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At least 613 records · Page 34

Fabricated ecosystem workshop: bridging laboratory to field science. Workshop report.

Lawrence Berkeley National Laboratory (Berkeley Lab) scientists held a workshop at the DOE BER Genomic Sciences PI meeting on the use of Fabricated Ecosystems in Washington D.C. on February 25th, 2020. Ecosystem fabrication is an approach to creating controlled microbial, soil and plant ecologies within a laboratory setting that enable discovery and dissection of environmental variables, activities, and interactions. At Berkeley Lab, we are developing two systems which span spatial and temporal scales — the EcoFAB and the EcoPOD. The participants of the workshop discussed the potential applications and challenges of using fabricated ecosystems as tools to tackle BER-relevant scientific questions. Specifically, they identified (1) research challenges that would benefit from ready access to this infrastructure (2) identified and prioritized technical challenges that currently limit these systems and (3) discussed how to use them to bridge the gap between lab and field research. To ensure that the fabricated ecosystems , in particular the larger-scale EcoPODs, are of use to as much of the BER community as possible, the workshop participants made the following recommendations: 1. Produce publicly available datasets for a set of control variables. Use for benchmarking, and assessing reproducibility between systems. 2. Implement data standards. 3. Develop/leverage nano/micro sensors and in situ root imaging. 4. Encourage the development of interdisciplinary teams to develop EcoPOD experiments. 5. Develop fabricated ecosystems with size and complexity that sits between the EcoFAB and EcoPOD to accelerate use and access.

42 ENGINEERING↗

Fast and accurate learned multiresolution dynamical downscaling for precipitation

Abstract. This study develops a neural-network-based approach for emulating high-resolution modeled precipitation data with comparable statistical properties but at greatly reduced computational cost. The key idea is to use combination of low- and high-resolution simulations (that differ not only in spatial resolution but also in geospatial patterns) to train a neural network to map from the former to the latter. Specifically, we define two types of CNNs, one that stacks variables directly and one that encodes each variable before stacking, and we train each CNN type both with a conventional loss function, such as mean square error (MSE), and with a conditional generative adversarial network (CGAN), for a total of four CNN variants. We compare the four new CNN-derived high-resolution precipitation results with precipitation generated from original high-resolution simulations, a bilinear interpolater and the state-of-the-art CNN-based super-resolution (SR) technique. Results show that the SR technique produces results similar to those of the bilinear interpolator with smoother spatial and temporal distributions and smaller data variabilities and extremes than the original high-resolution simulations. While the new CNNs trained by MSE generate better results over some regions than the interpolator and SR technique do, their predictions are still biased from the original high-resolution simulations. The CNNs trained by CGAN generate more realistic and physically reasonable results, better capturing not only data variability in time and space but also extremes such as intense and long-lasting storms. The new proposed CNN-based downscaling approach can downscale precipitation from 50 to 12 km in 14 min for 30 years once the network is trained (training takes 4 h using 1 GPU), while the conventional dynamical downscaling would take 1 month using 600 CPU cores to generate simulations at the resolution of 12 km over the contiguous United States.

54 ENVIRONMENTAL SCIENCES↗

Regional specialization in prefrontal cortex manifests in the reliability of task progression codes

The brain has the remarkable ability to guide the performance of complex tasks. Distinct prefrontal cortical areas make specific contributions to this ability, with the orbitofrontal cortex (OFC) critical for processing information related to trial outcomes and the dorsomedial prefrontal cortex (dmPFC) critical for sustained effort and selecting the right action at the right time. Yet, in both areas, neural activity represents both outcome- and action-related quantities. How similar neural representations support different functions remains unclear. Here, we compared OFC and dmPFC activity in rats performing a spatial alternation task. We show that, in contrast to other task-related variables, task progression is represented in both areas, but with distinct patterns of across-trial reliability that match each area’s previously documented functional specialization. Our results indicate that the engagement of reliable, task-phase-specific activity patterns differs across prefrontal regions in a manner well suited to engage different computations at different times.

