| 1. |
- Aquila, A., et al.
(författare)
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The linac coherent light source single particle imaging road map
- 2015
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Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 2:4
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Tidskriftsartikel (refereegranskat)abstract
- Intense femtosecond x-ray pulses from free-electron laser sources allow the imag-ing of individual particles in a single shot. Early experiments at the Linac CoherentLight Source (LCLS) have led to rapid progress in the field and, so far, coherentdiffractive images have been recorded from biological specimens, aerosols, andquantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLSheld a workshop to discuss the scientific and technical challenges for reaching theultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap towardreaching atomic resolution, 3D imaging at free-electron laser sources.
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| 2. |
- Metzger, Christine, et al.
(författare)
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CO2 fluxes and ecosystem dynamics at five European treeless peatlands - merging data and process oriented modeling
- 2015
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 12:1, s. 125-146
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Tidskriftsartikel (refereegranskat)abstract
- The carbon dioxide (CO2) exchange of five different peatland systems across Europe with a wide gradient in land use intensity, water table depth, soil fertility and climate was simulated with the process oriented CoupModel. The aim of the study was to find out whether CO2 fluxes, measured at different sites, can be explained by common processes and parameters or to what extend a site specific configuration is needed. The model was calibrated to fit measured CO2 fluxes, soil temperature, snow depth and leaf area index (LAI) and resulting differences in model parameters were analyzed. Finding site independent model parameters would mean that differences in the measured fluxes could be explained solely by model input data: water table, meteorological data, management and soil inventory data. Seasonal variability in the major fluxes was well captured, when a site independent configuration was utilized for most of the parameters. Parameters that differed between sites included the rate of soil organic decomposition, photosynthetic efficiency, and regulation of the mobile carbon (C) pool from senescence to shooting in the next year. The largest difference between sites was the rate coefficient for heterotrophic respiration. Setting it to a common value would lead to underestimation of mean total respiration by a factor of 2.8 up to an overestimation by a factor of 4. Despite testing a wide range of different responses to soil water and temperature, rate coefficients for heterotrophic respiration were consistently the lowest on formerly drained sites and the highest on the managed sites. Substrate decomposability, pH and vegetation characteristics are possible explanations for the differences in decomposition rates. Specific parameter values for the timing of plant shooting and senescence, the photosynthesis response to temperature, litter fall and plant respiration rates, leaf morphology and allocation fractions of new assimilates, were not needed, even though the gradient in site latitude ranged from 48 degrees N (southern Germany) to 68 degrees N (northern Finland) differed largely in their vegetation. This was also true for common parameters defining the moisture and temperature response for decomposition, leading to the conclusion that a site specific interpretation of these processes is not necessary. In contrast, the rate of soil organic decomposition, photosynthetic efficiency, and the regulation of the mobile carbon pool need to be estimated from available information on specific soil conditions, vegetation and management of the ecosystems, to be able to describe CO2 fluxes under different conditions.
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| 3. |
- Parkinson, Dilworth Y., et al.
(författare)
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Real-Time Data-Intensive Computing
- 2016
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Ingår i: Proceedings Of The 12Th International Conference On Synchrotron Radiation Instrumentation (SRI2015). - : Author(s). - 9780735413986
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Konferensbidrag (refereegranskat)abstract
- Today users visit synchrotrons as sources of understanding and discovery-not as sources of just light, and not as sources of data. To achieve this, the synchrotron facilities frequently provide not just light but often the entire end station and increasingly, advanced computational facilities that can reduce terabytes of data into a form that can reveal a new key insight. The Advanced Light Source (ALS) has partnered with high performance computing, fast networking, and applied mathematics groups to create a "super-facility", giving users simultaneous access to the experimental, computational, and algorithmic resources to make this possible. This combination forms an efficient closed loop, where data-despite its high rate and volume-is transferred and processed immediately and automatically on appropriate computing resources, and results are extracted, visualized, and presented to users or to the experimental control system, both to provide immediate insight and to guide decisions about subsequent experiments during beamtime. We will describe our work at the ALS ptychography, scattering, micro-diffraction, and micro-tomography beamlines.
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| 4. |
- Chadburn, Sarah E., et al.
