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At least 1,099 records · Page 61

Co-Active Subspace Methods for the Joint Analysis of Adjacent Computer Models

Active subspace (AS) methods are a valuable tool for understanding the relationship between the inputs and outputs of a Physics simulation. In this article, an elegant generalization of the traditional ASM is developed to assess the co-activity of two computer models. This generalization, which we refer to as a Co-Active Subspace (Co-AS) Method, allows for the joint analysis of two or more computer models allowing for thorough exploration of the alignment (or non-alignment) of the respective gradient spaces. We define co-active directions, co-sensitivity indices, and a scalar “concordance” metric (and complementary “discordance” pseudo-metric) and we demonstrate that these are powerful tools for understanding the behavior of a class of computer models, especially when used to supplement traditional AS analysis. Details for efficient estimation of the Co-AS and an accompanying R package (concordance) are provided. Practical application is demonstrated through analyzing a set of simulated rate stick experiments for PBX 9501, a high explosive, offering insights into complex model dynamics.

97 MATHEMATICS AND COMPUTING↗

Computation-guided optimization of split protein systems

Splitting bioactive proteins into conditionally reconstituting fragments is a powerful strategy for building tools to study and control biological systems. However, split proteins often exhibit a high propensity to reconstitute, even without the conditional trigger, limiting their utility. Current approaches for tuning reconstitution propensity are laborious, context-specific or often ineffective. Here, we report a computational design strategy grounded in fundamental protein biophysics to guide experimental evaluation of a sparse set of mutants to identify an optimal functional window. We hypothesized that testing a limited set of mutants would direct subsequent mutagenesis efforts by predicting desirable mutant combinations from a vast mutational landscape. This strategy varies the degree of interfacial destabilization while preserving stability and catalytic activity. We validate our method by solving two distinct split protein design challenges, generating both design and mechanistic insights. Furthermore, this new technology will streamline the generation and use of split protein systems for diverse applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Grid site availability evaluation and monitoring at CMS

The Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) uses distributed grid computing to store, process, and analyse the vast quantity of scientific data recorded every year. The computing resources are grouped into sites and organized in a tiered structure. Each site provides computing and storage to the CMS computing grid. Over a hundred sites worldwide contribute with resources from hundred to well over ten thousand computing cores and storage from tens of TBytes to tens of PBytes. In such a large computing setup scheduled and unscheduled outages occur continually and are not allowed to significantly impact data handling, processing, and analysis. Unscheduled capacity and performance reductions need to be detected promptly and corrected. CMS developed a sophisticated site evaluation and monitoring system for Run 1 of the LHC based on tools of the Worldwide LHC Computing Grid. For Run 2 of the LHC the site evaluation and monitoring system is being overhauled to enable faster detection/reaction to failures and a more dynamic handling of computing resources. Furthermore, enhancements to better distinguish site from central service issues and to make evaluations more transparent and informative to site support staff are planned.

43 PARTICLE ACCELERATORS↗

Advanced Simulation and Computing FY19 Implementation Plan, Rev. 1

The capabilities that the ASC Program provides at the national laboratories play a vital role in the Nuclear Security Enterprise and are necessary for fulfilling the stockpile stewardship and life extension requirements outlined for NNSA. The Program develops modern simulation tools that provide insights into stockpile aging issues, provide the computational and simulation tools that enable designers and analysts to certify the current stockpile and life-extended nuclear weapons, and inform the decision-making process when any modifications in nuclear warheads or the associated manufacturing processes are deemed necessary. Furthermore, ASC is enhancing the predictive simulation capabilities that are essential to evaluate weapons effects, design experiments, and ensure test readiness. The ASC Program continues to improve its unique tools to solve stockpile problems— with a focus on sufficient resolution, dimensionality, and scientific detail—to enable Quantification of Margins and Uncertainties (QMU) and to resolve the increasingly difficult analyses needed for stockpile stewardship. The needs of the Directed Stockpile Work (DSW) and major modernization programs also drive the requirements for simulation and computational resources. These requirements include planned LEPs, stockpile support activities, and mitigation efforts against the potential for technical surprise. All of the weapons within the current stockpile are in some stage of the life extension process. The simulation and computational capabilities are crucial for successful execution of these lifetime extensions and for ensuring NNSA can certify these life-extended weapons without conducting a UGT. Specific work activities and scope contained in this Implementation Plan (IP) represent the full-year annual operating plan for FY19. The Initial IP, effective August 8, 2018, should be consistent with the Department’s Base Table when operating under a Continuing Resolution (CR). The final IP, effective date TBD, is consistent with the final, enacted appropriation.