Biological and medical sciences↗

Variable Ion Compositions of Solar Energetic Particle Events in the Inner Heliosphere: A Field Line Braiding Model with Compound Injections

We propose a model for interpreting highly variable ion composition ratios in solar energetic particle (SEP) events recently observed by the Parker Solar Probe (PSP) at 0.3–0.45 au. We use numerical simulations to calculate SEP propagation in a turbulent interplanetary magnetic field with a Kolmogorov power spectrum from large scales down to the gyration scale of energetic particles. We show that when the source regions of different species are offset by a distance comparable to the size of the source regions, the observed energetic particle composition He/H can be strongly variable over more than two orders of magnitude, even if the source ratio is at the nominal value. Assuming a 3 He/ 4 He source ratio of 10% in impulsive 3 He-rich events and the same spatial offset of the source regions, the 3 He/ 4 He ratio at observation sites also vary considerably. The variability of the ion composition ratios depends on the radial distance, which can be tested by observations made at different radial locations. We discuss the implications of these results on the variability of ion composition of impulsive events and on further PSP and Solar Orbiter observations close to the Sun.

79 ASTRONOMY AND ASTROPHYSICS↗

RAVIS: Resource Forecast and Ramp Visualization for Situational Awareness - An Introduction to the Open-Source Tool and Use Cases

The Resource Forecast and Ramp Visualization for Situational Awareness (RAVIS) is an open-source tool for visualizing variable renewable resource forecasts and ramp alerts for significant up/down ramps in renewable resource and the consequent net-load. The modular dashboard of RAVIS contains configurable panes for viewing- probabilistic time series forecasts, ramp event alerts on the look-ahead timeline, spatially resolved resource sites and forecasts, and system simulation and market clearing data such as transmission lines utilization, nodal prices and available generation flexibility. RAVIS uses a technology suite that is assembled to provide optimum visualization facility while maintaining a wide pool of potential deployment and client environments. The tool is designed to take advantage of web application technologies, open source visualization libraries and tooling. Utilizing this technology will enable deployment in any environment, using any operating system, and is scalable to much higher spatial and temporal scales of visualization. As a prototype of the tool and demonstrating a use case of variable renewable integration, RAVIS currently integrates site-specific solar power forecasts in the California Independent System Operator (CAISO) and Mid-continent ISO (MISO) footprint from the IBM WattSun forecasting platform, and also superimposes market simulation data for CAISO footprint from as in-house NREL market clearing tool. The tool has the ability to alert the viewer for excessive up or down ramps for both individual solar sites as well as regionally aggregated net-load ramps, and alerts can also be qualified with respect to available flexible generation. This report will provide an introduction to the RAVIS tool, and summarize the above mentioned capabilities, typical use cases and possible extensions of the tool. The RAVIS development team believes there are likely to be high economic and reliability benefits of integrating probabilistic forecasts of variable renewables into control center visualizations and improved ramp events situational awareness for system operators and forecasting teams in the ISOs and electric utilities in comparison with their business as usual practices.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

The Evolution of Accreting Binaries: From Brown Dwarfs to Supermassive Black Holes

Circumbinary accretion occurs throughout the universe, from the formation of stars and planets to the aftermath of major galactic mergers. We present an extensive investigation of circumbinary accretion disks, studying circular binaries with mass ratios (q ≡ M 2 /M 1 ) from 0.01 to 1 and at each mass ratio probing the effects of disk thickness and viscosity. We study disks with aspect ratios H/r $\in$ {0.1, 0.05, 0.03} and vary both the magnitude and spatial dependence of viscosity. Although thin accretion disks have previously been found to promote rapid inspirals of equal-mass binaries, we find that gravitational torques become weaker at lower mass ratios and most binaries with 0.01 ≤ q ≤ 0.04 outspiral, which may delay the coalescence of black hole binaries formed from minor mergers and cause high-mass exoplanets to migrate outward. However, in a number of cases, the disks accreting onto binaries with mass ratios ~0.07 fail to develop eccentric modes, leading to extremely rapid inspirals. Variability in black hole accretion correlates with disk eccentricity, and we observe variability above the ~10% level even for mass ratios of 0.01. We demonstrate that the spatial dependence of the viscosity (e.g., α vs. constant ν) significantly affects the degree of preferential accretion onto the secondary, resolving discrepancies between previous studies. Colder circumbinary disks remain eccentric even at q ~ 0.01 and sustain deep, asymmetric cavities.

