Transforming Legacy Equation of State Databases into Interatomic Potentials via Machine Learning
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Presentation at LAMMPS workshop, content identical to recently submitted paper IR 1786384
This dataset contains data from a manipulative field study aimed at identifying critical thresholds for acute response of plants and ecosystems to water stress (TARP) that took place at Walker Branch Watershed in Oak Ridge, Tennessee from 2002-2005 (2002-06-20 to 2005-12-16). The study used understory tents for the removal of 100% of the growing-season throughfall and stem flow, to provide data on the impact of acute drought on mechanisms responsible for growth and mortality of deciduous forest canopy trees representative of common plant functional types (Liriodendron and Quercus). Through three years of manipulation (2003, 2004 and 2005; pretreatment measurements in 2002) various measures of tree response to surface moisture deficits were recorded including root and leaf traits, plant nonstructural carbohydrates status, hourly sapflow, basal area, and periodic observations of foliar photosynthesis and conductance. Additionally, environmental data such as air and soil temperature, soil water content, and soil matric potential were recorded. This dataset contains data 16 files in comma-separate (*.csv) format. Additional metadata are provided: 16 data dictionaries and a file-level metadata file in comma separate (*.csv) format and a user guide in PDF (*.pdf) format.
This data set reports tree growth measurements of mature Picea mariana and Larix laricina located in the S1-Bog permanent plots and the SPRUCE experimental study plots. Data have been collected annually from 2011 to 2024 (2011-02-23 to 2024-02-26) in late February/ early March to capture the productivity of the previous growing season (i.e. the February 2024 measurements track the 2023 growing season). Data collections are anticipated to continue through February of 2026 and this data set will be appended annually. Initial observations in 2011 included measurements of circumference at 1.3 m (diameter at breast height assessments; DBH) above the nominal bog hollow surface, tree heights and crown diameters. Subsequent annual measurements have focused on the measures of circumference at DBH. Supplemental tree height data collected via terrestrial lidar (Graham et al. 2019) were initiated in 2016 and have been maintained annually. Circumference measurements to the nearest 0.1 cm are converted to DBH in cm and basal area at DBH in (cm2). Tree height and crown diameter are measured to the nearest 0.1 m. This dataset contains one data file in comma separate (*.csv) format. User Note: In this Version 2, some previously released ‘Circum_Status’ values were updated to fix misread field measurements in previous years. The new data file, SPRUCE_Tree_Growth_Archive_20240620.csv, supersedes and replaces the previous, SPRUCE_Tree_Growth_Archive_20230327.csv.
This dataset contains empirical physiological, morphological, and chemical data collected on two dominant conifer species, Picea mariana and Larix laricina, between May 2016 and August 2017 at the SPRUCE (Spruce and Peatland Responses Under Changing Environments) experimental site within the Marcell Experimental Forest in northern Minnesota, USA. Analyses assessed the response of conifers to whole-ecosystem warming and elevated atmospheric carbon dioxide (CO2) concentrations. Measurements include light-saturated net photosynthesis and dark respiration at ambient atmospheric carbon dioxide (CO2) concentration (2016), CO2 response curves of light-saturated net photosynthesis (2017), leaf morphology (leaf mass per unit leaf area) and nitrogen content (on both mass and area basis). Leaf photosynthesis and respiration were measured with portable photosynthesis systems (LI6400XT, LI6800, LI-COR Biosciences, USA). In 2016, photosynthesis and respiration were measured at a common temperature of 25 ˚C to assess thermal acclimation, and at growth temperatures (for each of the five treatment temperatures) to assess field performance. In 2017, CO2 response curves of net photosynthesis (so-called A-Ci curves) were conducted at different leaf temperatures (15, 25, 32.5, 40 and 45 ˚C) for assessment of biochemical parameters and their temperature sensitivity. In addition, dark respiration measurements at different leaf temperatures (10, 15, 20, 25, 30, 35, 40, and 45 ºC) were also taken. This dataset contains one data file in comma-separate values (*.csv) and Microsoft Excel (*.xlsx) format. Additional metadata are provided: a data dictionary and a file-level metadata file in comma-separate values (.csv) format and a user guide in PDF (*.pdf) format.