97 MATHEMATICS AND COMPUTING↗

Advanced Simulation and Computing FY18 Implementation Plan, Rev. 1

The capabilities that the ASC Program provides at the national laboratories play a vital role in the Nuclear Security Enterprise and are necessary for fulfilling the stockpile stewardship and life extension requirements outlined for NNSA. The Program develops modern simulation tools that provide insights into stockpile aging issues, provide the computational and simulation tools that enable designers and analysts to certify the current stockpile and life-extended nuclear weapons, and inform the decision-making process when any modifications in nuclear warheads or the associated manufacturing processes are deemed necessary. Furthermore, ASC is enhancing the predictive simulation capabilities that are essential to evaluate weapons effects, design experiments, and ensure test readiness. The ASC Program continues to improve its unique tools to solve stockpile problems— with a focus on sufficient resolution, dimensionality, and scientific detail—to enable Quantification of Margins and Uncertainties (QMU) and to resolve the increasingly difficult analyses needed for stockpile stewardship. The needs of the Directed Stockpile Work (DSW) and major modernization programs also drive the requirements for simulation and computational resources. These requirements include planned LEPs, stockpile support activities, and mitigation efforts against the potential for technical surprise. All of the weapons within the current stockpile are in some stage of the life extension process. The simulation and computational capabilities are crucial for successful execution of these lifetime extensions and for ensuring NNSA can certify these life-extended weapons without conducting a UGT. Specific work activities and scope contained in this Implementation Plan (IP) represent the full-year annual operating plan for FY18. The Initial IP effective October 1, 2017, should be consistent with the Department’s Base Table when operating under a Continuing Resolution (CR). The final IP, effective March 24, 2018, is consistent with the final, enacted appropriation.

97 MATHEMATICS AND COMPUTING↗

JOBRUNNER

SF-23-071 Jobrunner is a command line tool to manage and deploy computing jobs, organize complex workloads, and enforce a directory based hierarchy to enable reuse of files and bash scripts within a project. Organization details of a directory tree are encoded in Jobfiles which serve as an index of files/scripts, and indicate their purpose when deploying or setting up a job. It is a flexible tool that allows users to design 16 their own directory structure, perserve their design, and maintain 17 consistency with increase in complexity of the project.

DHRUV, AKASH VIJAYKUMAR↗

A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in Sorghum

A better understanding of the genetic and metabolic mechanisms that confer stress resistance and tolerance in plants is key to engineering new crops through advanced breeding technologies. This requires a systems biology approach that builds on a genome-wide understanding of the regulation of gene expression, plant metabolism, physiology and growth. In this study, we examine the response to drought stress in Sorghum, as we leverage the tools for transcriptomics and plant metabolic modeling we have implemented at the U.S. Department of Energy Systems Biology Knowledgebase (KBase). KBase enables researchers worldwide to collaborate and advance research by allowing them to upload private or public data into the KBase Narrative Interface, empowering them to analyze this data using a rich, extensible array of computational and data-analytics tools, and allows them to securely share scientific workflows and conclusions. We demonstrate how to use the current RNA-seq tools in KBase, applicable to both plants and microbes, to assemble and quantify long transcripts and identify differentially expressed genes effectively. More specifically, we demonstrate the utility of the platform by identifying key genes that are differentially expressed during drought-stress in Sorghum bicolor, which is an important sustainable production crop plant. We then show how to use KBase tools to predict the membership of genes in metabolic pathways and examine expression data in the context of metabolic subsystems. We demonstrate the power of the platform by making the data analysis and interpretation available to the biologists in the reproducible, re-usable, point-and-click format of a KBase Narrative thus promoting FAIR (Findable, Accessible, Interoperable and Reusable) guiding principles for scientific data management and stewardship.

