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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Vision and Development of a Design, Implementation, and Verification Automation (DIVA) Software Platform for DNA Construction

Abstract DNA construction, while a prerequisite to many biological endeavors, is often a time-consuming distraction from an individual’s primary research objectives. We envisioned that with the right software infrastructure and cultural mindset, a single person could execute in parallel the batched DNA construction tasks of an entire research institute, at scales realizing efficiency gains through process and laboratory automation. In pursuit of this vision, we developed the Design, Implementation, and Verification Automation (DIVA) software platform. DIVA’s web interface enables researchers to design DNA constructs (using visual biological computer-aided design tools and biological parts repositories), submit designs for construction to dedicated staff, and track DNA construction as it progresses. DIVA supports the dedicated staff through the DNA construction process and records both successful and unsuccessful attempts toward improving the overall process. The platform is publicly available at public-diva.jbei.org and its open-source code through github.com/JBEI/DIVA.

Plahar, Hector [DOE Agile BioFoundry , , ,; DOE Jo↗
DOE OSTI2021

The Implementation of Framework for Improvement by Vertical Enhancement Into Energy Exascale Earth System Model

Abstract The low cloud bias in global climate models (GCMs) remains an unsolved problem. Coarse vertical resolution in GCMs has been suggested to be a significant cause of low cloud bias because planetary boundary layer parameterizations cannot resolve sharp temperature and moisture gradients often found at the top of subtropical stratocumulus layers. This work aims to ameliorate the low cloud problem by implementing a new computational method, the Framework for Improvement by Vertical Enhancement (FIVE), into the Energy Exascale Earth System Model (E3SM). Three physics schemes representing microphysics, radiation, and turbulence as well as vertical advection are interfaced to vertically enhanced physics (VEP), which allows for these processes to be computed on a higher vertical resolution grid compared to the rest of the E3SM model. We demonstrate the better representation of subtropical boundary layer clouds with FIVE while limiting additional computational cost from the increased number of levels. When the vertical resolution approaches the large eddy simulation‐like vertical resolution in VEP, the climatological low cloud amount shows a significant increase of more than 30% in the southeastern Pacific Ocean. Using FIVE to improve the representation of low‐level clouds does not come with any negative side effects associated with the simulation of mid‐ and high‐level cloud and precipitation, that can occur when running the full model at higher vertical resolution.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Implementation of an Orographic Drag Scheme Considering Orographic Anisotropy in All Flow Directions in the Earth System Model CAS‐ESM 2.0

Abstract A reasonable representation of orographic anisotropy in earth system models is vital for improving weather and climate modeling. In this study, we implement the orographic drag scheme, including 3‐D orographic anisotropy (3D‐AFD), into the Chinese Academy of Sciences Earth System Model version 2 (CAS‐ESM 2.0). Three groups of simulations named sensitivity run, medium‐range forecast, and seasonal forecast respectively are conducted using the updated CAS‐ESM model and validated against station observation and reanalysis data. These simulations are run using the three schemes—3D‐AFD scheme, the 3D orographic anisotropy scheme for the eight‐direction (3D‐8x), and the 2D isotropic scheme (2D)—to compare their performance in CAS‐ESM 2.0. Sensitivity runs show that the 3D‐AFD provide more continuous transition of calculated drag as function of wind direction than the 3D‐8x, while the drag calculated using the 2D scheme show no variation with change of wind direction. Enhanced drag in the medium range and seasonal forecast using the updated CAS‐ESM alleviates part of the winter wind speed bias over the Tibetan Plateau (TP) and the cold bias over TP and the Siberian polar region. It is shown that the 3D‐AFD scheme alleviates more bias than that of the 3D‐8x scheme (by wind speed reduction of 1 ∼ 2 m/s and temperature of 1 ∼ 2 K) especially in the seasonal forecast. The results suggest that reasonable representation of the orographic anisotropy is important in climate modeling.

