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At least 253 records · Page 14

Transport model comparison studies of intermediate-energy heavy-ion collisions

Transport models are the main method to obtain physics information on the nuclear equation of state and in-medium properties of particles from low to relativistic-energy heavy-ion collisions. The Transport Model Evaluation Project (TMEP) has been pursued to test the robustness of transport model predictions in reaching consistent conclusions from the same type of physical model. To this end, calculations under controlled conditions of physical input and set-up were performed with various participating codes. These included both calculations of nuclear matter in a box with periodic boundary conditions, which test separately selected ingredients of a transport code, and more realistic calculations of heavy-ion collisions. Over the years, six studies have been performed within this project. In this intermediate review, we summarize and discuss the present status of the project. We also provide condensed descriptions of the 26 participating codes, which contributed to some part of the project. These include the major codes in use today. After a compact description of the underlying transport approaches, we review the main results of the studies completed so far. They show, that in box calculations the differences between the codes can be well understood and a convergence of the results can be reached. These studies also highlight the systematic differences between the two families of transport codes, known under the names of Boltzmann–Uehling–Uhlenbeck (BUU) and Quantum Molecular Dynamics (QMD) type codes. However, when the codes were compared in full heavy-ion collisions using different physical models, as recently for pion production, they still yielded substantially different results. This calls for further comparisons of heavy-ion collisions with controlled models and of box comparisons of important ingredients, like momentum-dependent fields, which are currently underway. Furthermore, our evaluation studies often indicate improved strategies in performing transport simulations and thus can provide guidance to code developers. Results of transport simulations of heavy-ion collisions from a given code will have more significance if the code can be validated against benchmark calculations such as the ones summarized in this review.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Domesticating a food spoilage yeast into an organic acid–tolerant metabolic engineering host: Lactic acid production by engineered Zygosaccharomyces bailii

Lactic acid represents an important class of commodity chemicals, which can be produced by microbial cell factories. However, due to the toxicity of lactic acid at lower pH, microbial production requires the usage of neutralizing agents to maintain neutral pH. Zygosaccharomyces bailii, a food spoilage yeast, can grow under the presence of organic acids used as food preservatives. This unique trait of the yeast might be useful for producing lactic acid. With the goal of domesticating the organic acid!tolerant yeast as a metabolic engineering host, seven Z. bailii strains were screened in a minimal medium with 10 g/L of acetic, or 60 g/L of lactic acid at pH 3. The Z. bailii NRRL Y7239 strain was selected as the most robust strain to be en- gineered for lactic acid production. By applying a PAN!ARS!based CRISPR!Cas9 system consisting of a transfer RNA promoter and NAT selection, we demonstrated the targeted deletion of ADE2 and site!specific integration of Rhizopus oryzae ldhA coding for lactate dehydrogenase into the PDC1 locus. The resulting pdc1::ldhA strain produced 35 g/L of lactic acid without ethanol production. Here, this study de- monstrates the feasibility of the CRISPR!Cas9 system in Z. bailii, which can be applied for a fundamental study of the species.

59 BASIC BIOLOGICAL SCIENCES↗

Effects of surface diffusion in electrocatalytic CO 2 reduction on Cu revealed by kinetic Monte Carlo simulations

We report Kinetic Monte Carlo (KMC) methods are frequently used for mechanistic studies of thermally driven heterogeneous catalysis systems but are underused for electrocatalysis. Here, we develop a lattice KMC approach for electrocatalytic CO 2 reduction. The work is motivated by a prior experimental report that performed electroreduction of a mixed feed of 12 CO 2 and 13 CO on Cu; differences in the 13 C content of C2 products ethylene and ethanol (Δ 13 C) were interpreted as evidence of site selectivity. The lattice KMC model considers the effect of surface diffusion on this system. In the limit of infinitely fast diffusion (mean-field approximation), the key intermediates 12 CO* and 13 CO* would be well mixed on the surface and no evidence of site selectivity could have been observed. Using a simple two-site model and adapting a previously reported microkinetic model, we assess the effects of diffusion on the relative isotope fractions in the products using the estimated surface diffusion rate of CO* from literature reports. We find that the size of the active sites and the total surface adsorbate coverage can have a large influence on the values of Δ 13 C that can be observed. Δ 13 C is less sensitive to the CO* diffusion rate as long as it is within the estimated range. We further offer possible methods to estimate surface distribution of intermediates and to predict intrinsic selectivity of active sites based on experimental observations. This work illustrates the importance of considering surface diffusion in the study of electrochemical CO 2 reduction to multi-carbon products. Our approach is entirely based on a freely available open-source code, so will be readily adaptable to other electrocatalytic systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Overview of fast particle experiments in the first MAST Upgrade experimental campaigns

