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At least 1,243 records · Page 69

Highly efficient libraries design for saturation mutagenesis

Abstract Saturation mutagenesis is a semi-rational approach for protein engineering where sites are saturated either entirely or partially to include amino acids of interest. We previously reported on a codon compression algorithm, where a set of minimal degenerate codons are selected according to user-defined parameters such as the target organism, type of saturation and usage levels. Here, we communicate an addition to our web tool that considers the distance between the wild-type codon and the library, depending on its purpose. These forms of restricted collections further reduce library size, lowering downstream screening efforts or, in turn, allowing more comprehensive saturation of multiple sites. The library design tool can be accessed via http://www.dynamcc.com/dynamcc_d/. Graphical Abstract

59 BASIC BIOLOGICAL SCIENCES↗

Quasi-1D Coulomb Drag in the Nonlinear Regime

One-dimensional Coulomb drag has been an essential tool to probe the physics of interacting Tomonaga-Luttinger liquids. To date, most experimental work has focused on the linear regime while the predictions for Luttinger liquids beyond the linear response theory remain largely untested. In this Letter, we report measurements of reciprocal momentum transfer induced Coulomb drag between vertically coupled quasi-one-dimensional quantum wires in the nonlinear regime. Measurements were performed at ultralow temperatures between wires only 15 nm apart. Our results reveal a nonlinear dependence of the drag voltage as a function of the drive current superimposed with an oscillatory contribution, in agreement with theoretical predictions for Coulomb drag between Tomonaga-Luttinger liquids. Additionally, the observed current-voltage characteristics exhibit a nonmonotonic temperature dependence, further corroborating the presence of non-Fermi-liquid behavior in our system. In conclusion, these findings are observed both in the single and in the multiple subband regimes and in the presence of disorder, extending the onset of this behavior beyond the clean single channel Tomonaga-Luttinger regime where the predictions were originally formulated.

1-dimensional systems↗

CephFS experiments on stria.sandia.gov

This report is an institutional record of experiments conducted to explore performance of a vendor installation of CephFS on the SNL stria cluster. Comparisons between CephFS, the Lustre parallel file system, and NFS were done using the IOR and MDTEST benchmarking tools, a test program which uses the SEACAS/Trilinos IOSS library, and the checkpointing activity performed by the LAMMPS molecular dynamics simulation.

74 ATOMIC AND MOLECULAR PHYSICS↗

CephFS experiments on stria.sandia.gov

This report is an institutional record of experiments conducted to explore performance of a vendor installation of CephFS on the SNL stria cluster. Comparisons between CephFS, the Lustre parallel file system, and NFS were done using the IOR and MDTEST benchmarking tools, a test program which uses the SEACAS/Trilinos IOSS library, and the checkpointing activity performed by the LAMMPS molecular dynamics simulation.

97 MATHEMATICS AND COMPUTING↗

Soil, Foodstuffs, and Biota Program [Slides]

We use several environmental monitoring tools to assess ecosystem health and in part, risk to human health. Generally, the concentrations of chemicals we observe are below background and screening levels. All of our monitoring data are available in Intellus, and our analyses and results are reported in the Annual Site Environmental Report. Our program is only one of several monitoring programs at LANL, others include air, surface water, ground water, canyon sediments. We strive to improve the program by incorporating new monitoring techniques, monitoring new locations, monitoring new chemicals of interest, and by using robust statistical analyses.

54 ENVIRONMENTAL SCIENCES↗

Measuring Orbit Responses with Oscillating Trajectories in the Fermilab Linac

Recording changes in beam transverse positions re-ported by Beam Position Monitors (BPMs) in response to a beam deflection by an upstream dipole corrector (orbit response) is a powerful tool for analysis of accelerator optics and assisting with machine tuning. In the Fermilab Linac, orbit responses are recorded by oscillating the currents of up to 19 correctors, providing faster, drift-resistant measurements through frequency-domain analysis. This report describes the technique, including error estimations and consistency checks and shows an example of the measurements.