Xie, Jinbo↗
DOE OSTI2021

Implementation and Evaluation of a Unified Turbulence Parameterization Throughout the Canopy and Roughness Sublayer in Noah‐MP Snow Simulations

Abstract The Noah‐MP land surface model (LSM) relies on the Monin‐Obukhov (M‐O) Similarity Theory (MOST) to calculate land‐atmosphere exchanges of water, energy, and momentum fluxes. However, MOST flux‐profile relationships neglect canopy‐induced turbulence in the roughness sublayer (RSL) and parameterize within‐canopy turbulence in an ad hoc manner. We implement a new physics scheme (M‐O‐RSL) into Noah‐MP that explicitly parameterizes turbulence in RSL. We compare Noah‐MP simulations employing the M‐O‐RSL scheme (M‐O‐RSL simulations) and the default M‐O scheme (M‐O simulations) against observations obtained from 647 Snow Telemetry (SNOTEL) stations and two AmeriFlux stations in the western United States. M‐O‐RSL simulations of snow water equivalent (SWE) outperform M‐O simulations over 64% and 69% of SNOTEL sites in terms of root‐mean‐square‐error (RMSE) and correlation, respectively. The largest improvements in skill for M‐O‐RSL occur over closed shrubland sites, and the largest degradations in skill occur over deciduous broadleaf forest sites. Differences between M‐O and M‐O‐RSL simulated snowpack are primarily attributable to differences in aerodynamic conductance for heat underneath the canopy top, which modulates sensible heat flux. Differences between M‐O and M‐O‐RSL within‐canopy and below‐canopy sensible heat fluxes affect the amount of heat transported into snowpack and hence change snowmelt when temperatures are close to or above the melting point. The surface energy budget analysis over two AmeriFlux stations shows that differences between M‐O and M‐O‐RSL simulations can be smaller than other model biases (e.g., surface albedo). We intend for the M‐O‐RSL physics scheme to improve performance and uncertainty estimates in weather and hydrological applications that rely on Noah‐MP.

Meteorology & Atmospheric Sciences↗
DOE OSTI2025

Implementation and Evaluation of Physics-Driven Dynamic Entrainment-Mixing Parameterization in a Climate Model and Its Impact on Low-Cloud Simulation

The turbulent entrainment-mixing process in the Community Earth System Model version 1.2 (CESM1.2) is assumed to follow the extremely inhomogeneous entrainment-mixing. However, different entrainment-mixing scenarios can occur in real clouds. To address this deficiency, a unifying parameterization that represents different entrainment-mixing processes is implemented and evaluated in CESM1.2. The results indicate that the homogeneous mixing degree values simulated by the new parameterization in CESM1.2 are predominantly greater than 50%, suggesting a tendency toward homogeneous mixing. Compared to the extremely inhomogeneous mixing mechanism, the new parameterization increases the cloud droplet number concentration (Nc). More importantly, the new parameterization improves low-cloud fraction (CLDLOW) simulation in Northwest Pacific (NWP) and Southeast Pacific (SEP) regions, with relative improvements of 2.95% and 4.17%, respectively. Furthermore, the improvements reach up to 44.6% and 16.2% in the NWP and SEP regions, respectively, when considering the relationship between N c and CLDLOW. Further analysis reveals that the new parameterization enhances cloud optical depth, longwave radiative cooling effect, net condensation rate, cloud water mixing ratio, lower-troposphere stability, and CLDLOW by increasing N c . Additionally, these results underscore the importance of improving entrainment-mixing parameterization in climate models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Advancing Organized Convection Representation in the Unified Model: Implementing and Enhancing Multiscale Coherent Structure Parameterization