Abstract MAST-U is equipped with on-axis and off-axis neutral beam injectors (NBI), and these external sources of super-Alfvénic deuterium fast-ions provide opportunities for studying a wide range of phenomena relevant to the physics of alpha-particles in burning plasmas. The MeV range D-D fusion product ions are also produced but are not confined. Simulations with the ASCOT code show that up to 20% of fast ions produced by NBI can be lost due to charge exchange (CX) with edge neutrals. Dedicated experiments employing low field side (LFS) gas fuelling show a significant drop in the measured neutron fluxes resulting from beam-plasma reactions, providing additional evidence of CX-induced fast-ion losses, similar to the ASCOT findings. Clear evidence of fast-ion redistribution and loss due to sawteeth (ST), fishbones (FB), long-lived modes (LLM), Toroidal Alfvén Eigenmodes (TAE), Edge Localised Modes (ELM) and neoclassical tearing modes (NTM) has been found in measurements with a Neutron Camera (NCU), a scintillator-based Fast-Ion Loss Detector (FILD), a Solid-State Neutral Particle Analyser (SSNPA) and a Fast-Ion Deuterium- α (FIDA) spectrometer. Unprecedented FILD measurements in the range of 1–2 MHz indicate that fast-ion losses can be also induced by the beam ion cyclotron resonance interaction with compressional or global Alfvén eigenmodes (CAEs or GAEs). These results show the wide variety of scenarios and the unique conditions in which fast ions can be studied in MAST-U, under conditions that are relevant for future devices like STEP or ITER.

Physics↗

Genome-wide transcriptional regulation in Saccharomyces cerevisiae in response to carbon dioxide

Sugar metabolism by Saccharomyces cerevisiae produces ample amounts of CO 2 under both aerobic and anaerobic conditions. High solubility of CO 2 in fermentation media, contributing to enjoyable sensory properties of sparkling wine and beers by S. cerevisiae, might affect yeast metabolism. To elucidate the overlooked effects of CO 2 on yeast metabolism, we examined glucose fermentation by S. cerevisiae under CO 2 as compared to N 2 and O 2 limited conditions. While both CO 2 and N 2 conditions are considered anaerobic, less glycerol and acetate but more ethanol were produced under CO 2 condition. Transcriptomic analysis revealed that significantly decreased mRNA levels of GPP1 coding for glycerol-3-phosphate phosphatase in glycerol synthesis explained the reduced glycerol production under CO 2 condition. Besides, transcriptional regulations in signal transduction, carbohydrate synthesis, heme synthesis, membrane and cell wall metabolism, and respiration were detected in response to CO 2 . Interestingly, signal transduction was uniquely regulated under CO 2 condition, where upregulated genes (STE3, MSB2, WSC3, STE12, and TEC1) in the signal sensors and transcriptional factors suggested that MAPK signaling pathway plays a critical role in CO 2 sensing and CO 2 -induced metabolisms in yeast. Furthermore, our study identifies CO 2 as an external stimulus for modulating metabolic activities in yeast and a transcriptional effector for diverse applications.

59 BASIC BIOLOGICAL SCIENCES↗

Clifford transformations for fermionic quantum systems: From Pauli and Majorana operators to Dirac fermions

Clifford gates and transformations, which map products of elementary Pauli or Majorana operators to other such products, are foundational in quantum computing, underpinning the stabilizer formalism, error-correcting codes, magic state distillation, quantum communication and cryptography, and qubit tapering. Moreover, circuits composed entirely of Clifford gates are classically simulatable, highlighting their computational significance. In this article we extend the concept of Clifford transformations to Dirac fermions. We demonstrate that discrete Clifford transformations are generated by half-body and pair operators while continuous Clifford transformations are generated by number operators, providing a systematic framework for their characterization. Additionally, we establish connections with fermionic mean-field theories and applications in qubit tapering, offering insights into their broader implications in quantum computing.