Shemyakin, Alexander V. [Fermilab] (ORCID:00000001↗

Advancing Thermal-Hydraulic Modeling Capabilities for Molten Salt Reactors in Pronghorn

This is an M2 report for the NEAMS program. This work focuses on advancing the modeling and simulation capabilities for Molten Salt Reactors (MSRs) within Pronghorn, addressing key thermal-hydraulic challenges that must be addressed for the safe and efficient operation of these advanced reactors. This report summarizes the development and validation of the following new models in Pronghorn: (i) two-equation RANS turbulence models, (ii) near-wall turbulence corrections due to curvature and roughness, and (iii) multidimensional two-phase drift-flux models. For each of these cases, along with the experimental validation, an application study of interest to MSRs is presented. In addition, this report also presents recent improvements in the domain-overlapping coupling between Pronghorn and SAM to address the cases of weakly compressible flow and flow reversal. Finally, an MSR action that greatly simplifies the setup of MSR models using NEAMS tools is described.

42 ENGINEERING↗

Overview of the TJ-II stellarator research programme towards model validation in fusion plasmas

TJ-II stellarator results on modelling and validation of plasma flow asymmetries due to on-surface potential variations, plasma fuelling physics, Alfvén eigenmodes (AEs) control and stability, the interplay between turbulence and neoclassical (NC) mechanisms and liquid metals are reported. Regarding the validation of the neoclassically predicted potential asymmetries, its impact on the radial electric field along the flux surface has been successfully validated against Doppler reflectometry measurements. Research on the physics and modelling of plasma core fuelling with pellets and tracer encapsulated solid pellet injection has shown that, although post-injection particle radial redistributions can be understood qualitatively from NC mechanisms, turbulence and fluctuations are strongly affected during the ablation process. Advanced analysis tools based on transfer entropy have shown that radial electric fields do not only affect the radial turbulence correlation length but are also capable of reducing the propagation of turbulence from the edge into the scrape-off layer. Direct experimental observation of long range correlated structures show that zonal flow structures are ubiquitous in the whole plasma cross-section in the TJ-II stellarator. Alfvénic activity control strategies using ECRH and ECCD as well as the relation between zonal structures and AEs are reported. Finally, the behaviour of liquid metals exposed to hot and cold plasmas in a capillary porous system container was investigated.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A&L Annual Report: GRM-MAPS

Exploding Bridge Wire (EBW) is an important design for initiating detonators relevant to several LLNL systems. In such designs, a metal bridge wire is in direct contact with a porous secondary high explosive (HE), typically pressed to around 50% of its crystalline density. Initiation is believed to occur through shock waves generated when the bridge wire is made to explode via the rapid passing of a strong current pulse. Permeametry is an important characterization tool for the porous powdered HE (PETN, HMX, etc.) component in such devices. Such powders are well known to coarsen with age, with an accompanying deterioration in performance, which includes increased function time and sensitivity. Among various material characteristics, one that has been shown to correlate the most with such performance parameters is the flow-permeable surface area (FSSA), measured using air-permeametry. Commercially available permeametry apparatuses, such as that from Fisher Scientific or a more modern version from Micromeritics suffer from a few drawbacks, most notably as related to monitoring age-related changes in FSSA. This is because it requires re-compaction of the aged powder into the permeametry tube, which in most cases leads to an unwanted increase in FSSA. To address this and a few other shortcomings, we have been developing a modern version of the permeameter, Gee-Reinstein-Maiti Modern Air-Permeametry System (GRM-MAPS). In this report, we summarize progress made in FY25 toward perfecting and calibrating the instrument, which we aim at deploying within surveillance in FY26.

36 MATERIALS SCIENCE↗

Multireference Methods are Realistic and Useful Tools for Modeling Catalysis

Abstract Highly correlated systems, in particular those that include transition metals, are ubiquitous in catalysis. The significant static correlation found in such systems is often poorly accounted for using Kohn Sham density functional theory methods, as they are single determinantal in nature. Applications to catalysis of more rigorous and appropriate multiconfigurational methods have been reported in select instances, but their use remains rare. We discuss obstacles that hinder the routine application of multireference (MR) wave function theoretical calculations to catalytic systems and the current state of the art with respect to removing those obstacles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Navigation and Meteorological Data from Multiple Sensors on Airborne Platform (NAVMET-AIR) Value-Added Product Report