To address the effect of stratiform latent heating on meso- to large-scale circulations, an enhanced implementation of the Multiscale Coherent Structure Parameterization (MCSP) is developed for the Met Office Unified Model. MCSP represents the top-heavy stratiform latent heating from under-resolved organized convection in general circulation models. We couple the MCSP with a mass-flux convection scheme (CoMorph-A) to improve storm lifecycle continuity. The improved MCSP trigger is specifically designed for mixed-phase deep convective cloud, combined with a background vertical wind shear, both known to be crucial for stratiform development. We also test a cloud top temperature dependent convective-stratiform heating partitioning, in contrast to the earlier fixed partitioning. Assessments from ensemble weather forecasts and decadal simulations demonstrate that MCSP directly reduces cloud deepening and precipitation areas by moderating mesoscale circulations. Indirectly, it amends tropical precipitation biases, notably correcting dry and wet biases over India and the Indian Ocean, respectively. Remarkably, the scheme outperforms a climate model ensemble by improving seasonal precipitation cycle predictions in these regions. The scheme also improves Madden-Julian Oscillation (MJO) spectra, achieving better alignment with observational and reanalysis data by intensifying the simulated MJO over the Indian Ocean during phases 4 to 5. However, the scheme increases precipitation overestimation over the Western Pacific. Shifting from fixed to temperature-dependent convective-stratiform partitioning reduces the Pacific precipitation overestimation and further improves the seasonal cycle in India. Spatially correlated biases highlight the necessity for advances beyond deterministic approaches to align MCSP with environmental conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Implementation of Sub‐Grid Scale Temperature Perturbations Induced by Non‐Orographic Gravity Waves in WACCM6

Abstract Atmospheric gravity waves can play a significant role on atmospheric chemistry through temperature fluctuations. A recent modeling study introduced a method to implement subgrid‐scale orographic gravity‐wave‐induced temperature perturbations in the Whole Atmosphere Community Climate Model (WACCM). The model with a wave‐induced temperature parameterization was able to reproduce for example, the influence of mountain wave events on atmospheric chemistry, as highlighted in previous literature. Here we extend the subgrid‐scale wave‐induced temperature parameterization to also include non‐orographic gravity waves arising from frontal activity and convection. We explore the impact of these waves on middle atmosphere chemistry, particularly focusing on reactions that are strongly sensitive to temperature. The non‐orographic gravity waves increase the variability of chemical reaction rates, especially in the lower mesosphere. As an example, we show that this, in turn, leads to increases in the daytime ozone variability. To demonstrate another impact, we briefly investigate the role of non‐orographic gravity waves in cirrus cloud formation in this model. Consistent with findings from the previous study focusing on orographic gravity waves, non‐orographic waves also enhance homogeneous nucleation and increase cirrus clouds. The updated method used enables the global chemistry‐climate model to account for both orographic and non‐orographic gravity‐wave‐induced subgrid‐scale dynamical perturbations in a consistent manner.

Yook, Simchan [Department of Earth Atmospheric and↗
DOE OSTI2025

Implementation and Evaluation of Emission‐Driven Land‐Atmosphere Coupled Simulation in E3SMv2.1

Emissions-driven (prognostic CO 2 ) simulations are essential for representing two-way carbon-climate feedback in Earth System Models. We present an emissions-driven land–atmosphere coupled biogeochemistry (BGC) configuration (BGCLNDATM_progCO2) in version 2.1 of the Energy Exascale Earth System Model (E3SMv2.1). This is the first E3SM configuration that performs land-atmosphere emission-hindcasts. Here, we document its implementation, evaluate the model's performance against observations and other models, and propose a structured evaluation protocol for such emissions-driven simulations. We conducted transient historical simulations (1850–2014) with BGCLNDATM_progCO2 and compare them to reference simulations—a land-atmosphere coupled simulation without BGC and a standalone land simulation with BGC, both using prescribed CO 2 concentrations—and to observations. BGCLNDATM_progCO2 overestimates atmospheric CO 2 concentrations by 11–23 ppm yet stays within the 40-ppm spread CMIP6 emission-driven models and retains physical climate properties comparable to the reference runs. The CO 2 biases are partly attributed to underrepresented oceanic CO 2 uptake and inadequate representations of some terrestrial processes. In general, introducing prognostic CO 2 did not change physical climate metrics at the global scale but had larger regional effects, particularly over land where spatially heterogeneous CO 2 and prognostic leaf area index influenced surface energy balance. Finally, we propose a general evaluation protocol including spin-up assessment, atmospheric CO 2 benchmarking, physical climate evaluation, and land biogeochemical analysis to support scientific rigor and facilitate inter-model comparisons. The new configuration lays the groundwork for future enhancements, including improved terrestrial biogeochemical processes, integrated marine biogeochemistry, and additional human–Earth system interactions. These developments advance E3SM toward fully coupled emissions-driven simulations, enabling more accurate carbon–climate feedback projections and informing mitigation policy by providing physically consistent carbon-budget metrics for mitigation scenarios.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Numerical Water Tracers in the Atmospheric Component of the Energy Exascale Earth System Model: Implementation and Changes in Moisture Origin

