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DOE OSTI2024

ZFP: A compressed array representation for numerical computations

HPC trends favor algorithms and implementations that reduce data motion relative to FLOPS. We investigate the use of lossy compressed data arrays in place of traditional IEEE floating point arrays to store the primary data of calculations. Simulation is fundamentally an exercise in controlled approximation, and error introduced by finite-precision arithmetic (or lossy compression) is just one of several sources of error that need to be managed to ensure sufficient accuracy in a computed result. We describe ZFP, a compressed numerical format designed for in-memory storage of multidimensional arrays, and summarize theoretical results that demonstrate that the error of repeated lossy compression can be bounded and controlled. Furthermore, we establish a relationship between grid resolution and compression-induced errors and show that, contrary to conventional floating point, ZFP reduces finite-difference errors with finer grids. We present example calculations that demonstrate data reduction by 4x or more with negligible impact on solution accuracy. Our results further demonstrate several orders-of-magnitude increase in accuracy using ZFP over IEEE floating point and Posits for the same storage budget.

Lindstrom, Peter↗

DOE OSTI2016

Development of a reduced tri-propylene glycol monomethyl ether– n -hexadecane–poly-aromatic hydrocarbon mechanism and its application for soot prediction

A reduced chemical kinetic mechanism for Tri-Propylene Glycol Monomethyl Ether (TPGME) has been developed and applied to computational fluid dynamics (CFD) calculations for predicting combustion and soot formation processes. The reduced TPGME mechanism was combined with a reduced n-hexadecane mechanism and a Poly-Aromatic Hydrocarbon (PAH) mechanism to investigate the effect of fuel oxygenation on combustion and soot emissions. The final version of the TPGME-n-hexadecane-PAH mechanism consists of 144 species and 730 reactions and was validated with experiments in shock tubes as well as in a constant volume spray combustion vessel (CVCV) from the Engine Combustion Network (ECN). The effects of ambient temperature, varying oxygen content in the tested fuels on ignition delay, spray liftoff length and soot formation under diesel-like conditions were analyzed and addressed using multidimensional reacting flow simulations and the reduced mechanism. Here, the results show that the present reduced mechanism gives reliable predictions of the combustion characteristics and soot formation processes. In the CVCV simulations, two important trends were identified. First, increasing the initial temperature in the CVCV shortens the ignition delay and lift-off length, reduces the fuel-air mixing, thereby increasing the soot levels. Secondly, fuel oxygenation introduces more oxygen into the central region of a fuel jet and reduces residence times of fuel rich area in active soot forming regions, thereby reducing soot levels.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2020

A data-driven mobility–energy typology framework for New York State

Exploring multidimensional aspects of differences in technology adoption, travel, and vehicle ownership across settlement types can help inform energy-efficient and affordable mobility system goals. Concurrently, mapping key enablers, barriers, and risks for successfully meeting ambitious goals and targets (e.g. by geography, age, income, education, population density) offer important explanatory power as to context-specific challenges and opportunities. This paper explores how a highly geographically resolved understanding of social, economic, techno-infrastructural, environmental, and governance (SET EG) factors shape variations in technology adoption and associated mobility and energy outcomes in diverse communities of New York State, in terms of electric vehicle adoption rates, alternative commute mode choices, vehicles per household, and vehicle fuel economy. Results indicate the range of two to three times higher adoption rates for electric vehicles by more highly educated, wealthier, “Core Urban” populations relative to the other identified typologies, given the labels “Rural”, “Suburban”, and “Urban” populations. Additionally, commute mode choice is closely linked with population and employment density—more than 89% of Core Urbanites use transit or active modes, compared with just 26% and 18% of Suburban and Rural residents, respectively. Household vehicle ownership varies from approximately 1.9 vehicles per household in Rural areas to only 0.6 in Core Urban settings. Findings on differences among the four settlement types, which go beyond simply rural to urban contexts, suggest an important need to explore how best to manage and anticipate very different types of services that may be supportive in achieving energy-efficient and affordable mobility systems statewide.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Solid-state NMR of unlabeled plant cell walls: high-resolution structural analysis without isotopic enrichment