(författare)
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Carbon stocks and fluxes in the high latitudes : using site-level data to evaluate Earth system models
- 2017
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Ingår i: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 14:22, s. 5143-5169
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Tidskriftsartikel (refereegranskat)abstract
- It is important that climate models can accurately simulate the terrestrial carbon cycle in the Arctic due to the large and potentially labile carbon stocks found in permafrost-affected environments, which can lead to a positive climate feedback, along with the possibility of future carbon sinks from northward expansion of vegetation under climate warming. Here we evaluate the simulation of tundra carbon stocks and fluxes in three land surface schemes that each form part of major Earth system models (JSBACH, Germany; JULES, UK; ORCHIDEE, France). We use a site-level approach in which comprehensive, high-frequency datasets allow us to disentangle the importance of different processes. The models have improved physical permafrost processes and there is a reasonable correspondence between the simulated and measured physical variables, including soil temperature, soil moisture and snow. We show that if the models simulate the correct leaf area index (LAI), the standard C3 photosynthesis schemes produce the correct order of magnitude of carbon fluxes. Therefore, simulating the correct LAI is one of the first priorities. LAI depends quite strongly on climatic variables alone, as we see by the fact that the dynamic vegetation model can simulate most of the differences in LAI between sites, based almost entirely on climate inputs. However, we also identify an influence from nutrient limitation as the LAI becomes too large at some of the more nutrient-limited sites. We conclude that including moss as well as vascular plants is of primary importance to the carbon budget, as moss contributes a large fraction to the seasonal CO2 flux in nutrient-limited conditions. Moss photosynthetic activity can be strongly influenced by the moisture content of moss, and the carbon uptake can be significantly different from vascular plants with a similar LAI. The soil carbon stocks depend strongly on the rate of input of carbon from the vegetation to the soil, and our analysis suggests that an improved simulation of photosynthesis would also lead to an improved simulation of soil carbon stocks. However, the stocks are also influenced by soil carbon burial (e.g. through cryoturbation) and the rate of heterotrophic respiration, which depends on the soil physical state. More detailed below-ground measurements are needed to fully evaluate biological and physical soil processes. Furthermore, even if these processes are well modelled, the soil carbon profiles cannot resemble peat layers as peat accumulation processes are not represented in the models. Thus, we identify three priority areas for model development: (1) dynamic vegetation including (a) climate and (b) nutrient limitation effects; (2) adding moss as a plant functional type; and an (3) improved vertical profile of soil carbon including peat processes.
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| 5. |
- Daurer, Benedikt J., et al.
(författare)
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Nanosurveyor : a framework for real-time data processing
- 2017
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Ingår i: Advanced Structural and Chemical Imaging. - : Springer Science and Business Media LLC. - 2198-0926. ; 3:7
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Tidskriftsartikel (refereegranskat)abstract
- Background: The ever improving brightness of accelerator based sources is enabling novel observations and discov-eries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality.Results: Here we present an integrated software/algorithmic framework designed to capitalize on high-throughput experiments through efficient kernels, load-balanced workflows, which are scalable in design. We describe the streamlined processing pipeline of ptychography data analysis.Conclusions: The pipeline provides throughput, compression, and resolution as well as rapid feedback to the micro-scope operators
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| 6. |
- Marchesini, Stefano, et al.
(författare)
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SHARP : a distributed GPU-based ptychographic solver
- 2016
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Ingår i: Journal of applied crystallography. - 0021-8898 .- 1600-5767. ; 49, s. 1245-1252
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Tidskriftsartikel (refereegranskat)abstract
- Ever brighter light sources, fast parallel detectors and advances in phase retrieval methods have made ptychography a practical and popular imaging technique. Compared to previous techniques, ptychography provides superior robustness and resolution at the expense of more advanced and time-consuming data analysis. By taking advantage of massively parallel architectures, high-throughput processing can expedite this analysis and provide microscopists with immediate feedback. These advances allow real-time imaging at wavelength-limited resolution, coupled with a large field of view. This article describes a set of algorithmic and computational methodologies used at the Advanced Light Source and US Department of Energy light sources. These are packaged as a CUDA-based software environment named SHARP (http://camera.lbl.gov/sharp), aimed at providing state-of-the-art high-throughput ptychography reconstructions for the coming era of diffraction-limited light sources.
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| 7. |
- Peltola, O., et al.
(författare)
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Studying the spatial variability of methane flux with five eddy covariance towers of varying height
- 2015
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Ingår i: Agricultural and Forest Meteorology. - : Elsevier BV. - 1873-2240 .- 0168-1923. ; 214, s. 456-472
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Tidskriftsartikel (refereegranskat)abstract
- In this study, the spatial representativeness of eddy covariance (EC) methane (CH4) measurements was examined by comparing parallel CH4 fluxes from three short (6 m) towers separated by a few kilometres and from two higher levels (20 m and 60 m) at one location. The measurement campaign was held on an intensively managed grassland on peat soil in the Netherlands. The land use and land cover types are to a large degree homogeneous in the area. The CH4 fluxes exhibited significant variability between the sites on 30-min scale. The spatial coefficient of variation (CVspa) between the three short towers was 56% and it was of similar magnitude as the temporal variability, unlike for the other fluxes (friction velocity, sensible heat flux) for which the temporal variability was considerably larger than the spatial variability. The CVspa decreased with temporal averaging, although less than what could be expected for a purely random process (1/root N), and it was 14% for 26-day means of CH4 flux. This reflects the underlying heterogeneity of CH4 flux in the studied landscape at spatial scales ranging from 1 ha (flux footprint) to 10 km(2) (area bounded by the short towers). This heterogeneity should be taken into account when interpreting and comparing EC measurements. On an annual scale, the flux spatial variability contributed up to 50% of the uncertainty in CH4 emissions. It was further tested whether EC flux measurements at higher levels could be used to acquire a more accurate estimate of the spatially integrated CH4 emissions. Contrarily to what was expected, flux intensity was found to both increase and decrease depending on measurement height. Using footprint modelling, 56% of the variation between 6 m and 60 m CH4 fluxes was attributed to emissions from local anthropogenic hotspots (farms). Furthermore, morning hours proved to be demanding for the tall tower EC where fluxes at 60 m were up to four-fold those at lower heights. These differences were connected with the onset of convective mixing during the morning period. (C) 2015 The Authors. Published by Elsevier B.V.
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