The Navigation and Meteorological Data from Multiple Sensors on Airborne Platform (NAVMET-AIR) value-added product encompasses the aafnaviwg data set in the ARM Data Center (ADC), known as the IWG file, named for the Inter-Agency Working Group for Airborne Data and Telemetry Systems (IWGADTS). Its purpose is to produce a suite of tools to promote standardization of instrument interface, data format, and data processing. This data set’s contents are navigational and meteorological state variables at 1 Hz. It also contains higher-order data flags created by ARM Aerial Facility (AAF) scientists to aid analysis such as periods when the aircraft is flying level, operating in maneuvers, or flying through cloud. Due to the nature of research flights, the payload of the aircraft consists of many duplicate and overlapping instruments to ensure, in case of instrument failure, there is a backup to record the data. Measurements from multiple instruments are consolidated into a single file. Each variable of this data set is carefully chosen from the onboard instrumentation and quality checked by AAF scientists to create this wholistic and most accurate data set for airborne research. This document is intended to be a hub towards the individual “read me” files produced for each campaign. For reference about what instrument was used for calculations on specific days, the read me files are located in the ARM IOP archive at the addresses listed, or access the IOP (intensive operational period) database at https://www.archive.arm.gov/.

54 ENVIRONMENTAL SCIENCES↗

Natural Charge-Transfer Analysis: Eliminating Spurious Charge-Transfer States in Time-Dependent Density Functional Theory via Diabatization, with Application to Projection-Based Embedding

For many types of vertical excitation energies, linear-response time-dependent density functional theory (LR-TDDFT) offers a useful degree of accuracy combined with unrivaled computational efficiency, although charge-transfer excitation energies are often systematically and dramatically underestimated, especially for large systems and those that contain explicit solvent. As a result, low energy electronic spectra of solution-phase chromophores often contain tens to hundreds of spurious charge-transfer states, making LR-TDDFT needlessly expensive in bulk solution. More nefariously, intensity borrowing by the low-energy charge-transfer states can affect intensities of the valence excitations even if those excitation energies are accurate. At higher excitation energies, it is difficult to distinguish spurious CT states from genuine charge-transfer-to-solvent (CTTS) excitations. In this work, we introduce an automated diabatization scheme that enables fast and effective screening of the CTTS acceptor space in bulk solution. Our procedure introduces the concept of “natural charge-transfer orbitals”, which provide a means to isolate characteristic pairs of orbitals that are most likely to participate in a CTTS excitation. The projection of these orbitals onto solvent-centered virtual orbitals provides a criterion for defining the most important solvent molecules in a given excitation. We apply this method to analyze an ab initio molecular dynamics (MD) trajectory of I-(aq) and report the lowest-energy CTTS band in the absorption spectrum. Our results are in excellent agreement with experimental measurements for bulk I-(aq), and only one-third of the water molecules in the I-(H2O)96 simulation cell need to be described with LR-TDDFT in order to obtain excitation energies that are converged to < 0.1 eV. The tools introduced herein will improve the accuracy, efficiency, and usability of LR-TDDFT in solution-phase environments

Carter-Fenk, Kevin D.↗

Energy Resilient Recovery in Puerto Rico: Hurricane Maria Recovery Support

This report covers microgrids as a special application of distributed energy resources (DERs) in Puerto Rico. This is one of a series of reports describing the U.S. Department of Energy (DOE) multi-laboratory efforts undertaken. To ensure the sustainable, long-term recovery of Puerto Rico's electric power grid from hurricanes Maria and Irma and to build capacity to manage future potential natural disasters in the most secure and resilient way, DOE convened experts from multiple national laboratories to develop a comprehensive set of data, models, analytic tools, and studies, considering inputs from a wide variety of stakeholder groups, to support technically sound recommendations for Puerto Rico's energy investment decisions. In Phase 1 of the multi-laboratory effort to support Puerto Rico's recovery, the National Renewable Energy Laboratory (NREL) provided the utility company Puerto Rico Electric Power Authority (PREPA) recommendations for a new framework of interconnection standards to accelerate the integration of utility-scale, transmission-connected, renewable electrical generation and energy storage that ensure cross-technology compatibility and enable high deployment levels without compromising grid reliability, safety, or security (https://www.nrel.gov/docs/fy19osti/73848.pdf). In Phase 2, NREL published a report focused on the interconnection of distributed energy resources (DERs) to the electric distribution system in Puerto Rico (https://www.nrel.gov/docs/fy21osti/77127.pdf). This report familiarized the reader with Puerto Rico's distribution infrastructure and operational practices and procedures that are relevant to DER interconnection. The report also provided considerations for streamlining the interconnection process given the expected increase in deployments resulting from Puerto Rico's renewable portfolio standard goal of 100% renewables by 2050. Accordingly, the report identifies considerations and concerns associated with the increase in intermittent generation, strategies for DER interconnection best practices, and the potential use of the latest technological solutions identified in the latest revision of the Institute of Electrical and Electronics Engineers 1547-2018 interconnection standard. Additionally, the report identified ways to improve the physical resiliency of installed DERs. This task describes how distributed energy systems may participate in and contribute to improving the resiliency of Puerto Rico's energy infrastructure in the future. This report presents an analysis of the Puerto Rico grid to illustrate the possible different microgrid and minigrid scenarios. The capability to form sustained microgrids and minigrids has the potential to provide a high level of resiliency during disturbances on the grid. DERs, on the other hand, have the capability to aid in the microgrid operation by providing grid support as well as grid-forming functionality. Other tasks in Phase 3 include voltage regulation in distribution networks using DERs and transmission-and-distribution co-simulation.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Economic Model for Estimation of GDP Losses in the MACCS Offsite Consequence Analysis Code