Abstract Background Multidimensional solid-state nuclear magnetic resonance (ssNMR) spectroscopy has emerged as an indispensable technique for resolving polymer structure and intermolecular packing in primary and secondary plant cell walls. Isotope ( 13 C) enrichment provides feasible sensitivity for measuring 2D/3D correlation spectra, but this time-consuming procedure and its associated expenses have restricted the application of ssNMR in lignocellulose analysis. Results Here, we present a method that relies on the sensitivity-enhancing technique Dynamic Nuclear Polarization (DNP) to eliminate the need for 13 C-labeling. With a 26-fold sensitivity enhancement, a series of 2D 13 C– 13 C correlation spectra were successfully collected using the unlabeled stems of wild-type Oryza sativa (rice). The atomic resolution allows us to observe a large number of intramolecular cross peaks for fully revealing the polymorphic structure of cellulose and xylan. NMR relaxation and dipolar order parameters further suggest a sophisticated change of molecular motions in a ctl1 ctl2 double mutant: both cellulose and xylan have become more dynamic on the nanosecond and microsecond timescale, but the motional amplitudes are uniformly small for both polysaccharides. Conclusions By skipping isotopic labeling, the DNP strategy demonstrated here is universally extendable to all lignocellulose materials. This time-efficient method has landed the technical foundation for understanding polysaccharide structure and cell wall assembly in a large variety of plant tissues and species.

09 BIOMASS FUELS↗

DOE OSTI2025

Nitrogen limitation causes a seismic shift in redox state and phosphorylation of proteins implicated in carbon flux and lipidome remodeling in Rhodotorula toruloides

Background: Oleaginous yeast are prodigious producers of oleochemicals, offering alternative and secure sources for applications in foodstuff, skincare, biofuels, and bioplastics. Nitrogen starvation is the primary strategy used to induce oil accumulation in oleaginous yeast as part of a global stress response. While research has demonstrated that post-translational modifications (PTMs), including phosphorylation and protein cysteine thiol oxidation (redox PTMs), are involved in signaling pathways that regulate stress responses in metazoa and algae, their role in oleaginous yeast remain understudied and unexplored. Results: Towards linking the yeast oleaginous phenotype to protein function, we integrated lipidomics, redox proteomics, and phosphoproteomics to investigate Rhodotorula toruloides under nitrogen-rich and starved conditions over time. Our lipidomics results unearthed interactions involving sphingolipids and cardiolipins with ER stress and mitophagy. Our redox and phosphoproteomics data highlighted the roles of the AMPK, TOR, and calcium signaling pathways in regulation of lipogenesis, autophagy, and oxidative stress response. As a first, we also demonstrated that lipogenic enzymes including fatty acid synthase are modified as a consequence of shifts in cellular redox states due to nutrient availability. Conclusions: We conclude that lipid accumulation is largely a consequence of carbon rerouting and autophagy governed by changes to PTMs, and not increases in the abundance of enzymes involved in central carbon metabolism and fatty acid biosynthesis. Our systems-level approach sets the stage for acquiring multidimensional data sets for protein structural modeling and predicting the functional relevance of PTMs using Artificial Intelligence/Machine Learning (AI/ML). Coupled to those bioinformatics approaches, the putative PTM switches that we delineate will enable advanced metabolic engineering strategies to decouple lipid accumulation from nitrogen limitation.

Lipid Signalling↗

DOE OSTI2023

Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics

This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1–0.2 ppt and brackish 0.3–1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10–100 kyr old), MP (105–120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

Microbial metal resistance and metabolism across dynamic landscapes: high-throughput environmental microbiology

Multidimensional gradients of inorganic compounds influence microbial activity in diverse pristine and anthropogenically perturbed environments. Here, we suggest that high-throughput cultivation and genetics can be systematically applied to generate quantitative models linking gene function, microbial community activity, and geochemical parameters. Metal resistance determinants represent a uniquely universal set of parameters around which to study and evaluate microbial fitness because they represent a record of the environment in which all microbial life evolved. By cultivating microbial isolates and enrichments in laboratory gradients of inorganic ions, we can generate quantitative predictions of limits on microbial range in the environment, obtain more accurate gene annotations, and identify useful strategies for predicting and engineering the trajectory of natural ecosystems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2016

Towards a Consolidated Approach for the Assessment of Evaluation Models of Nuclear Power Reactors