59 BASIC BIOLOGICAL SCIENCES↗

Developing tools and process controls to manufacture energy-efficient powders for additive manufacturing feedstocks: Computational analysis of metal powder manufacturing via machining

Traditionally, metal powders have been produced through methods such as grinding, atomization, and electrolysis. In contrast to these techniques, Metal Powder Works, Inc. has pioneered a methodology based on metal cutting. This innovative approach utilizes a vibrating cutting tool to machine metal particles, in the form of chips, from a workpiece. This technique allows for control of powder particle size, morphology, and avoids any thermally induced material changes. This collaboration aims to elucidate metal cutting characteristics and assess performance on tough materials like Inconel alloys. Computational models, using FEA and SPH techniques, will be developed initially, focusing on aluminum alloy (Al 7075-T6) for studying mesh sensitivity, cutting forces, and chip morphology.

99 GENERAL AND MISCELLANEOUS↗

Electricity Bill Calculator (elecprice) v0.1.0

The Electricity Bill Calculator Library is a generic tool for manipulating the tariffs of electricity, with an emphasis on commercial Time-Of-Use (TOU) rates in the U.S. and residential Net Energy Metering tariffs in CA. Typical uses of the package are price signal generation and bill computation. To generate price signals from a specific tariff and given a time window, the tool creates a pandas dataframes containing the various components of the electricity charges, at each time step. This is particularly useful for Demand Response (DR) applications, such as price-based optimization of energy in buildings. The tool also computes bills given a building's power consumption and a specific tariff and returning the corresponding cost of electricity, as well as a breakdown per type of rate.

Prakash, Anand Krishnan↗

Classical shadows for quantum process tomography on near-term quantum computers

Quantum process tomography is a powerful tool for understanding quantum channels and characterizing the properties of quantum devices. Inspired by recent advances using classical shadows in quantum state tomography [H.-Y. Huang, R. Kueng, and J. Preskill, .], we have developed ShadowQPT, a classical shadow method for quantum process tomography. We introduce two related formulations with and without ancilla qubits. ShadowQPT stochastically reconstructs the Choi matrix of the device allowing for an classical evaluation of the device on arbitrary inputs with respect to arbitrary outputs. Using shadows, we then show how to compute overlaps, generate all k -weight reduced processes, and perform reconstruction via Hamiltonian learning. These latter two tasks are efficient for large systems as the number of quantum measurements needed scales only logarithmically with the number of qubits. A number of additional approximations and improvements are developed, including the use of a pair-factorized Clifford shadow and a series of postprocessing techniques that significantly enhance the accuracy for recovering the quantum channel. We have implemented ShadowQPT using both Pauli and Clifford measurements on the IonQ trapped ion quantum computer for quantum processes up to n = 4 qubits, and we achieved good performance. Published by the American Physical Society 2024

Levy, Ryan (ORCID:0000000349527156)↗

A computational workflow for designing silicon donor qubits

Developing devices that can reliably and accurately demonstrate the principles of superposition and entanglement is an on-going challenge for the quantum computing community. Modeling and simulation offer attractive means of testing early device designs and establishing expectations for operational performance. However, the complex integrated material systems required by quantum device designs are not captured by any single existing computational modeling method. We examine the development and analysis of a multi-staged computational workflow that can be used to design and characterize silicon donor qubit systems with modeling and simulation. Our approach integrates quantum chemistry calculations with electrostatic field solvers to perform detailed simulations of a phosphorus dopant in silicon. We show how atomistic details can be synthesized into an operational model for the logical gates that define quantum computation in this particular technology. In conclusion, the resulting computational workflow realizes a design tool for silicon donor qubits that can help verify and validate current and near-term experimental devices.

97 MATHEMATICS AND COMPUTING↗

Large exotic spin torques in antiferromagnetic iron rhodium.

Spin torque is a promising tool for driving magnetization dynamics for computing technologies. These torques can be easily produced by spin-orbit effects, but for most conventional spin source materials, a high degree of crystal symmetry limits the geometry of the spin torques produced. Magnetic ordering is one way to reduce the symmetry of a material and allow exotic torques, and antiferromagnets are particularly promising because they are robust against external fields. We present spin torque ferromagnetic resonance (ST-FMR) measurements and second harmonic Hall measurements characterizing the spin torques in anti -ferromagnetic iron rhodium alloy. We report extremely large, strongly temperature-dependent exotic spin torques with a geometry apparently defined by the magnetic ordering direction. We find the spin torque efficiency of iron rhodium to be (207 +/- 94)% at 170 K and (88 +/- 32)% at room temperature. We support our conclusions with theoretical calculations showing how the antiferromagnetic ordering in iron rhodium gives rise to such exotic torques.

