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At least 109 records · Page 6

Expanded genome and proteome reallocation in a novel, robust Bacillus coagulans strain capable of utilizing pentose and hexose sugars

Bacillus coagulans, a Gram-positive thermophilic bacterium, is recognized for its probiotic properties and recent development as a microbial cell factory. Despite its importance for biotechnological applications, the current understanding of B. coagulans’ robustness is limited, especially for undomesticated strains. To fill this knowledge gap, we characterized the metabolic capability and performed functional genomics and systems analysis of a novel, robust strain, B. coagulans B-768. Genome sequencing revealed that B-768 has the largest B. coagulans genome known to date (3.94 Mbp), about 0.63 Mbp larger than the average genome of sequenced B. coagulans strains, with expanded carbohydrate metabolism and mobilome. Functional genomics identified a well-equipped genetic portfolio for utilizing a wide range of C5 (xylose, arabinose), C6 (glucose, mannose, galactose), and C12 (cellobiose) sugars present in biomass hydrolysates, which was validated experimentally. For growth on individual xylose and glucose, the dominant sugars in biomass hydrolysates, B-768 exhibited distinct phenotypes and proteome profiles. Faster growth and glucose uptake rates resulted in lactate overflow metabolism, which makes B. coagulans a lactate overproducer; however, slower growth and xylose uptake diminished overflow metabolism due to the high energy demand for sugar assimilation. Carbohydrate Transport and Metabolism (COG-G), Translation (COG-J), and Energy Conversion and Production (COG-C) made up 60%–65% of the measured proteomes but were allocated differently when growing on xylose and glucose. The trade-off in proteome reallocation, with high investment in COG-C over COG-G, explains the xylose growth phenotype with significant upregulation of xylose metabolism, pyruvate metabolism, and tricarboxylic acid (TCA) cycle. Strain B-768 tolerates and effectively utilizes inhibitory biomass hydrolysates containing mixed sugars and exhibits hierarchical sugar utilization with glucose as the preferential substrate.

carbohydrate metabolism↗

New Time Integrators and Capabilities in SUNDIALS Versions 6.2.0-7.4.0

SUNDIALS is a well-established numerical library that provides robust and efficient time integrators and nonlinear solvers. This article overviews several significant improvements and new features added over the last 3 years to support scientific simulations run on high-performance computing systems. Notably, three new classes of one-step methods have been implemented: low storage Runge–Kutta, symplectic partitioned Runge–Kutta, and operator splitting. In addition, we describe new timestep adaptivity support for multirate methods, adjoint sensitivity analysis capabilities for explicit Runge–Kutta methods, additional options for Anderson acceleration in nonlinear solvers, and improved error handling and logging.

Computer science↗

Bacteria isolated from the grape phyllosphere capable of degrading guaiacol, a main volatile phenol associated with smoke taint in wine

Recent wildfires near vineyards in the Pacific United States have caused devastating financial losses due to smoke taint in wine. When wine grapes (Vitis vinifera) are exposed to wildfire smoke, their berries absorb volatile phenols derived from the lignin of burning plant material. Volatile phenols are released during the winemaking process giving the finished wine an unpleasant, smokey, and ashy taste known as smoke taint. Bacteria are capable of undergoing a wide variety of metabolic processes and therefore present great potential for bioremediation applications in many industries. In this study, we identify two strains of the same species that colonize the grape phyllosphere and are able to degrade guaiacol, a main volatile phenol responsible for smoke taint in wine. We identify the suite of genes that enable guaiacol degradation in Gordonia alkanivorans via RNAseq of cells growing on guaiacol as a sole carbon source. Additionally, we knockout guaA, a cytochrome P450 gene involved in the conversion of guaiacol to catechol; ΔguaA cells cannot catabolize guaiacol in vitro, providing evidence that GuaA is necessary for this process. Furthermore, we analyze the microbiome of berries and leaves exposed to smoke in the vineyard to investigate the impact of smoke on the grape microbial community. We found smoke has a significant but small effect on the microbial community, leading to an enrichment of several genera belonging to the Bacilli class. Collectively, this research shows that studying microbes and their enzymes has the potential to identify novel tools for alleviating smoke taint.