79 ASTRONOMY AND ASTROPHYSICS↗

The Evolution of Accreting Binaries: From Brown Dwarfs to Supermassive Black Holes

Circumbinary accretion occurs throughout the universe, from the formation of stars and planets to the aftermath of major galactic mergers. We present an extensive investigation of circumbinary accretion disks, studying circular binaries with mass ratios (q ≡ M 2 /M 1 ) from 0.01 to 1 and at each mass ratio probing the effects of disk thickness and viscosity. We study disks with aspect ratios H/r ϵ {0.1, 0.05, 0.03} and vary both the magnitude and spatial dependence of viscosity. Although thin accretion disks have previously been found to promote rapid inspirals of equal-mass binaries, we find that gravitational torques become weaker at lower mass ratios and most binaries with 0.01 ≤ q ≤ 0.04 outspiral, which may delay the coalescence of black hole binaries formed from minor mergers and cause high-mass exoplanets to migrate outward. However, in a number of cases, the disks accreting onto binaries with mass ratios ~0.07 fail to develop eccentric modes, leading to extremely rapid inspirals. Variability in black hole accretion correlates with disk eccentricity, and we observe variability above the ~10% level even for mass ratios of 0.01. We demonstrate that the spatial dependence of the viscosity (e.g., α vs. constant ν) significantly affects the degree of preferential accretion onto the secondary, resolving discrepancies between previous studies. Colder circumbinary disks remain eccentric even at q ~ 0.01 and sustain deep, asymmetric cavities.

79 ASTRONOMY AND ASTROPHYSICS↗

Large Ensemble Particle Filter for Spatial Climate Reconstructions Using a Linear Inverse Model

Proxy records that document the last 2000 years of climate provide evidence for the wide range of the natural climate variability from inter-annual to secular timescales not captured by the short window of recent direct observations. Assessing climate models ability to reproduce such natural variations is crucial to understand climate sensitivity and impacts of future climate change. Paleoclimate data assimilation (PDA) offers a powerful way to extend the short instrumental period by optimally combining the physics described by General Circulation Climate Models (GCMs) with information from available proxy records while taking into account their uncertainties. Here we present a new PDA approach based on a sequential importance resampling (SIR) Particle filter (PF) that uses Linear Inverse Modeling (LIM) as an emulator of several CMIP-class GCMs. We examine in a perfect-model framework the skill of the various LIMs to forecast the dynamics of the surface temperatures and provide spatial field reconstructions over the last millennium in a SIR PF. Our results show that the LIMs allow for skillful ensemble forecasts at 1-year lead-time based on GCMs dynamical knowledge with best prediction in the tropics and the North Atlantic. The PDA further provides a set of physically consistent spatial fields allowing robust uncertainty quantification related to climate models biases and proxy spatial sampling. Our results indicate that the LIM yields dynamical memory improving climate variability reconstructions and support the use of the LIM as a GCM-emulator in real reconstruction to propagate large ensembles of particles at low cost in SIR PF.

54 ENVIRONMENTAL SCIENCES↗

Random strain induced correlations in materials with intertwined nematic and magnetic orders

Electronic nematicity is rarely observed as an isolated instability of a correlated electron system. Instead, in iron pnictides and in certain cuprates and heavy-fermion materials, nematicity is intertwined with an underlying spin-stripe or charge-stripe state. As a result, random strain, ubiquitous in any real crystal, creates both random-field disorder for the nematic degrees of freedom and random-bond disorder for the spin or charge ones. Here, we put forward an Ashkin-Teller model with random Baxter fields to capture the dual role of random strain in nematic systems for which nematicity is a composite order arising from a stripe state. Using Monte Carlo to simulate this random Baxter-field model, we find not only the expected break-up of the system into nematic domains, but also the emergence of nontrivial disorder-promoted magnetic correlations. Such correlations enhance and tie up the fluctuations associated with the two degenerate magnetic stripe states from which nematicity arises, leaving characteristic signatures in the spatial profile of the magnetic domains, in the configurational space of the spin variables, and in the magnetic noise spectrum. We discuss possible experimental manifestations of these effects in iron-pnictide superconductors. Furthermore, our work establishes the random Baxter-field model as a more complete alternative to the random-field Ising model to describe complex electronic nematic phenomena in the presence of disorder.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Global root traits (GRooT) database