The MACCS (MELCOR Accident Consequence Code System) code is the U.S. Nuclear Regulatory Commission (NRC) tool used to perform probabilistic health and economic consequence assessments for atmospheric releases of radionuclides. It is also used by international organizations, both reactor owners and regulators. It is intended and most commonly used for hypothetical accidents that could potentially occur in the future rather than to evaluate past accidents or to provide emergency response during an ongoing accident. It is designed to support probabilistic risk and consequence analyses and is used by the NRC, U.S. nuclear licensees, the Department of Energy, and international vendors, licensees, and regulators. This report describes the modeling framework, implementation, verification, and benchmarking of a GDP-based model for economic losses that has recently been developed as an alternative to the original cost-based economic loss model in MACCS. The GDP-based model has its roots in a code developed by Sandia National Laboratories for the Department of Homeland Security to estimate short-term losses from natural and manmade accidents, called the Regional Economic Accounting analysis tool (REAcct). This model was adapted and modified for MACCS and is now called the Regional Disruption Economic Impact Model (RDEIM). It is based on input-output theory, which is widely used in economic modeling. It accounts for direct losses to a disrupted region affected by an accident, indirect losses to the national economy due to disruption of the supply chain, and induced losses from reduced spending by displaced workers. RDEIM differs from REAcct in its treatment and estimation of indirect loss multipliers, elimination of double counting associated with inter-industry trade in the affected area, and that it is designed to be used to estimate impacts for extended periods that can occur from a major nuclear reactor accident, such as the one that occurred at the Fukushima Daiichi site in Japan. Most input-output models do not account for economic adaptation and recovery, and in this regard RDEIM differs from its parent, REAcct, because it allows for a user-definable national recovery period. Implementation of a recovery period was one of several recommendations made by an independent peer review panel to ensure that RDEIM is state-of-practice. For this and several other reasons, RDEIM differs from REAcct. Both the original and the RDEIM economic loss models account for costs from evacuation and relocation, decontamination, depreciation, and condemnation. Where the original model accounts for an expected rate of return, based on the value of property, that is lost during interdiction, the RDEIM model instead accounts for losses of GDP based on the industrial sectors located within a county. The original model includes costs for disposal of crops and milk that the RDEIM model currently does not, but these costs tend to contribute insignificantly to the overall losses. This document discusses three verification exercises to demonstrate that the RDEIM model is implemented correctly in MACCS. It also describes a benchmark study at five nuclear power plants chosen to represent the spectrum of U.S. commercial sites. The benchmarks provide perspective on the expected differences between the RDEIM and the original cost-based economic loss models. The RDEIM model is shown to consistently predict larger losses than the original model, probably in part because it accounts for national losses by including indirect and induced losses; whereas, the original model only accounts for regional losses. Nonetheless, the RDEIM model predicts losses that are remarkably consistent with the original cost-based model, differing by 16% at most for the five sites combined with three source terms considered in this benchmark.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