Castro, Claudia [United States Department of Agric↗

Advanced Test Reactor (ATR) Capabilities in Support of Advanced Reactor Development [Slides]

A primary mission of the Advanced Test Reactor (ATR) is to support the next generation of nuclear reactors. This is an overview of ATR irradiation capabilities in support of advanced reactor development. Topics include an overview of the ATR facility and reactor, experiment design overview, thermal and fast spectrum testing, as well as advanced material testing.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Demonstrating MeV-Scale Physics Capabilities of Large Neutrino LArTPCs with Ambient Blip Activity in MicroBooNE

Large neutrino liquid argon time projection chamber (LArTPC) experiments can broaden their physics reach by incorporating isolated MeV-scale features present in their data. We use data from MicroBooNE, an 85 tonne LArTPC exposed to Fermilab neutrino beams from 2015 until 2021, to demonstrate new calorimetric and particle discrimination capabilities for isolated ~O(1 MeV) energy depositions referred to as "blips". We observe concentrations of blips near fiberglass support struts along the TPC edge, with an energy spectrum indicative of specific gamma-ray decays. These and other blip sources are being used to validate calibrations in MicroBooNE's data by leveraging spectral features. This work further reports on the progress towards distinguishing between low-energy protons and electrons in large LArTPCs using cosmogenic data. The composition of proton-like blips selected using this new technique is being studied to evaluate the accuracy of cosmic ray flux models used in LArTPCs

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

FARM supervisory capabilities for thermal energy storage

The FARM (Feasible Actuator Range Modifier) module is a component of the RAVEN-based FORCE framework for the analysis of Integrated Energy Systems (IES). FARM aids HERON in the solution of the power dispatch problem by evaluating feasible set-point signals to be issued to the control systems of the different IES unit components. Set-points need to satisfy limits on both production variables (i.e., the variables to be optimized such as the electrical power, etc.) and process variables tied to the service life of equipment (e.g., steam flowrate, vessel pressure, turbine firing temperature, etc.). To enforce all these limits, a two-stage approach is adopted. First, the power dispatcher algorithm in HERON module estimates set-points that meet the constraints on the production variables, e.g., power levels and power ramp rate limits. These constraints are called explicit constraints. Then, if necessary, FARM adjusts these set-points to ensure the respect of the limits on the process variables of interest, given the knowledge of the system dynamics acquired through machine learning algorithms. These constraints are called implicit constraints. From this standpoint, FARM constitutes a bridge between the HERON power dispatcher that adopts a simplified description of the IES unit (low-resolution physics) and the HYBRID high-fidelity models (high-resolution physics). In this report, an overview of the major capabilities of the latest release of FARM is provided, along with a summary of the tool demonstration campaign conducted at the Dynamic Energy Technology and Integration Laboratory (DETAIL) facility. These results assess the performance of the control system architecture embedding FARM both as a Validator of the HERON power dispatcher and as a real time Supervisory control scheme. Additionally, the report outlines the areas that FARM might benefit from, along with proposed solutions.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

The NETL DAC Center: Design and Capabilities

Description of NETL's Direct Air Capture (DAC) Center, including design and capabilities of research units being installed for the evaluation of processes removing carbon dioxide from air.

Hoffman, James↗

Framework for Optimization, Quantification of Uncertainty, and Surrogates, and CCSI2 Toolset Capabilities

This poster will present key features and capabilities of the CCSI2 software platform to relevant technical and research audience members at the 2024 FECM / NETL Carbon Management Research Project Review Meeting. Attendees will learn about available process models in the CCSI2 Toolset, as well as design of experiments and machine learning features in the Framework for Optimization, Quantification of Uncertainty, and Surrogates (FOQUS) software to support pilot plant work.

Paul, Brandon↗

WarpX: Delivering Unprecedented Particle-in-Cell Simulation Capability

Since 1939, more than 30 percent of all Nobel prizes in physics and four of the past 14 prizes in chemistry have been awarded for work with particle accelerators. These tools are now used to treat cancer and produce medical supplies, support research in applied fields such as pharmaceuticals, create microcircuits, and sterilize food—and the applications list continues to grow. However, the size of the facilities needed to house these machines—which are often dozens of kilometers long—has limited their future potential. Thus, researchers are motivated to create novel particle accelerator designs that provide new imaging capability but have a much smaller footprint. The Exascale Computing Project’s WarpX application captures the full complexity of the acceleration processes within plasma-based design, supporting the rapid and cost-efficient development of tens of thousands of new particle accelerators for various applications from improving human health to nuclear fusion reactors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Developing Capabilities in Physical and Computational Sciences