Gibbons, Jonathan↗

Cell-machine interfaces for characterizing gene regulatory network dynamics

Gene regulatory networks and the dynamic responses theyproduce offer a wealth of information about how biologicalsystems process information about their environment.Recently, researchers interested in dissecting these networkshave been outsourcing various parts of their experimentalworkflow to computers. Here we review how, using microfluidicor optogenetic tools coupled with fluorescence imaging, it isnow possible to interface cells and computers. These platformsenable scientists to perform informative dynamic stimulationsof genetic pathways and monitor their reaction. It is alsopossible to close the loop and regulate genes in real time,providing an unprecedented view of how signals propagatethrough the network. Finally, we outline new tools that can beused within the framework of cell–machine interfaces.

59 BASIC BIOLOGICAL SCIENCES↗

Calibration and Uncertainty Estimation Using the Ensemble Kalman Filter with a Large Subsurface Flow and Transport Model - 20321

At routinely monitored groundwater contamination sites, periodically measured environmental conditions such as groundwater levels and contaminant concentrations are used to inform and confirm a conceptual site model (CSM) and guide the development and calibration of a numerical groundwater flow and transport model. The calibration of groundwater flow and transport models after each measurement (sampling) event can illuminate deficiencies in a CSM, identify areas where additional monitoring is warranted, and predict the behavior of the system to guide decision making. However, manual and automated (e.g. PEST) model calibration tools can be time-consuming and computationally expensive to implement after each sampling event. Perhaps as a result, such calibration tools generally utilize all available monitoring data simultaneously rather than sequentially assimilating monitoring data one sampling event at a time as the results from sampling become available. A more real-time data assimilation approach may reduce parameter uncertainty, quantify the value of additional monitoring data, and produce a usable model more quickly and with less effort. To mitigate the potential time-consuming aspects of manual and widely applied automated calibration techniques, a data assimilation algorithm called the ensemble Kalman filter (EnKF) was evaluated as a relatively efficient method of model calibration and uncertainty assessment via the sequential integration of monitoring data into a model. The EnKF was able to successfully and efficiently assimilate monitoring and modeling data to calibrate a complex flow and transport model at a real-world site with significant subsurface heterogeneity, uncertainty, and 12 years of monitoring data (over 4,000 individual measurements of groundwater levels and over 2,500 measurements of contaminant concentrations). Starting with an uncalibrated model data from annual sampling events were sequentially assimilated, and the resultant predication errors and estimated parameter uncertainties were tracked. After all monitoring data were assimilated, both flow and transport residuals at the end of the EnKF process were comparable to those produced via a concurrent PEST calibration effort but required fewer model simulations. Both uncertainty and prediction errors decreased over time. In a real-time application, the adequacy of the model could be assessed after each sampling event. The benefits of such a real-time approach to utilizing monitoring data include reduced costs (in the form of model updates or site characterization efforts), early flagging of possible errors in the CSM, and a reduced risk of overfitting and corresponding increased confidence in model predictions. This tool may be particularly useful compared to other calibration techniques (e.g. manual, PEST) when model runtimes are long, calibration parameters are many, or parameter uncertainty is large. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

FAST.Farm Response to Varying Wind Inflow and Discretization

FAST.Farm is a newly developed multiphysics, midfidelity engineering tool that can be used to predict turbine power and structural loads of wind turbines in a wind farm. Previous studies have shown the similarities and differences between FAST.Farm and large-eddy simulations (LES) using the same LES-precursor-generated ambient wind inflow. The ability to generate ambient wind inflow using a synthetic turbulence engineering model (e.g., TurbSim or the Mann model) has recently been integrated into FAST.Farm to potentially enable more computationally efficient usage of the tool. This work aims to: 1) compare FAST.Farm simulations using LES-generated inflow to those using synthetically generated inflow from TurbSim, and 2) establish guidelines by which TurbSim-generated inflow should be generated for wind farm analysis. It was found that properly setting spatial coherence parameters for the transverse wind velocity components is necessary to accurately predict wake meandering. It is shown that TurbSim-generated inflow can be used in FAST.Farm to accurately predict thrust, power, speed, and torque for waked and unwaked turbines; wake meandering behavior across different atmospheric conditions; and averaged wake-deficit advection and evolution effects.