Numerical water tracers are implemented in the Energy Exascale Earth System Model version 2. Simulations performed with the water‐tag‐enabled model for both pre‐industrial and future greenhouse gas concentrations reveal a marked increase in the role of mid‐latitude and southern subtropical regions as exporters of atmospheric moisture—to the extratropical upper troposphere and the tropical free troposphere. For the latter, the northward shift of the Intertropical Convergence Zone increases cross‐hemispheric transport of subtropical water vapor to the Northern Hemisphere. In the polar regions, most of the lower tropospheric moistening instead arises from increases in local evaporation. These findings illustrate the utility of the water tags, underscore critical changes in global hydrologic cycle, and provide insight into atmospheric dynamics under future climate scenarios. For applications when a global grid is desired, we additionally propose a novel statistical reconstruction, based on copula modeling, of the joint distribution of origin of water vapor, which reduces the number of tracers from order $\mathcal{O}\left({n}^{2}\right)$to order $\mathcal{O}(n)$, substantially ameliorating the considerable computational cost of water tracers. This statistical reconstruction is particularly beneficial to the interpretation of the relationship between latitude and longitude of origin of moisture over the tropical oceans and in the lower troposphere over land.

copula modeling↗
DOE OSTI2023

Decision making for implementing non-traditional water sources: a review of challenges and potential solutions

Abstract The effects of climate change, population growth, and future hydrologic uncertainties necessitate increased water conservation, new water resources, and a shift towards sustainable urban water supply portfolios. Diversifying water portfolios with non-traditional water sources can play a key role. Rooftop harvested rainwater (RHRW), atmospheric and condensate harvesting, stormwater, recycled wastewater and greywater, and desalinated seawater and brackish water are all currently utilized and rapidly emerging non-traditional water sources. This review explores the status and trends around these non-traditional water sources, and reviews approaches and models for prioritizing, predicting, and quantifying metrics of concern. The analysis presented here suggests that understanding the challenges of location specific scenarios, socioeconomic knowledge gaps, water supply technologies, and/or water management structure is the crucial first step in establishing a model or framework approach to provide a strategy for improvement going forward. The findings of this study also suggest that clear policy guidance and onsite maintenance is necessary for variable water quality concerns of non-traditional sources like harvested rainwater and greywater. In addition, use of stormwater or reuse of wastewater raises public health concerns due to unknown risks and pathogen levels, thus rapid monitoring technologies and transparent reporting systems can facilitate their adoption. Finally, cost structure of desalination varies significantly around the world, largely due to regulatory requirements and local policies. Further reduction of its capital cost and energy consumption is identified as a hurdle for implementation. Overall, models and process analyses highlight the strength of comparative assessments across scenarios and water supply options.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Implementation of FAIR principles in the IPCC: the WGI AR6 Atlas repository