74 ATOMIC AND MOLECULAR PHYSICS↗

Performance Analysis of Speculative Parallel Adaptive Local Timestepping for Conservation Laws

Stable simulation of conservation laws, such as those used to model fluid dynamics and plasma physics applications, requires the satisfaction of the so-called Courant-Friedrichs-Lewy condition. By allowing regions of the mesh to advance with different timesteps that locally satisfy this stability constraint, significant work reduction can be attained when compared to a time integration scheme using a single timestep size. However, parallelizing this algorithm presents considerable difficulty. Since the stability condition depends on the state of the system, dependencies become dynamic and potentially non-local. In this article, we present an adaptive local timestepping algorithm using an optimistic (Timewarp-based) parallel discrete event simulation. We introduce waiting heuristics to limit misspeculation and a semi-static load balancing scheme to eliminate load imbalance as parts of the mesh require finer or coarser timesteps. Last, we outline an interface for separating the physics of the specific conservation law from the temporal integration allowing for productive adoption of our proposed algorithm. We present a misspeculation study for three conservation laws, demonstrating both the productivity of the local timestepping API, for which 74% of the lines of code are reused across different conservation laws, and the robustness of the waiting heuristics—at most 1.5% of element updates are rolled back. Our performance studies demonstrate up to a 2.8× speedup versus a baseline unoptimized local timestepping approach, a 4x improvement in per-node throughput compared to an MPI parallelization of synchronous timestepping, and scalability up to 3,072 cores on NERSC’s Cori Haswell partition.

97 MATHEMATICS AND COMPUTING↗

MatRIS: Multi-level Math Library Abstraction for Heterogeneity and Performance Portability using IRIS Runtime

Vendor libraries are tuned for a specific architecture and are not portable to others. Moreover, they lack support for heterogeneity and multi-device orchestration, which is required for efficient use of contemporary HPC and cloud resources. To address these challenges, we introduce MatRIS—a multilevel math library abstraction for scalable and performance-portable sparse/dense BLAS/LAPACK operations using IRIS runtime. The MatRIS-IRIS co-design introduces three levels of abstraction to make the implementation completely architecture agnostic and provide highly productive programming. We demonstrate that MatRIS is portable without any change in source code and can fully utilize multi-device heterogeneous systems by achieving high performance and scalability on Summit, Frontier, and a CADES cloud node equipped with four NVIDIA A100 GPUs and four AMD MI100 GPUs. A detailed performance study is presented in which MatRIS demonstrates multi-device scalability. When compared, MatRIS provides competitive and even better performance than libraries from vendors and other third parties.

Monil, M. A. H.↗

Ciel

Compiler optimizations can alter the numerical results of scientific computing applications. When numerical results differ significantly between compilers, optimization levels, and floating-point hardware, these numerical inconsistencies can impact programming productivity. Ciel is a framework that helps programmers identify locations in the source code that are affected by compiler optimizations in CPU and GPU code. Ciel uses a floating-point precision enhancement strategy, guided by a recursive bisection search algorithm with increasing search granularity, to identify the program expressions that induce numerical inconsistencies due to compiler optimizations.

Miao, Wenjun↗

The Rodinia Benchmark Suite in SYCL

As opposed to the Open Computing Language (OpenCL) programming model in which host and device codes are generally written in different programming languages, SYCL can combine host and device codes for an application in a type-safe way to improve development productivity and performance portability. Rodinia is a widely used benchmark suite for heterogeneous computing. Hence, we port the OpenCL implementations of the benchmark suite to SYCL manually. The SYCL benchmark suite is an opensource project for tracking the development of the mainstream SYCL compilers, and for developers and researchers interested in programming productivity, performance analysis, and portability across different computing platforms. We organize the remainder of the report as follows. Section II introduces the SYCL programming model, shows the major differences between an OpenCL program and a SYCL program, and gives a summary of the benchmark suite. In Section III, we describe our SYCL implementations in more details. We evaluate the SYCL benchmarks on the Intel® central processing units (CPUs) and graphics processing units (GPUs) in Section IV. Section V concludes the report.

97 MATHEMATICS AND COMPUTING↗

Novel Geometric Operations for Linear Programming

This report summarizes the work performed under the project "Linear Programming in Strongly Polynomial Time." Linear programming (LP) is a classic combinatorial optimization problem heavily used directly and as an enabling subroutine in integer programming (IP). Specifically IP is the same as LP except that some solution variables must take integer values (e.g. to represent yes/no decisions). Together LP and IP have many applications in resource allocation including general logistics, and infrastructure design and vulnerability analysis. The project was motivated by the PI's recent success developing methods to efficiently sample Voronoi vertices (essentially finding nearest neighbors in high-dimensional point sets) in arbitrary dimension. His method seems applicable to exploring the high-dimensional convex feasible space of an LP problem. Although the project did not provably find a strongly-polynomial algorithm, it explored multiple algorithm classes. The new medial simplex algorithms may still lead to solvers with improved provable complexity. We describe medial simplex algorithms and some relevant structural/complexity results. We also designed a novel parallel LP algorithm based on our geometric insights and implemented it in the Spoke-LP code. A major part of the computational step is many independent vector dot products. Our parallel algorithm distributes the problem constraints across processors. Current commercial and high-quality free LP solvers require all problem details to fit onto a single processor or multicore. Our new algorithm might enable the solution of problems too large for any current LP solvers. We describe our new algorithm, give preliminary proof-of-concept experiments, and describe a new generator for arbitrarily large LP instances.