17 WIND ENERGY↗

FAST.Farm Response to Varying Wind Inflow Techniques: Preprint

FAST.Farm is a newly developed multiphysics, midfidelity engineering tool that can be used to predict turbine power and structural loads of wind turbines in a wind farm. Previous studies have shown the similarities and differences between FAST.Farm and large-eddy simulations (LES) using the same LES-precursor-generated ambient wind inflow. The ability to generate ambient wind inflow using a synthetic turbulence engineering model (e.g., TurbSim or the Mann model) has recently been integrated into FAST.Farm to potentially enable more computationally efficient usage of the tool. This work aims to: 1) compare FAST.Farm simulations using LES-generated inflow to those using synthetically generated inflow from TurbSim, and 2) establish guidelines by which TurbSim-generated inflow should be generated for wind farm analysis. It was found that properly setting spatial coherence parameters for the transverse wind velocity components is necessary to accurately predict wake meandering. It is shown that TurbSim-generated inflow can be used in FAST.Farm to accurately predict thrust, power, speed, and torque for waked and unwaked turbines; wake meandering behavior across different atmospheric conditions; and averaged wake-deficit advection and evolution effects.

17 WIND ENERGY↗

A map of the inorganic ternary metal nitrides

Exploratory synthesis in new chemical spaces is the essence of solid-state chemistry. However, uncharted chemical spaces can be difficult to navigate, especially when materials synthesis is challenging. Nitrides represent one such space, where stringent synthesis constraints have limited the exploration of this important class of functional materials. Here, we employ a suite of computational materials discovery and informatics tools to construct a large stability map of the inorganic ternary metal nitrides. Our map clusters the ternary nitrides into chemical families with distinct stability and metastability, and highlights hundreds of promising new ternary nitride spaces for experimental investigation - from which we experimentally realized seven new Zn- and Mg-based ternary nitrides. As a result, by extracting the mixed metallicity, ionicity and covalency of solid-state bonding from the density functional theory (DFT)-computed electron density, we reveal the complex interplay between chemistry, composition and electronic structure in governing large-scale stability trends in ternary nitride materials.

36 MATERIALS SCIENCE↗

WE-H-BRA-04: Biological Geometries for the Monte Carlo Simulation Toolkit TOPASNBio

Purpose: New advances in radiation therapy are most likely to come from the complex interface of physics, chemistry and biology. Computational simulations offer a powerful tool for quantitatively investigating radiation interactions with biological tissue and can thus help bridge the gap between physics and biology. The aim of TOPAS-nBio is to provide a comprehensive tool to generate advanced radiobiology simulations. Methods: TOPAS wraps and extends the Geant4 Monte Carlo (MC) simulation toolkit. TOPAS-nBio is an extension to TOPAS which utilizes the physics processes in Geant4-DNA to model biological damage from very low energy secondary electrons. Specialized cell, organelle and molecular geometries were designed for the toolkit. Results: TOPAS-nBio gives the user the capability of simulating biological geometries, ranging from the micron-scale (e.g. cells and organelles) to complex nano-scale geometries (e.g. DNA and proteins). The user interacts with TOPAS-nBio through easy-to-use input parameter files. For example, in a simple cell simulation the user can specify the cell type and size as well as the type, number and size of included organelles. For more detailed nuclear simulations, the user can specify chromosome territories containing chromatin fiber loops, the later comprised of nucleosomes on a double helix. The chromatin fibers can be arranged in simple rigid geometries or within factual globules, mimicking realistic chromosome territories. TOPAS-nBio also provides users with the capability of reading protein data bank 3D structural files to simulate radiation damage to proteins or nucleic acids e.g. histones or RNA. TOPAS-nBio has been validated by comparing results to other track structure simulation software and published experimental measurements. Conclusion: TOPAS-nBio provides users with a comprehensive MC simulation tool for radiobiological simulations, giving users without advanced programming skills the ability to design and run complex simulations.

60 APPLIED LIFE SCIENCES↗