The Sixth Assessment Report (AR6) of the Intergovernmental Panel on Climate Change (IPCC) has adopted the FAIR Guiding Principles. We present the Atlas chapter of Working Group I (WGI) as a test case. We describe the application of the FAIR principles in the Atlas, the challenges faced during its implementation, and those that remain for the future. We introduce the open source repository resulting from this process, including coding (e.g., annotated Jupyter notebooks), data provenance, and some aggregated datasets used in some figures in the Atlas chapter and its interactive companion (the Interactive Atlas), open to scrutiny by the scientific community and the general public. We describe the informal pilot review conducted on this repository to gather recommendations that led to significant improvements. Finally, a working example illustrates the re-use of the repository resources to produce customized regional information, extending the Interactive Atlas products and running the code interactively in a web browser using Jupyter notebooks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Implementation and analysis of quantum computing application to Higgs boson reconstruction at the large Hadron Collider

With the advent of the High-Luminosity Large Hadron Collider (HL-LHC) era, high energy physics (HEP) event selection will require new approaches to rapidly and accurately analyze vast databases. The current study addresses the enormity of HEP databases in an unprecedented manner—a quantum search using Grover’s Algorithm (GA) on an unsorted database, ATLAS Open Data, from the ATLAS detector. A novel method to identify rare events at 13 TeV in CERN’s LHC using quantum computing (QC) is presented. As indicated by the Higgs boson decay channel H→ZZ*→4l , the detection of four leptons in one event may be used to reconstruct the Higgs boson and, more importantly, evince Higgs boson decay to some new phenomena, such as H→ZZ d →4l . Searching the dataset for collisions resulting in detection of four leptons using a Jupyter Notebook, a classical simulation of GA, and several quantum computers with multiple qubits, the current application was found to make the proper selection in the unsorted dataset. Quantum search efficacy was analyzed for the incoming HL-LHC by implementing the QC method on multiple classical simulators and IBM’s quantum computers with the IBM Qiskit Open Source Software. The current QC application provides a novel, high-efficiency alternative to classical database searches, demonstrating its potential utility as a rapid and increasingly accurate search method in HEP.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Implementation of a Talbot–Lau x-ray deflectometer diagnostic platform for the OMEGA EP laser

A Talbot–Lau X-ray Deflectometer (TXD) was implemented in the OMEGA EP laser facility to characterize the evolution of an irradiated foil ablation front by mapping electron densities >10 22 cm -3 by means of Moiré deflectometry. The experiment used a short-pulse laser (30–100 J, 10 ps) and a foil copper target as an x-ray backlighter source. In the first experimental tests performed to benchmark the diagnostic platform, grating survival was demonstrated and x-ray backlighter laser parameters that deliver Moiré images were described. Finally, the necessary modifications to accurately probe the ablation front through TXD using the EP-TXD diagnostic platform are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2020

A pulsed-power implementation of “Laser Gate” for increasing laser energy coupling and fusion yield in magnetized liner inertial fusion (MagLIF)

Magnetized Liner Inertial Fusion (MagLIF) at Sandia National Laboratories involves a laser preheating stage,where a few-ns laser pulse passes through a few-micron-thick plastic window to preheat gaseous fusion fuel contained within the MagLIF target. Interactions with this window reduce heating e ciency and mix window and target materials into the fuel. A recently proposed idea called \Laser Gate" involves removing the window well before the preheating laser is applied. In this article, we introduce experimental proof-of-principle results for a pulsed-power implementation of Laser Gate, where a thin current-carrying wire weakens the perimeter of the window, allowing the fuel pressure to push the window open and away from the preheating laser path. For this e ort, transparent targets were fabricated and a test facility capable of studying this version of Laser Gate was developed. A 12-frame bright- eld laser schlieren/shadowgraphy imaging system captured the window opening dynamics on microsecond timescales. The images exhibit that the window remains largely intact as it opens and detaches from the target. A column of escaping pressurized gas appears to prevent the detached window from inadvertently moving into the preheating laser path.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Analytic evaluation of energy first derivatives for spin–orbit coupled-cluster singles and doubles augmented with noniterative triples method: General formulation and an implementation for first-order properties