Motivation: Trait data are fundamental to the quantitative description of plant form and function. Although root traits capture key dimensions related to plant responses to changing environmental conditions and effects on ecosystem processes, they have rarely been included in large-scale comparative studies and global models. For instance, root traits remain absent from nearly all studies that define the global spectrum of plant form and function. Thus, to overcome conceptual and methodological roadblocks preventing a widespread integration of root trait data into large-scale analyses we created the Global Root Trait (GRooT) Database. GRooT provides readyto- use data by combining the expertise of root ecologists with data mobilization and curation. Specifically, we (a) determined a set of core root traits relevant to the description of plant form and function based on an assessment by experts, (b) maximized species coverage through data standardization within and among traits, and (c) implemented data quality checks. Main types of variables contained: GRooT contains 114,222 trait records on 38 continuous root traits. Spatial location and grain: Global coverage with data from arid, continental, polar, temperate and tropical biomes. Data on root traits were derived from experimental studies and field studies. Time period and grain: Data were recorded between 1911 and 2019. Major taxa and level of measurement: GRooT includes root trait data for which taxonomic information is available. Trait records vary in their taxonomic resolution, with subspecies or varieties being the highest and genera the lowest taxonomic resolution available. It contains information for 184 subspecies or varieties, 6,214 species, 1,967 genera and 254 families. Owing to variation in data sources, trait records in the database include both individual observations and mean values. Software format: GRooT includes two csv files. A GitHub repository contains the csv files and a script in R to query the database.

59 BASIC BIOLOGICAL SCIENCES↗

3D Nanocrystallography and the Imperfect Molecular Lattice

Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatiotemporal evolution of melt ponds on Arctic sea ice

Melt ponds on sea ice play an important role in the Arctic climate system. Their presence alters the partitioning of solar radiation: decreasing reflection, increasing absorption and transmission to the ice and ocean, and enhancing melt. The spatiotemporal properties of melt ponds thus modify ice albedo feedbacks and the mass balance of Arctic sea ice. The Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition presented a valuable opportunity to investigate the seasonal evolution of melt ponds through a rich array of atmosphere-ice-ocean measurements across spatial and temporal scales. In this study, we characterize the seasonal behavior and variability in the snow, surface scattering layer, and melt ponds from spring melt to autumn freeze-up using in situ surveys and auxiliary observations. We compare the results to satellite retrievals and output from two models: the Community Earth System Model (CESM2) and the Marginal Ice Zone Modeling and Assimilation System (MIZMAS). During the melt season, the maximum pond coverage and depth were 21% and 22 ± 13 cm, respectively, with distribution and depth corresponding to surface roughness and ice thickness. Compared to observations, both models overestimate melt pond coverage in summer, with maximum values of approximately 41% (MIZMAS) and 51% (CESM2). This overestimation has important implications for accurately simulating albedo feedbacks. During the observed freeze-up, weather events, including rain on snow, caused high-frequency variability in snow depth, while pond coverage and depth remained relatively constant until continuous freezing ensued. Both models accurately simulate the abrupt cessation of melt ponds during freeze-up, but the dates of freeze-up differ. MIZMAS accurately simulates the observed date of freeze-up, while CESM2 simulates freeze-up one-to-two weeks earlier. This work demonstrates areas that warrant future observation-model synthesis for improving the representation of sea-ice processes and properties, which can aid accurate simulations of albedo feedbacks in a warming climate.

54 ENVIRONMENTAL SCIENCES↗

Quantifying and Understanding the Access Time to Dockless Micromobility: A Case Study in Washington, D.C.