97 MATHEMATICS AND COMPUTING↗

pLiner

Compiler optimizations can alter significantly the numerical results of scientific computing applications. When numerical results differ significantly between compilers, optimization levels, and floating-point hardware, these numerical inconsistencies can impact programming productivity. pLiner is a framework that helps programmers identify locations in the source code that are highly affected by compiler optimizations. pLiner uses a novel approach to identify such code locations by enhancing the floatingpoint precision of variables and expressions. Using a guided search to locate the most significant code regions, pLiner can report to users such locations at different granularities, file, function, and line of code.

Laguna Peralta, Ignacio↗

Using Griffin's Transmutation Solver to Calculate Radiation Damage

Displacement Radiation Damage originates from all nuclides, not just those that are naturally occurring. Currently only damage from naturally-occurring nuclides, or sometimes damage from one transmutation product is considered. It is proposed that the transmutation solvers implemented in many codes be used to calculate this radiation damage. This would explicitly treat damage from all sources without additionally burdening the user. A proof-of-concept implementation was created in Griffin. The implementation showed that only minor code modifications are necessary to add this feature. When compared against an analytical benchmark the results Griffin could calculate were very accurate.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

PUFFIn – A user friendly fast interface for calculating and visualizing the dose distribution in materials

This article describes a new graphical user interface that uses the PENELOPE Monte Carlo code to calculate dose distributions in materials. It is named PUFFIn, for the Penelope User-Friendly Fast Interface and was developed as an educational and scoping analysis tool for non-experts in radiation modeling. PUFFIn enables the user to visualize and compare the dose distributions in objects (e.g., sterilized healthcare products) irradiated with cobalt-60 gamma-rays, electron beam (E-beam) or X-rays. From such comparisons, the user can determine the most efficient product and/or packaging designs for any given radiation field – whether for conceptual or existing products and packaging. PUFFIn is distributed in a complete, self-contained package of software, including the PENELOPE radiation transport code, a standard graphics package, and a set of simple exercises. The package is available to any user at no cost and requires a minimal amount of training compared to other similar software. PUFFIn's capabilities are described, as well as validation measurements performed at Texas A&M University E-beam facility and the Aerial E-beam Facility in France.

97 MATHEMATICS AND COMPUTING↗

Deployment of the HFIRCON transport and depletion tool for plutonium-238 production studies

Irradiation of {sup 237}Np-bearing targets in Oak Ridge National Laboratory's (ORNL) High Flux Isotope Reactor (HFIR) results in the efficient production of {sup 238}Pu, which, in the form of heat source PuO{sub 2}, is used as a reliable power source for deep-space and planetary NASA missions. A technology demonstration subproject was initiated at ORNL in 2011 to develop and implement the technology required to establish a {sup 238}Pu supply chain. A systematic progression of NpO{sub 2}/Al cermet (20 vol.% NpO{sub 2}) activities to date has successfully demonstrated target fabrication, irradiation, and chemical recovery processes. Recent program tasks have included the development of the HFIRCON transport and depletion tool for efficient reactor physics analyses and the evaluation of increased NpO{sub 2} loadings (i.e., beyond 20 vol.%) and NpN-based targets. This paper documents the deployment of the HFIRCON code to assess various Np concentrations in NpO{sub 2}- and NpN-based targets in HFIR's inner small vertical experiment facilities. Results indicate that {sup 238}Pu production and quality can be enhanced with increased Np loadings; however, target conversion rates are reduced. The results recorded in this paper, thermal and material balance evaluations, and testing requirement planning will be used to determine whether increased NpO{sub 2} loadings or NpN-based targets will be further considered. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Substantial and overlooked greenhouse gas emissions from deep Arctic lake sediment - supporting data and code