This data set contains the geographic coordinates of the GWAS population described in Tuskan et. al, 2011 and Evans, et. al, 2014. These genotypes have been used in numerous experiments since then, and have been propogated in common gardens. The most recent common garden geo referenced dataset for Davis, California is also available.
A 6-year study in Sumter Co., SC, to determine crown and leaf attributes, supplemental water and fertilization effects on dry weight productivity, and clonal variation accounts in biomass traits. Eight commercially available clones -- ‘ST148’, ‘S2C20’, ‘3167’, ‘ST72’ ‘20WV’, ‘S7C1’, ‘ST70’, and ‘S7C15’, were studied. Drip irrigation rates were used to maintain soil tension of 33 kPa at 15% volumetric soil moisture or 1500 kPa at 10%. Application of macro- and micronutrients occurred via drip irrigation at a high and low rate. The high rate included an initial application of 85 kg elemental nitrogen ha-1, which increased to 182 kg ha-1 at age 3, which then was reduced to 135 kg ha-1 for remainder of the study. The low treatment received 50% (w/v) of the high treatment. Individual tree measurements across time are provided in this dataset.
We report intrinsic photoconductivity studies on one of the least examined layered compounds, ZrS 2 .Few-atomic layer ZrS 2 field-effect transistors were fabricated on the Si/SiO 2 substrate and photoconductivity measurements were performed using both two- and four-terminal configurations under the illumination of 532 nm laser source. We measured photocurrent as a function of the incident optical power at several source-drain (bias) voltages. We observe a significantly large photoconductivity when measured in the multiterminal (four-terminal) configuration compared to that in the two-terminal configuration. For an incident optical power of 90 nW, the estimated photosensitivity and the external quantum efficiency (EQE) measured in two-terminal configuration are 0.5 A/W and 120%, respectively, under a bias voltage of 650 mV. Under the same conditions, the four-terminal measurements result in much higher values for both the photoresponsivity (R) and EQE to 6 A/W and 1400%, respectively. This significant improvement in photoresponsivity and EQE in the four-terminal configuration may have been influenced by the reduction of contact resistance at the metal-semiconductor interface, which greatly impacts the carrier mobility of low conducting materials. This suggests that photoconductivity measurements performed through the two-terminal configuration in previous studies on ZrS 2 and other 2D materials have severely underestimated the true intrinsic properties of transition metal dichalcogenides and their remarkable potential for optoelectronic applications.
Silicon is considered as a promising anode material for the next-generation lithium-ion battery (LIB) due to its high capacity at nanoscale. However, silicon expands up to 300% during lithiation, which induces high stresses and leads to fractures. To design silicon nanostructures that could minimize fracture, it is important to understand and characterize stress states in the silicon nanostructures during lithiation. Synchrotron X-ray microdiffraction has proven to be effective in revealing insights of mechanical stress and other mechanics considerations in small-scale crystalline structures used in many important technological applications, such as microelectronics, nanotechnology, and energy systems. In the present study, an in situ synchrotron X-ray microdiffraction experiment was conducted to elucidate the mechanical stress states during the first electrochemical cycle of lithiation in single-crystalline silicon nanowires (SiNWs) in an LIB test cell. Morphological changes in the SiNWs at different levels of lithiation were also studied using scanning electron microscope (SEM). It was found from SEM observation that lithiation commenced predominantly at the top surface of SiNWs followed by further progression toward the bottom of the SiNWs gradually. The hydrostatic stress of the crystalline core of the SiNWs at different levels of electrochemical lithiation was determined using the in situ synchrotron X-ray microdiffraction technique. We found that the crystalline core of the SiNWs became highly compressive (up to -325.5 MPa) once lithiation started. In conclusion, this finding helps unravel insights about mechanical stress states in the SiNWs during the electrochemical lithiation, which could potentially pave the path toward the fracture-free design of silicon nanostructure anode materials in the next-generation LIB.