Micromobility has been widely deployed in many cities. Similar as how access time/distance affects the travel demand to use public transit and informs transit system design, access time/distance to micromobility service measures its service efficiency and also serves as an equity indicator to inform city agencies from a regulation perspective. Though there is an increasing need to understand it, access to micromobility has not been sufficiently studied. This paper developed a framework to quantity the access time to dockless micromobility service (i.e., the minimum time needed to walk to reach the closest dockless micromobility vehicles). Based on the real-time vehicle location data collected from Washington, DC, this research quantified the access time to dockless micromobility, analyzed its spatial and temporal variation patterns and investigated its relationship with socio-demographic variables (i.e., population density, employment density and low-income population). The results revealed that the access time to dockless micromobility ranges between 0 to 4 minutes with the most frequently observed range of 0.5 to 1 minutes, and the city center area tends to have shorter access time than the outskirts areas. Results also indicate a quite stable access time level in DC with access time standard deviation of 0.2 to 0.5 minutes. After correlating the access time at census-block-group level with socio-demographic data, it was discovered that shorter access time usually aligns with larger population and employment density, and the proportion of low-income population was found not helpful with explaining the access time variation, which indicating a relatively equitable micromobility program.

access time↗

Evolution of microstructures in radiation fields using a coupled binary-collision Monte Carlo phase field approach

The simulation of radiation effects in materials broadly falls into two categories. At short time and length scales lies the modeling of primary radiation damage, such as point defect creation, energy deposition, and ballistic mixing. This is followed by the modeling at longer time scales of thermally activated microstructure evolution and defect reactions, such as recombination, clustering, and coarsening. The binary collision Monte Carlo method is an established, numerically efficient method for the computation of primary radiation damage. Conversely, the phase field method is a state of the art method for microstructure evolution on longer time and length scales. Here we present a concurrent coupling of these two methods, overcoming the difference between the discrete object Monte Carlo paradigm for primary radiation damage and the continuum field variable approach for microstructure evolution. The coupling is bidirectional, in which the microstructure evolution in the MOOSE finite element frame- work provides the spatial scattering data set for the charged particle trans- port and receives point defect, mass transport, and heat source terms from the simulated collision cascades that contribute to the field variable evolution. The concurrent coupling scheme is implemented in the code Magpie and demonstrated by investigating patterning for a model irradiated immiscible binary alloy. The results from the coupled binary collision Monte Carlo/phase field simulations reproduce the results of analytical models for phase separation, phase mixing, and patterning, supporting the approach and indicating its utility for modeling real materials systems.

36 MATERIALS SCIENCE↗

Modeling Spatial Asymmetries in Teleconnected Extreme Temperatures

Abstract Combining strengths from deep learning and extreme value theory can help describe complex relationships between variables where extreme events have significant impacts (e.g., environmental or financial applications). Neural networks learn complicated nonlinear relationships from large datasets under limited parametric assumptions. By definition, the number of occurrences of extreme events is small, which limits the ability of the data-hungry, nonparametric neural network to describe rare events. Inspired by recent extreme cold winter weather events in North America caused by atmospheric blocking, we examine several probabilistic generative models for the entire multivariate probability distribution of daily boreal winter surface air temperature. We propose metrics to measure spatial asymmetries, such as long-range anticorrelated patterns that commonly appear in temperature fields during blocking events. Compared to vine copulas, the statistical standard for multivariate copula modeling, deep learning methods show improved ability to reproduce complicated asymmetries in the spatial distribution of ERA5 temperature reanalysis, including the spatial extent of in-sample extreme events.