This data package contains data, descriptions, and code-based analyses that were used to support conclusions drawn in “Substantial and overlooked greenhouse gas emissions from deep Arctic lake sediment”, by Freitas et al. (2025) (https://doi.org/10.1038/s41561-024-01614-y). The study evaluated greenhouse gas production along a deep sediment core (20 m) taken in 2018 from below Goldstream Lake, a field site approximately 15 km north of Fairbanks, Alaska.The file “ESSDive_NFreitas_2024_flmd.csv” includes an overview of all other csv files in this data package, namely: sediment descriptions (depth and type of sediment), sediment characterizations (bulk density, gravimetric water content, total carbon, etc.), calculated respiration and temperature sensitivity values associated with year-long incubations of the sediment core, and the R code used to process the dataset. Additional details regarding the content of these files and how the calculations were performed are described in the Methods section of this archive. The “data_dictionary_ESSDive_NFreitas_2024_dd.csv” is a data dictionary for all files included in the data package. Each row in the data dictionary represents a column name in a given file. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).Data package updates- August 2024: Title was updated, R code now includes a process for calculating potential production across the whole sediment column, the "sediment_column_production_potentials_ESSDive_NFreitas_2024.csv" is the associated data output file, and the file level metadata and data dictionaries were updated to reflect the contents of the additional csv file.- October 2024: Title was updated, and a statement was added to Step 2 of the Methods that describes that samples were collected (and exported) in a responsible manner and in accordance with relevant permits and local laws.- January 2025: Updated the associated manuscript details in the Abstract (manuscript title, publication date, DOI link) and in the Related References section (full citation).

54 ENVIRONMENTAL SCIENCES↗

Hydrogen Refueling Reference Station Lot Size Analysis for Urban Sites

Hydrogen Fueling Infrastructure Research and Station Technology (H2FIRST) is a project initiated by the DOE in 2015 and executed by Sandia National Laboratories and the National Renewable Energy Laboratory to address R&D barriers to the deployment of hydrogen fueling infrastructure. One key barrier to the deployment of fueling stations is the land area they require (i.e. "footprint"). Space is particularly a constraint in dense urban areas where hydrogen demand is high but space for fueling stations is limited. This work presents current fire code requirements that inform station footprint, then identifies and quantifies opportunities to reduce footprint without altering the safety profile of fueling stations. Opportunities analyzed include potential new methods of hydrogen delivery, as well as alternative placements of station technologies (i.e. rooftop/underground fuel storage). As interest in heavy-duty fueling stations and other markets for hydrogen grows, this study can inform techniques to reduce the footprint of heavy-duty stations as well. This work characterizes generic designs for stations with a capacity of 600 kg/day hydrogen dispensed and 4 dispenser hoses. Three base case designs (delivered gas, delivered liquid, and on-site electrolysis production) have been modified in 5 different ways to study the impacts of recently released fire code changes, colocation with gasoline refueling, alternate delivery assumptions, underground storage of hydrogen, and rooftop storage of hydrogen, resulting in a total of 32 different station designs. The footprints of the base case stations range from 13,000 to 21,000 ft 2 . A significant focus of this study is the NFPA 2 requirements, especially the prescribed setback distances for bulk gaseous or liquid hydrogen storage. While the prescribed distances are large in some cases, these setback distances are found to have a nuanced impact on station lot size; considerations of the delivery truck path, traffic flow, parking, and convenience store location are also important. Station designs that utilize underground and rooftop storage can reduce footprint but may not be practical or economical. For example, burying hydrogen storage tanks underground can reduce footprint, but the cost savings they enable depend on the cost of burial and the cost land. Siting and economic analysis of station lot sizes illustrate the benefit of smaller station footprints in the flexibility and cost savings they can provide. This study can be used as a reference that provides examples of the key design differences that fueling stations can incorporate, the approximate sizes of generic station lots, and considerations that might be unique to particular designs.

08 HYDROGEN↗

Time-dependent variational principle for mixed matrix product states in the thermodynamic limit

Here, we describe a time evolution algorithm for quantum spin chains whose Hamiltonians are composed of an infinite uniform left and right bulk part, and an arbitrary finite region in between. The left and right bulk parts are allowed to be different from each other. The algorithm is based on the time-dependent variational principle (TDVP) of matrix product states. It is inversion-free and very simple to adapt from an existing TDVP code for finite systems. The importance of working in the projective Hilbert space is highlighted. We study the quantum Ising model as a benchmark and an illustrative example. The spread of information after a local quench is studied in both the ballistic and the diffusive case. We also offer a derivation of TDVP directly from symplectic geometry.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