting architecture.

Nguyen, Thien↗

DOE OSTI2022

Power Converter Circuit Design Automation using Parallel Monte Carlo Tree Search

The tidal waves of modern electronic/electrical devices have led to increasing demands for ubiquitous application-specific power converters. A conventional manual design procedure of such power converters is computation- and labor-intensive, which involves selecting and connecting component devices, tuning component-wise parameters and control schemes, and iteratively evaluating and optimizing the design. To automate and speed up this design process, we propose an automatic framework that designs custom power converters from design specifications using Monte Carlo Tree Search. Specifically, the framework embraces the upper-confidence-bound-tree (UCT), a variant of Monte Carlo Tree Search, to automate topology space exploration with circuit design specification-encoded reward signals. Moreover, our UCT-based approach can exploit small offline data via the specially designed default policy and can run in parallel to accelerate topology space exploration. Further, it utilizes a hybrid circuit evaluation strategy to substantially reduce design evaluation costs. Empirically, we demonstrated that our framework could generate energy-efficient circuit topologies for various target voltage conversion ratios. Compared to existing automatic topology optimization strategies, the proposed method is much more computationally efficient --- the sequential version can generate topologies with the same quality while being up to 67% faster. Here, the parallelization schemes can further achieve high speedups compared to the sequential version.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

PANDORA: A Parallel Dendrogram Construction Algorithm for Single Linkage Clustering on GPU

This paper introduces Pandora, a parallel algorithm for computing dendrograms, the hierarchical cluster trees for single linkage clustering (SLC). Current parallel approaches construct dendrograms by partitioning a minimum spanning tree and removing edges. However, they struggle with skewed, hard-to-parallelize real-world dendrograms. Consequently, computing dendrograms is the sequential bottleneck in HDBSCAN*[21], a popular SLC variant. Pandora uses recursive tree contraction to address this limitation. Pandora contracts nodes to construct progressively smaller trees. It computes the smallest contracted dendrogram and expands it by inserting contracted edges. This recursive strategy is highly parallel, skew-independent, work-optimal, and well-suited for GPUs and multicores. We develop a performance portable implementation of Pandora in Kokkos[31] and evaluate its performance on multicore CPUs and multi-vendor GPUs (e.g., Nvidia, AMD) for dendrogram construction in HDBSCAN*. Multithreaded Pandora is 2.2x faster than the current best-multithreaded implementation. Our GPU version achieves 6-20x speedup on AMD GPUs and 10-37x on NVIDIA GPUs over multithreaded Pandora. Pandora removes HDBSCAN*’s sequential bottleneck, greatly boosting efficiency, particularly with GPUs.

Sao, Piyush↗

DOE OSTI2023

Flow Injection Electrochemical Quartz Crystal Microbalance with ICP-OES Detection: Electroprecipitation and Stripping of Lanthanum and Neodymium in a Flow Cell

We used an improved version of our hyphenated analysis technique, flow injection electrochemical quartz crystal microbalance (EQCM) with inductively coupled optical emission spectroscopy, to investigate the electroprecipitation of lanthanum and neodymium from flowing solutions. The improved version has two independent flow injection circuits, allowing different conditions for electrochemical precipitation (pH=4.3 or 2.6) and quick stripping (2% HNO3) with EQCM mass detection and ICP-OES elemental analysis. Lanthanum or neodymium ions in a 500 uL sample were injected into a carrier stream and deposited onto an EQCM housed in a micro flow cell, owing to a localized high-pH layer. The deposits are subsequently stripped from the electrode using HNO3 and analyzed downstream using an ICP-OES. We found that using acidic solutions without supporting electrolyte leads to an increase of the amount of lanthanum detected by 4-fold. The enhanced deposition can be attributed to enhanced mass transfer by migration. Furthermore, we showed that by applying chronopotentiometry, we can detect a change in the hydrogen evolution reaction mechanism that enables the precipitation of lanthanides on the surface of the electrode. Understanding and enhancing the deposition of lanthanides is relevant for elemental or isotopic detection in nuclear forensics.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2021

F3C v0.1

Fast Free Fermion Compiler (F3C) is an application-specific quantum circuit compiler for time-evolution circuits of spin Hamiltonian systems that can be mapped to free fermions. F3C is the Matlab software version and the related F3C++ is the C++ software version.

Van Beeumen, RoelMaria Franciscus↗

DOE OSTI2021

HyRAM+ (Hydrogen Plus Other Alternative Fuels Risk Assessment Models) v.4.0

HyRAM+ is a software toolkit for conducting quantitative risk assessment (QRA) and consequence modeling for hydrogen and other alternative fuels infrastructure and transportation systems. HyRAM+ contains validated, simplified release behavior models, a standardized QRA approach, and engineering models and generic data relevant to hydrogen installations. HyRAM (hydrogen-only) versions 1.0 to 3.1 were developed by Sandia for the U.S. Department of Energy (DOE) Hydrogen and Fuel Cell Technologies Office (HFTO). The U.S. DOE Vehicle Technologies Office (VTO) and U.S. Department of Transportation (DOT) Pipeline and Hazardous Material Safety Administration (PHMSA) contributed to the development of HyRAM+ version 4.0 regarding the addition of methane (natural gas) and propane models. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-10862 O