First Plant Cell Atlas symposium report

The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these needs and accelerate progress. This report details the presentations and discussions focused on the possibility of a data synthesis center for a PCA and the expected impacts of such a center on advancing science and technology globally. Community discussions focused on topics such as data analysis tools and annotation standards; computational expertise and cyber-infrastructure; modes of community organization and engagement; methods for ensuring a broad reach in the PCA community; recruitment, training, and nurturing of new talent; and the overall impact of the PCA initiative. These targeted discussions facilitated dialogue among the participants to gauge whether PCA might be a vehicle for formulating a data synthesis center. The conversations also explored how online tools can be leveraged to help broaden the reach of the PCA (i.e., online contests, virtual networking, and social media stakeholder engagement) and decrease costs of conducting research (e.g., virtual REU opportunities). Major recommendations for the future of the PCA included establishing standards, creating dashboards for easy and intuitive access to data, and engaging with a broad community of stakeholders. The discussions also identified the following as being essential to the PCA's success: identifying homologous cell-type markers and their biocuration, publishing datasets and computational pipelines, utilizing online tools for communication (such as Slack), and user-friendly data visualization and data sharing. In conclusion, the development of a data synthesis center will help the PCA community achieve these goals by providing a centralized repository for existing and new data, a platform for sharing tools, and new analytical approaches through collaborative, multidisciplinary efforts. A data synthesis center will help the PCA reach milestones, such as community-supported data evaluation metrics, accelerating plant research necessary for human and environmental health.

59 BASIC BIOLOGICAL SCIENCES↗

Neutron imaging the spatial progression of chemical oxidation of lithium-ion cathode material in a packed bed reactor

Emerging electrochemical systems relevant to energy applications including redox targeted flow batteries rely on chemical redox of solid electroactive materials using dissolved redox couples. One configuration to facilitate contact between the redox shuttles and solid material which is volume efficient is a packed bed reactor. While methods have been reported to assess the overall progression by analysis of the packed bed reactor effluent, herein analysis of the spatial progression of the chemical redox will be reported. Combination of neutron and x-ray tomography enabled assessing the pore and particle structure in the packed bed reactor and the spatial homogeneity of the reaction at different overall extents of conversion of the reactor bed. Finally, these characterization tools provide methods to probe the chemical redox processes occurring within the reactor environment.

25 ENERGY STORAGE↗

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

The members of the tribe Brassiceae share a whole-genome triplication (WGT), and one proposed model for its formation is a two-step pair of hybridizations producing hexaploid descendants. However, evidence for this model is incomplete, and the evolutionary and functional constraints that drove evolution after the hexaploidy are even less understood. Here, we report a new genome sequence of Crambe hispanica , a species sister to most sequenced Brassiceae. Using this new genome and three others that share the hexaploidy, we traced the history of gene loss after the WGT using the Polyploidy Orthology Inference Tool (POInT). We confirm the two-step formation model and infer that there was a significant temporal gap between those two allopolyploidizations, with about a third of the gene losses from the first two subgenomes occurring before the arrival of the third. We also, for the 90,000 individual genes in our study, make parental subgenome assignments, inferring, with measured uncertainty, from which of the progenitor genomes of the allohexaploidy each gene derives. We further show that each subgenome has a statistically distinguishable rate of homoeolog losses. There is little indication of functional distinction between the three subgenomes: the individual subgenomes show no patterns of functional enrichment, no excess of shared protein-protein or metabolic interactions between their members, and no biases in their likelihood of having experienced a recent selective sweep. We propose a "mix and match" model of allopolyploidy, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.

59 BASIC BIOLOGICAL SCIENCES↗

Simulated Feasibility of 3-D Lightning Mapping From Space

In addition to the awe it inspires, lightning can illuminate the microphysical processes hidden away within deep convection. The current generation of space-based lightning mapping uses mostly 2-D optical imaging to connect overall flash characteristics to their parent storm dynamics, but are missing a dimension’s worth of information. With lightning now classified as an essential climate variable, future spaceborne mappers will need improved capabilities to take advantage of the 3-D structure of lightning flashes to support meteorological and climate modeling. We report here on a study of the feasibility of high-resolution 3-D lightning mapping using a radio frequency (RF)-based network of satellites from low-Earth orbit (LEO). Lightning sources are simulated using existing lightning mapping array (LMA) tools, modified for orbital detection, and spatially reconstructed using a Levenberg–Marquardt geolocation algorithm to assess sources of uncertainty in these solutions. We analyze the benefits and limitations of this approach compared to existing orbital and ground-based methods. Results of this study show that lightning can be mapped in 3-D with a vertical location accuracy better than 2 km using as few as five satellites in LEO capable of measuring the time-of-arrival of impulsive RF signals in the very high-frequency (VHF) band. The consequence of this study is that high-resolution, spaceborne 3-D mapping of lightning is achievable across most of the globe, having crucial implications for our understanding of not only lightning, but also severe weather development, climate science, and more.

47 OTHER INSTRUMENTATION↗