Spatial heterogeneity in methane (CH 4 ) flux requires a reliable upscaling approach to reach accurate regional CH 4 budgets in the Arctic tundra. In this study, we combined the CLM-Microbe model with three footprint algorithms to scale up CH 4 flux from a plot level to eddy covariance (EC) tower domains (200 m × 200 m) in the Alaska North Slope, for three sites in Utqiaġvik (US-Beo, US-Bes, and US-Brw), one in Atqasuk (US-Atq) and one in Ivotuk (US-Ivo), for a period of 2013–2015. Three footprint algorithms were the homogenous footprint (HF) that assumes even contribution of all grid cells, the gradient footprint (GF) that assumes gradually declining contribution from center grid cells to edges, and the dynamic footprint (DF) that considers the impacts of wind and heterogeneity of land surface. Simulated annual CH 4 flux was highly consistent with the EC measurements at US-Beo and US-Bes. In contrast, flux was overestimated at US-Brw, US-Atq, and US-Ivo due to the higher simulated CH 4 flux in early growing seasons. The simulated monthly CH 4 flux was consistent with EC measurements but with different accuracies among footprint algorithms. At US-Bes in September 2013, RMSE and NNSE were 0.002 μmol m −2 s −1 and 0.782 using the DF algorithm, but 0.007 μmol m −2 s −1 and 0.758 using HF and 0.007 μmol m −2 s −1 and 0.765 using GF, respectively. DF algorithm performed better than the HF and GF algorithms in capturing the temporal variation in daily CH 4 flux each month, while the model accuracy was similar among the three algorithms due to flat landscapes. Temporal variations in CH 4 flux during 2013–2015 were predominately explained by air temperature (67–74%), followed by precipitation (22–36%). Spatial heterogeneities in vegetation fraction and elevation dominated the spatial variations in CH 4 flux for all five tower domains despite relatively weak differences in simulated CH 4 flux among three footprint algorithms. The CLM-Microbe model can simulate CH 4 flux at both plot and landscape scales at a high temporal resolution, which should be applied to other landscapes. Integrating land surface models with an appropriate algorithm provides a powerful tool for upscaling CH 4 flux in terrestrial ecosystems.
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Microbial decomposition of soil organic carbon (SOC) in the thawing Arctic permafrost is one of the most important, but poorly understood, processes in determining the greenhouse gases feedback of tundra ecosystems to climate. Here in this paper, we examine changes in microbial community structure during an anoxic incubation at either –2 or 8 °C for up to 122 days using both an organic and a mineral soil collected from the Barrow Environmental Observatory in northern Alaska, USA. Soils were characterized for SOC chemistry, and GeoChips were used to determine microbial community structure and functional genes associated with C degradation and Fe(III) reduction. We observed notable decreases in functional gene diversity (at P < 0.05) in response to warming at 8 °C, particularly in the organic soil. A number of genes associated with SOC degradation, fermentation, methanogenesis, and iron cycling decreased significantly (P < 0.05) after 122 days of incubation, which coincided well with decreasing labile SOC content, soil respiration, methane production, and iron reduction. The soil type (i.e., organic vs. mineral) and the availability of labile SOC were among the most significant environmental factors impacting the functional community structure. In contrast, the functional structure was largely unchanged in the –2 °C incubation due to low microbial activity resulting in less competition or exclusion. These results demonstrate the vulnerability of SOC in Arctic tundra to warming, facilitated by iron reduction and methanogenesis, and the importance of microbial communities in moderating such vulnerability.