Groth, Katrina↗

DOE OSTI2022

MEASUR - Manufacturing Energy Assessment Software for Utility Reduction

MEASUR your energy savings with the free DOE MEASUR software The Department of Energy (DOE), with Oak Ridge National Laboratory (ORNL), released version 1.0 of their energy efficiency software tool MEASUR (Manufacturing Energy Assessment Software for Utility Reduction). MEASUR has been available for several years as a beta version, being tested by industry experts and real users, and will continue to be updated and improved in the coming years. It is an integrated suite of tools to aid manufacturers in improving the efficiency of energy systems and equipment within a plant, including motors, pumps, fans, process heating, steam, and compressed air. Additionally, there are modules for wastewater energy analysis and to help perform energy treasure hunts. Several calculators are also included, allowing users to independently perform smaller calculations and analyses (such as estimating pump head, performing a fan traverse analysis, estimating waste heat recovery potential, and cataloging compressed air leaks). The MEASUR modules are based on previous DOE software tools that have been used by industry since the early 2000s (such as MotorMaster, AirMaster+, PSAT, PHAST, and FSAT). The original tools only ran on Windows operating systems, and by Windows 10, most of them were inoperable. DOE started their energy efficiency software tool revitalization effort in 2016, first with PSAT (for pumps), then began to integrate the other tools and expand their functionality and utility. The new MEASUR suite provides an extensively more user-friendly, modern, and versatile set of tools. All the assessment modules and most of the calculators have several visual components and graphs and detailed help text for every user input. To help reach international users, the tool utilizes Google translate and users can easily change unit systems, even converting existing user inputs if desired. The assessment files can be organized within the internal file system and easily shared to other users, regardless of their operating system. The entire suite is free, open-source, and can be downloaded on Windows, Mac, or Linux operating systems.

Accawi, Gina [Oak Ridge National Lab. (ORNL), Oak ↗

DOE OSTI2022

R-Stream

R-Stream version 3.21.3, including its TensorFlow front-end (TFRCC) and LLVM 9 front-end. This version includes the features developed in the Portacy Phase II contract. R-Stream is a source-to-source automatic parallelization engine. For usage, please refer to the manuals (In particular, user guide and release notes) available in the package.

Meister, Benoit [Reservoir Labs, Inc., Portland, O↗

DOE OSTI2022

HyRAM+ (Hydrogen Plus Other Alternative Fuels Risk Assessment Models) v.4.1.1

Groth, Katrina↗

DOE OSTI2020

SAM™ (System Advisor Model™) [SWR-16-02, SWR-10-13]

See the SAM™ website to build a desktop version of the National Laboratory of the Rockies' (NLR's) System Advisor Model™ (SAM). https://sam.nlr.gov/ The System Advisor Model™ (SAM™) is a free techno-economic software model that facilitates decision-making for people in the renewable energy industry: -Project managers and engineers -Policy analysts -Technology developers -Researchers SAM can model many types of renewable energy systems: -Photovoltaic systems, from small residential rooftop to large utility-scale systems -Battery storage with Lithium ion, lead acid, or flow batteries for front-of-meter or behind-the-meter applications -Concentrating Solar Power systems for electric power generation, including parabolic trough, power tower, and linear Fresnel -Industrial process heat from parabolic trough and linear Fresnel systems -Wind power, from individual turbines to large wind farms -Marine energy wave and tidal systems -Solar water heating -Fuel cells -Geothermal power generation -Biomass combustion for power generation -High concentration photovoltaic systems SAM's financial models are for the following types of projects: -Residential and commercial projects where the renewable energy system is on the customer side of the electric utility meter (behind the meter), and power from the system is used to reduce the customer's electricity bill. -Power purchase agreement (PPA) projects where the system is connected to the grid at an interconnection point, and the project earns revenue through power sales. The project may be owned and operated by a single owner or by a partnership involving a flip or leaseback arrangement. -Third party ownership where the system is installed on the customer's (host) property and owned by a separate entity (developer), and the host is compensated for power generated by the system through either a PPA or lease agreement. For a more detailed description of SAM, see Blair et al. (2018), System Advisor Model (SAM) General Description (Version 2017.9.5), NREL/TP-6A20-70414. https://www.nrel.gov/docs/fy18osti/70414.pdf

Ryberg, David↗

DOE OSTI2021

Griffin-m

Griffin-m is a MOOSE-based reactor multiphysics application that streamlines the analysis of a variety of nuclear multiphysics simulations, including steady-state and transient radiation transport, core performance, fuel depletion, criticality and decay heat calculations, reprocessing and post-irradiation examination. This streamlining is accomplished via enhanced flexibility of the tools, uniform syntax in the MOOSE framework, dynamic linking of all relevant physics and a single point of execution. The design for flexible multi-physics, multi-radiation, multi-scheme tasks demands and ultimately makes Griffin-m a highly extendable code system. A software quality assurance (SQA) procedure is enforced during Griffin-m development. The Griffin-m version will be the main production version and it includes the MCC3 code, which was originally developed at Argonne National Laboratory to prepare cross sections for fast reactors.

Ortensi, Javier [Idaho National Laboratory (INL), ↗

DOE OSTI2020

ames-market/psst

Python version of the AMES Wholesale Power Market Test Bed; no GUI. Previously hosted by Iowa State University; PNNL has assumed hosting. AMES existed in a non-version controlled and inconsistent form. PNNL added price-sensitive loads for transactive systems, with various other bug fixes and features.

McDermott, Tom↗