The Physical and Computational Sciences Directorate (PCSD) performs fundamental research in support of the science missions of Offices of Basic Energy Sciences (BES), Advanced Scientific Computing Research (ASCR), High Energy Physics (HEP), Nuclear Physics (NP), and Fusion Energy Sciences (FES), and others within the domains of the chemical, materials, computational sciences, mathematics, and physics. This LDRD project aims to provide funding to develop/demonstrate research capabilities for proposals and publications to support these science missions. Staff will propose small research tasks/projects to be performed under this overall project.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Implications of new Reasoning Capabilities for Science and Security: Results from a Quick Initial Study

On Thursday, September 12 OpenAI released “a new series of models designed to spend more time thinking… they can reason through complex tasks and solve harder problems than previous models in science, coding, and math.” These models are referred to as o1-preview and o1-mini and appear to be first results of what had been a closely held project called Strawberry within OpenAI. The models are not described as successors in the earlier GPT series because they provide a qualitatively different type of capability, especially step-by-step reasoning.

97 MATHEMATICS AND COMPUTING↗

Using AMReX's Embedded Boundaries to Support MFIX-Exa’s Geometry Capabilities

MFIX-Exa is an AMReX-based application used for the simulation of chemically reacting multiphase flows inside reactors. The reactor geometry is mostly a combination of primitive shapes such as cylinders, cubes and spheres of varying dimensions connected together with potentially a lot of dead space between them. Additionally, the reactors may have particle-laden jets introduced at different parts of their geometry to enhance reactant mixing. This talk presents how MFIX-Exa uses OpenSCAD’s csg format to allow users to define the embedded boundary (EB) geometry and how it supports specifying inflow through certain sections of the EB. The talk will describe how MFIX-Exa leverages the EB features of grid-pruning, restart files and redistribution. Finally, the talk goes over some capabilities which are currently not available in MFIX-Exa but planned for the future, such as moving parts of the reactor geometry.

embedded boundaries↗

Multilayer Electrodes with Metalized Polymer Current Collector for High-Energy Lithium-Ion Batteries with Extreme-Fast-Charging Capability

The pursuit of batteries capable of extreme fast charging (XFC), that also satisfy high energy and safety criteria, poses a significant challenge to current lithium-ion battery technologies. Additionally, the increasing demand for aluminum (Al) and copper (Cu) in electrification, and vehicle lightweighting is driving these metals towards near-critical status in the medium term. This study introduced metalized polymer films by depositing an Al or Cu thin layer onto two sides of a polyethylene terephthalate (PET) film – named mPET/Al and mPET/Cu, as lightweight, cost-effective alternatives to traditional metal current collectors in LIBs.

25 ENERGY STORAGE↗

NIF Enhanced Yield Capability Conceptual Design Review Report

The purpose of the NIF Enhanced Yield Capability (EYC) Conceptual Design Review was to evaluate key aspects of the design and assess readiness to move to the next phase of the project. The NNSA accepted the NIF Integrated Product Review Board (IPRB) process as an appropriate means of conducting the review. The review committee finds that the NIF EYC Design Team has successfully addressed the review scope objectives. No Type 1 action items or liens were identified during the technical review. Some recommendations and observations are recorded below to assist the team.

42 ENGINEERING↗

Advancing understanding and predictive capability for fast-ion driven instabilities and associated anomalous transport in NSTX-U

This project advanced predictive capability for the spherical tokamak (ST) by (a) experimental validation of physics models in GTC for simulating fast-ion driven instabilities and their fast-ion and energy transport in the ST, and (b) verification of GTC with linear theory and validation using experimental measurements in the high frequency regime in the ST.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Reassessment of Boiling Water Reactor Rod Cusping Capability of VERA-MPACT

This technical report assesses the current modeling capabilities of the Virtual Environment for Reactor Applications (VERA) for minimizing control rod cusping in boiling water reactors. Assessment is performed on a 10 × 10 General Electric (GE)-14 assembly as well as a simplified version of the same assembly. Runs were performed using VERA for three available cusping treatments in the Michigan PArallel Characteristics Transport (MPACT) code: no treatment, subplane treatment, and fitted polynomial correction treatment. Subplane treatment is discussed, but specific results are not provided because of failures in the method of implementation for boiling water reactors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

SCEPTRE: A Cyber-Physical Emulation Capability

Cyber-physical systems form a critical but vulnerable backbone to US critical infrastructure. Recent high-profile cyber-attacks have shown the need for increased assessment and hardening of these systems. However, such assessments and investigations into advanced technologies to harden these systems is difficult due to their operational nature. Instead, modeling of these systems is heavily leveraged. Investigation into these complex systems and their potential cascading failures requires comprehensive modeling of both the cyber and physical components of the system. This paper introduces SCEPTRE, an emulation capability to address this need.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