Warming temperatures in continuous permafrost zones of the Arctic will alter both hydrological and geochemical soil conditions, which are strongly linked with heterotrophic microbial carbon (C) cycling. Heterogeneous permafrost landscapes are often dominated by polygonal features formed by expanding ice wedges: water accumulates in low centered polygons (LCPs), and water drains outward to surrounding troughs in high centered polygons (HCPs). These geospatial differences in hydrology cause gradients in biogeochemistry, soil C storage potential, and thermal properties. Presently, data quantifying carbon dioxide (CO 2 ) and methane (CH 4 ) release from HCP soils are needed to support modeling and evaluation of warming-induced CO 2 and CH 4 fluxes from tundra soils. This study quantifies the distribution of microbial CO 2 and CH 4 release in HCPs over a range of temperatures and draws comparisons to previous LCP studies. Arctic tundra soils were initially characterized for geochemical and hydraulic properties. Laboratory incubations at −2, +4, and +8°C were used to quantify temporal trends in CO 2 and CH 4 production from homogenized active layer organic and mineral soils in HCP centers and troughs, and methanogen abundance was estimated from mcrA gene measurements. Results showed that soil water availability, organic C, and redox conditions influence temporal dynamics and magnitude of gas production from HCP active layer soils during warming. At early incubation times (2–9 days), higher CO 2 emissions were observed from HCP trough soils than from HCP center soils, but increased CO 2 production occurred in center soils at later times (>20 days). HCP center soils did not support methanogenesis, but CH 4 -producing trough soils did indicate methanogen presence. Consistent with previous LCP studies, HCP organic soils showed increased CO 2 and CH 4 production with elevated water content, but HCP trough mineral soils produced more CH 4 than LCP mineral soils. HCP mineral soils also released substantial CO 2 but did not show a strong trend in CO 2 and CH 4 release with water content. Knowledge of temporal and spatial variability in microbial C mineralization rates of Arctic soils in response to warming are key to constraining uncertainties in predictive climate models.
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The high energy densities deposited in materials by focused X-ray laser pulses generate shock waves which travel away from the irradiated region, and can generate complex wave patterns or induce phase changes. We determined the time-pressure histories of shocks induced by X-ray laser pulses in liquid water microdrops, by measuring the surface velocity of the microdrops from images recorded during the reflection of the shock at the surface. Measurements were made with ~30 µm diameter droplets using 10 keV X-rays, for X-ray pulse energies that deposited linear energy densities from 3.5 to 120 mJ/m; measurements were also made with ~60 µm diameter drops for a narrower energy range. At a distance of 15 µm from the X-ray beam, the peak shock pressures ranged from 44 to 472 MPa, and the corresponding time-pressure histories of the shocks had a fast quasi-exponential decay with positive pressure durations estimated to range from 2 to 5 ns. Knowledge of the amplitude and waveform of the shock waves enables accurate modeling of shock propagation and experiment designs that either maximize or minimize the effect of shocks.
Transfer of graphene, grown by chemical vapor deposition (CVD), to a substrate of choice, typically involves the deposition of a polymeric layer (for example, poly(methyl methacrylate) (PMMA), or polydimethylsiloxane, PDMS). These polymers are quite hard to remove without leaving some residues behind. One method to improve the graphene transfer is to coat the graphene with a thin protective oxide layer, followed by the deposition of a very thin polymer layer on top of the oxide layer (much thinner than the usual thickness), followed by a more aggressive polymeric removal method, thus leaving the graphene intact. At the same time, having an oxide layer on graphene may serve applications, such as channeled transistors or sensing devices. Here, we study the transfer of graphene with a protective thin oxide layer grown by atomic layer deposition (ALD). We follow the transfer process from the graphene growth stage through oxide deposition until completion. We report on the nucleation growth process of oxides on graphene, their resultant strain and their optical transmission.
Serial femtosecond crystallography (SFX) data were recorded at the European X-ray free-electron laser facility (EuXFEL) with protein microcrystals delivered via a microscopic liquid jet. An XFEL beam striking such a jet may launch supersonic shock waves up the jet, compromising the oncoming sample. To investigate this efficiently, we employed a novel XFEL pulse pattern to nominally expose the sample to between zero and four shock waves before being probed. Analyzing hit rate, indexing rate, and resolution for diffraction data recorded at MHz pulse rates, we found no evidence of damage. Notably, however, this conclusion could only be drawn after careful identification and assimilation of numerous interrelated experimental factors, which we describe in detail. Failure to do so would have led to an erroneous conclusion. Femtosecond photography of the sample-carrying jet revealed critically different jet behavior from that of all homogeneous liquid jets studied to date in this manner.