The STARS project at the Paul Scherrer Institut (PSI) has adopted the TRACE thermal-hydraulic (T-H) code for best-estimate system transient simulations of the Swiss Light Water Reactors (LWRs). For analyses involving interactions between system and core, a coupling of TRACE with the SIMULATE-3K (S3K) LWR core simulator has also been developed. In this configuration, the TRACE code and associated nuclear power reactor simulation models play a central role to achieve a comprehensive safety analysis capability. Thus, efforts have now been undertaken to consolidate the validation strategy by implementing a more rigorous and structured assessment approach for TRACE applications involving either only system T-H evaluations or requiring interfaces to e.g. detailed core or fuel behavior models. The first part of this paper presents the preliminary concepts of this validation strategy. The principle is to systematically track the evolution of a given set of predicted physical Quantities of Interest (QoIs) over a multidimensional parametric space where each of the dimensions represent the evolution of specific analysis aspects, including e.g. code version, transient specific simulation methodology and model "nodalisation". If properly set up, such environment should provide code developers and code users with persistent (less affected by user effect) and quantified information (sensitivity of QoIs) on the applicability of a simulation scheme (codes, input models, methodology) for steady state and transient analysis of full LWR systems. Through this, for each given transient/accident, critical paths of the validation process can be identified that could then translate into defining reference schemes to be applied for downstream predictive simulations. In order to illustrate this approach, the second part of this paper presents a first application of this validation strategy to an inadvertent blowdown event that occurred in a Swiss BWR/6. The transient was initiated by the spurious actuation of the Automatic Depressurization System (ADS). The validation approach progresses through a number of dimensions here: First, the same BWR system simulation model is assessed for different versions of the TRACE code, up to the most recent one. The second dimension is the "nodalisation" dimension, where changes to the input model are assessed. The third dimension is the "methodology" dimension. In this case imposed power and an updated TRACE core model are investigated. For each step in each validation dimension, a common set of QoIs are investigated. For the steady-state results, these include fuel temperatures distributions. For the transient part of the present study, the evaluated QoIs include the system pressure evolution and water carry-over into the steam line.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Modeling In-Reactor Temperature Gradients in Lithium Aluminate Ceramic Pellets

In reactor thermal performance of lithium aluminate ceramic pellets are calculated to determine operating temperatures if internal components shift during irradiation. A 2D conduction model was setup to model this scenario with additional physics, including thermal expansion of components to reactor temperatures, creep down of the cladding due to differential pressure between the inside of the rod and reactor coolant system, and net radiation exchange between components. The non-linear coupling of the governing equations presented convergence challenges due to the very different effects from a small temperature change on the radiation vs radial and circumferential conduction equations. Initial temperature guesses for the multidimensional solution were provided from conservative 1D models simulating bounding scenarios. Convergence was greatly improved by taking small steps towards the root solutions and averaging with initial guesses. The final method robustly converged all 132 points at an axial plane after a few dozen iterations. The temperature results show that the additional physics have a secondary effect as the dominant heat transfer mechanism is radial conduction across the gas gap followed by circumferential conduction around components. Circumferential conduction in the lithium aluminate pellets is enhanced by the relatively high thermal conductivity of this ceramic.

Carstens, Nathan A.↗

DOE OSTI2016

Quasi-rotating frame: accurate line shape determination with increased efficiency in noncollinear 2D optical spectroscopy

Multidimensional spectroscopies correlate the oscillation frequencies of an atomic or molecular resonance during at least two different time periods. For two-dimensional (2D) optical spectroscopy, oscillations in the first coherence period are sampled in the time domain point-bypoint. Here, we present a general method for accelerating this often lengthy task, the Quasi-Rotating Frame (QRF), through heterodyne detection of the nonlinear signal pulse with a systematic variably delayed local oscillator pulse in a non-collinear (box-CARS) geometry four wave mixing experiment. 2D infrared (2D IR) vibrational echo experiments are conducted to demonstrate the QRF technique, and the results are compared to data obtained in the stationary frame. We describe straightforward techniques to configure QRF detection, prevent experimental artifacts, appropriately calibrate the rotating frame frequencies, and process the resulting data such that accurate liquid structural dynamics may be extracted from a series of waiting-timedependent 2D spectral line shapes.