Krock, Mitchell L.↗

Formation of Linear Plasmonic Heterotrimers Using Nanoparticle Docking to DNA Origami Cages

The fabrication of complex assemblies with interesting collective properties from plasmonic nanoparticles (NPs) is often challenging. While DNA-directed self-assembly has emerged as one of the most promising approaches to forming such complex assemblies, the resulting structures tend to have large variability in gap sizes and shapes, as the DNA strands used to organize these particles are flexible, and the polydispersity of the NPs leads to variability in these critical structural features. Here, we use a new strategy termed docking to DNA origami cages (D-DOC) to organize spherical NPs into a linear heterotrimer with a precisely defined geometrical arrangement. Instead of binding NPs to the exterior of the DNA templates, D-DOC binds the NPs to either the interior or the opening of a 3D cage, which significantly reduces the variability of critical structural features by incorporating multiple diametrically arranged capture strands to tether NPs. Additionally, such a spatial arrangement of the capture strand can work synergistically with shape complementarity to achieve tighter confinement. To assemble NPs via D-DOC, we developed a multistep assembly process that first encapsulates an NP inside a cage and then binds two other NPs to the openings. Microscopic characterization shows low variability in the bond angles and gap sizes. Both UV–vis absorption and surface-enhanced Raman scattering (SERS) measurements showed strong plasmonic coupling that aligned with predictions by electrodynamic simulations, further confirming the precision of the assembly. These results suggest D-DOC could open new opportunities in biomolecular sensing, SERS and fluorescence spectroscopies, and energy harvesting through the self-assembly of NPs into more complex 3D assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Median Isn’t the Message: soil nutrient hot spots have a disproportionate influence on biogeochemical structure across years, seasons, and depths

Abstract Soil nutrient distribution is heterogeneous in space and time, potentially altering nutrient acquisition by trees and microorganisms. Ecologists have distinguished “hot spots” (HSs) as areas with enhanced and sustained rates of nutrient fluxes relative to the surrounding soil matrix. We evaluated the spatial and temporal patterns in nutrient flux HSs in two mixed-conifer forest soils by repeatedly sampling the soil solution at the same spatial locations (horizontally and vertically) over multiple seasons and years using ion exchange resins incubated in situ. The climate of these forests is Mediterranean, with intense fall rains occurring following summers with little precipitation, and highly variable winter snowfall. Hot spots formed most often for NO 3 − and Na + . Although nutrient HSs often occurred in the same spatial location multiple times, HSs persisted more often for PO 4 3− NH 4 + , and NO 3 − , and were more transient for Ca 2+ , Mg 2+ , and Na + . Sampling year (annual precipitation ranged from 558 to 1223 mm) impacted the occurrence of HSs for most nutrients, but season was only significant for PO 4 3− , NH 4 + , NO 3 − , and Na + , with HSs forming more often after fall rains than after spring snowmelt. The frequency of HSs significantly decreased with soil depth for all nutrients, forming most commonly immediately below the surficial organic horizon. Although HSs accounted for less than 17% of the sampling volume, they were responsible for 56–88% of PO 4 3− , NH 4 + , and NO 3 − resin fluxes. Our results suggest that macronutrient HSs have a disproportional contribution to soil biogeochemical structure, with implications for vegetation nutrient acquisition strategies and biogeochemical models. Graphical abstract

54 ENVIRONMENTAL SCIENCES↗

Downscaling atmospheric chemistry simulations with physically consistent deep learning

Abstract. Recent advances in deep convolutional neural network (CNN)-based super resolution can be used to downscale atmospheric chemistry simulations with substantially higher accuracy than conventional downscaling methods. This work both demonstrates the downscaling capabilities of modern CNN-based single image super resolution and video super-resolution schemes and develops modifications to these schemes to ensure they are appropriate for use with physical science data. The CNN-based video super-resolution schemes in particular incur only 39 % to 54 % of the grid-cell-level error of interpolation schemes and generate outputs with extremely realistic small-scale variability based on multiple perceptual quality metrics while performing a large (8×10) increase in resolution in the spatial dimensions. Methods are introduced to strictly enforce physical conservation laws within CNNs, perform large and asymmetric resolution changes between common model grid resolutions, account for non-uniform grid-cell areas, super-resolve lognormally distributed datasets, and leverage additional inputs such as high-resolution climatologies and model state variables. High-resolution chemistry simulations are critical for modeling regional air quality and for understanding future climate, and CNN-based downscaling has the potential to generate these high-resolution simulations and ensembles at a fraction of the computational cost.

54 ENVIRONMENTAL SCIENCES↗