The paper reports a formulation of analytic energy first derivatives for the coupled-cluster singles and doubles augmented with noniterative triples [CCSD(T)] method with spin–orbit coupling included at the orbital level and an implementation for evaluation of first-order properties. Here, the new development extends the applicability of relativistic coupled cluster methods for heavy-element chemistry and spectroscopy. Benchmark calculations of first-order properties including dipole moments and electric-field gradients using the corresponding exact two-component property integrals are presented for heavy-element containing molecules to demonstrate the usefulness of the present analytic scheme.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Equation-of-motion coupled-cluster method with double electron-attaching operators: Theory, implementation, and benchmarks

We report a production-level implementation of the equation-of-motion (EOM) coupled-cluster (CC) method with double electron-attaching (DEA) EOM operators of 2 p and 3 p 1 h types, EOM-DEA-CCSD. This ansatz, suitable for treating electronic structure patterns that can be described as two-electrons-in-many orbitals, represents a useful addition to the EOM-CC family of methods. We analyze the performance of EOM-DEA-CCSD for energy differences and molecular properties. By considering reduced quantities, such as state and transition one-particle density matrices, we compare EOM-DEA-CCSD wave functions with wave functions computed by other EOM-CCSD methods. The benchmarks illustrate that EOM-DEA-CCSD is capable of treating diradicals, bond-breaking, and some types of conical intersections.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Volumetric recombination in EMC3-EIRENE: Implementation and first application to the pre-fusion power operation phase in ITER

An upgrade to the 3D plasma boundary model EMC3-EIRENE for detached divertor plasmas is introduced and evaluated. Stabilization of the iterative approximation of a self-consistent plasma–neutral gas solution is required at low divertor plasma temperatures, and this has been achieved by linearization of the energy loss term associated with the electron–neutral gas interaction. An implicit method for volumetric recombination has been implemented, which improves agreement with SOLPS-ITER results for the pre-fusion power operation phase in ITER. Resonant magnetic perturbations for control of edge localized modes are found to result in a partially detached divertor plasma with a significantly broader reduction of particle loads in the traditional strike zone, which is attributed to volumetric recombination. The additional non-axisymmetric far scrape-off layer strike points, on the other hand, remain attached at relatively high temperature so that volumetric recombination is not effective there.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Toward implementing autonomous adaptive data acquisition for scanning hyperspectral imaging of biological systems

Autonomous experimentation is an emerging area of research, primarily related to autonomous vehicles, scientific combinatorial discovery approaches in materials science and drug discovery, and iterative research loops of planning, experimentation, and analysis. However, autonomous approaches developed in these contexts are difficult to apply to high-dimensional mapping technologies, such as scanning hyperspectral imaging of biological systems, due to sample complexity and heterogeneity. We briefly cover the history of adaptive sampling algorithms and surrogate modeling in order to define autonomous adaptive data acquisition as an objective-based, flexible building block for future biological imaging experimentation driven by intelligent infrastructure. We subsequently summarize the recent implementations of autonomous adaptive data acquisition (AADA) for scanning hyperspectral imaging, assess how these address the difficulties of autonomous approaches in hyperspectral imaging, and highlight the AADA design variation from a goal-oriented perspective. Finally, we present a modular AADA architecture that embeds AADA-driven flexible building blocks to address the challenge of time resolution for high-dimensional scanning hyperspectral imaging of nonequilibrium dynamical systems. In our example research-driven experimental design case, we propose an AADA infrastructure for time-resolved, noninvasive, and label-free scanning hyperspectral imaging of living biological systems. This AADA infrastructure can accurately target the correct state of the system for experimental workflows that utilize subsequent expensive, high-information-content analytical techniques.

59 BASIC BIOLOGICAL SCIENCES↗