14 SOLAR ENERGY↗

DOE OSTI2022

Enhanced stimulated Raman scattering during intense laser propagation

Stimulated Raman scattering is ubiquitous in many high-intensity laser environments. Parametric four-wave mixing between the pump and Raman sidebands can affect the Raman gain, but stringent phase matching requirements and strongly nonlinear dynamics obscure clear understanding of its effects at high laser powers. Here we investigate four-wave mixing in the presence of strong self-focusing and weak ionization at laser powers above the Kerr critical power. Theoretical analysis shows that the plasma generated at focus naturally leads to phase matching conditions suitable for enhanced Raman gain, almost without regard to the initial phase mismatch. Multidimensional nonlinear optical simulations with multiphoton and collisional ionization confirm the enhancement and suggest that it may lead to significantly higher Raman losses in some high-intensity laser environments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Single-shot measurements of shaped XUV FEL pulses with frequency-resolved optical gating

The ability to control the amplitude and phase of extreme ultraviolet (XUV) and X-ray free-electron laser (FEL) pulses can allow for the extension of optical techniques, such as multidimensional spectroscopy or coherent control, to higher photon energies, for probing and controlling core electronic transitions. However, this requires the ability to make single-shot, and complete, electric field measurements of potentially complex FEL pulses, in order to develop, and verify, pulse shaping strategies. Here, we present direct, single-shot measurements of XUV pulses generated under special operating configurations for producing specific pulse shapes from a laser-seeded XUV FEL. To do this, we built upon our past work using transient grating (TG) cross correlation frequency-resolved optical gating (FROG), where an optical reference pulse is diffracted from an XUV TG produced by a pair of interfering FEL pulses. The resulting nonlinear signal versus frequency and delay, i.e., the FROG trace, contains the electric field of the FEL pulse. The FEL pulse electric field is reconstructed from the FROG trace using a phase retrieval algorithm. Here we confirmed three different pulse shaping strategies for generating chirped, double and multiple FEL pulses by tuning the seed laser and FEL parameters and measuring the resulting shaped FEL pulses with TG XFROG. This work paves the way for generating on-demand pulse shapes with a seeded FEL by improving the characterization of FEL pulses, for transform-limited to more complex shapes.

Elverson, Francesca↗

DOE OSTI2016

Simultaneous generation of sub-5-femtosecond 400 nm and 800 nm pulses for attosecond extreme ultraviolet pump–probe spectroscopy

Few-cycle laser pulses with wavelengths centered at 400 nm and 800 nm are simultaneously attained through wavelength separation of ultrashort, spectrally broadened Vis-NIR laser pulses spanning 350-1100 nm wavelengths. The 400 nm and 800 nm pulses are separately compressed, yielding pulses with 4.4 fs and 3.8 fs duration, respectively. The pulse energy exceeds 5 μJ for the 400 nm pulses and 750 μJ for the 800 nm pulses. Intense 400 nm few-cycle pulses have a broad range of applications in nonlinear optical spectroscopy, which include the study of photochemical dynamics, semiconductors, and photovoltaic materials on few-femtosecond to attosecond time scales. Furthermore, the ultrashort 400 nm few-cycle pulses generated here not only extend the spectral range of the optical pulse for NIR-XUV attosecond pump-probe spectroscopy but also pave the way for two-color, three-pulse, multidimensional optical-XUV spectroscopy experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform ( RPX ) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars

The genetics and responses to biotic stressors of tetraploid switchgrass (Panicum virgatum L.) lowland cultivar ‘Kanlow’ and upland cultivar Summer are distinct and can be exploited for trait improvement. In general, there is a paucity of data on the basal differences in transcription across tissue developmental times for switchgrass cultivars. Here, the changes in basal and temporal expression of genes related to leaf functions were evaluated for greenhouse grown ‘Kanlow’, and ‘Summer’ plants. Three biological replicates of the 4 th leaf pooled from 15 plants per replicate were harvested at regular intervals beginning from leaf emergence through senescence. Increases and decreases in leaf chlorophyll and N content were similar for both cultivars. Likewise, multidimensional scaling (MDS) analysis indicated both cultivar-independent and cultivar-specific gene expression. Cultivar-independent genes and gene-networks included those associated with leaf function, such as growth/senescence, carbon/nitrogen assimilation, photosynthesis, chlorophyll biosynthesis, and chlorophyll degradation. However, many genes encoding nucleotide-binding leucine rich repeat (NB-LRRs) proteins and wall-bound kinases associated with detecting and responding to environmental signals were differentially expressed. Several of these belonged to unique cultivar-specific gene co-expression networks. Analysis of genomic resequencing data provided several examples of NB-LRRs genes that were not expressed and/or apparently absent in the genomes of Summer plants. It is plausible that cultivar (ecotype)-specific genes and gene-networks could be one of the drivers for the documented differences in responses to leaf-borne pathogens between these two cultivars. Incorporating broad resistance to plant pathogens in elite switchgrass germplasm could improve sustainability of biomass production under low-input conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

System identity and transformation in petroleum jurisdictions: A multi-method approach for the North Slope Borough, Alaska

Capturing the multidimensionality of a bounded social-environmental system (SES) presents a range of challenges to interdisciplinary researchers due to the need to integrate divergent scientific paradigms, scalar data, and social theories. Contemporary Arctic circumpolar SESs studied under conditions of rapid and unprecedented climatic, ecological, economic, and sociopolitical change, defy any singular established methodological approach that aims to schematize and interpret the system for decision-making purposes. As a small interdisciplinary team working within a large Arctic SES modeling effort, we have found that developing systems models to support resilience in the Arctic requires an understanding of system dynamics that is attentive to holistic indicators of change, measured both quantitatively and qualitatively. Using the Alaska North Slope Borough as a case study, we apply three convergent frameworks to capture significant dimensions of the system for improved problem definition in confronting the challenges of Arctic climate change. We describe contemporary “oil and gas” social-ecological system components and dynamics, the historical processes and transformations that fundamentally altered the system, and the scientific projections for the most likely catalysts of future change. This analysis results in a typology for defining subnational Arctic hydrocarbon SESs. We conclude that the future of oil and gas development as a policy pathway in different locations experiencing rapid climate change can be evaluated when difficult-to-quantify variables are included.

Lovecraft, Amy Lauren↗

DOE OSTI2026

Observation of spin‑wave altermagnetic splitting in MnF2

-Contents of the Data Repository: - Polarized neutron diffraction data acquired in the (HK0) scattering plane. - Inelastic neutron scattering (INS) data from both unpolarized and polarized measurements with an incident neutron energy of Ei =9 meV.- - Reduced multidimensional single-crystal datasets (MDE) and corresponding S(Q,ω) slices used to generate all figures presented in the manuscript. - Julia source code and supporting input files used for spin-wave calculations, model fitting, and simulation of neutron scattering intensity maps.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Exploring the physics of cesium lead halide perovskite quantum dots via Bayesian inference of the photoluminescence spectra in automated experiment

The unique optoelectronic properties of metal halide perovskite quantum dots (QDs) make them promising candidates for applications in light-emitting diodes (LEDs), scintillators, and other photonic devices. The automated micropipetting synthesis platform equipped with an optical reader enables the opportunity for high throughput synthesis and photoluminescent (PL) characterization of metal halide perovskite QDs for the first time. Here, we explore the compositional dependence of the PL behavior and stability of the combinatorial library of cesium lead halide (CsPbX 3 ) perovskites QDs via the automated platform. To study the stability of synthesized QDs in the binary and ternary configurations, we study the time-dependent PL properties using previously developed machine learning analysis. Additionally, to systematically explore the PL behavior in the ternary CsPbX 3 QDs system, we introduce the Bayesian inference framework that allows the probabilistic fit of multiple models to the PL data and establishes both optimal model and model parameter robustly. Furthermore, these behaviors can be used as a control parameter for the navigation of the multidimensional compositional spaces in automated synthesis. Furthermore, this analysis shows the nonuniformity of the PL peak behavior in the ternary CsPbX 3 QDs system. Further, the analysis confirms narrow size distribution and good quality of CsPbBr 3 QDs alloyed with low concentrations of iodide and chloride. We note that Bayesian Inference fit parameters can be further used as a control signal for navigation of the chemical spaces in automated synthesis.

36 MATERIALS SCIENCE↗