7 research outputs found
Computational Physics on Graphics Processing Units
The use of graphics processing units for scientific computations is an
emerging strategy that can significantly speed up various different algorithms.
In this review, we discuss advances made in the field of computational physics,
focusing on classical molecular dynamics, and on quantum simulations for
electronic structure calculations using the density functional theory, wave
function techniques, and quantum field theory.Comment: Proceedings of the 11th International Conference, PARA 2012,
Helsinki, Finland, June 10-13, 201
UAV-Based Characterization of Tree-Attributes and Multispectral Indices in an Uneven-Aged Mixed Conifer-Broadleaf Forest
Unmanned aerial vehicles (UAVs) have contributed considerably to forest monitoring. However, gaps in the knowledge still remain, particularly for natural forests. Species diversity, stand heterogeneity, and the irregular spatial arrangement of trees provide unique opportunities to improve our perspective of forest stands and the ecological processes that occur therein. In this study, we calculated individual tree metrics, including several multispectral indices, in order to discern the spectral reflectance of a natural stand as a pioneer area in Mexican forests. Using data obtained by UAV DJI 4, and in the free software environments OpenDroneMap and QGIS, we calculated tree height, crown area, number of trees and multispectral indices. Digital photogrammetric procedures, such as the ForestTools, Structure from Motion and Multi-View Stereo algorithms, yielded results that improved stand mapping and the estimation of stand attributes. Automated tree detection and quantification were limited by the presence of overlapping crowns but compensated by the novel stand density mapping and estimates of crown attributes. Height estimation was in line with expectations (R2 = 0.91, RMSE = 0.36) and is therefore a useful parameter with which to complement forest inventories. The diverse spectral indices applied yielded differential results regarding the potential vegetation activity present and were found to be complementary to each other. However, seasonal monitoring and careful estimation of photosynthetic activity are recommended in order to determine the seasonality of plant response. This research contributes to the monitoring of natural forest stands and, coupled with accurate in situ measurements, could refine forest productivity parameters as a strategy for the validity of results. The metrics are reliable and rapid and could serve as model inputs in modern inventories. Nevertheless, increased efforts in the configuration of new technologies and algorithms are required, including full consideration of the costs implied by their adoption
UAV-Based Characterization of Tree-Attributes and Multispectral Indices in an Uneven-Aged Mixed Conifer-Broadleaf Forest
Unmanned aerial vehicles (UAVs) have contributed considerably to forest monitoring. However, gaps in the knowledge still remain, particularly for natural forests. Species diversity, stand heterogeneity, and the irregular spatial arrangement of trees provide unique opportunities to improve our perspective of forest stands and the ecological processes that occur therein. In this study, we calculated individual tree metrics, including several multispectral indices, in order to discern the spectral reflectance of a natural stand as a pioneer area in Mexican forests. Using data obtained by UAV DJI 4, and in the free software environments OpenDroneMap and QGIS, we calculated tree height, crown area, number of trees and multispectral indices. Digital photogrammetric procedures, such as the ForestTools, Structure from Motion and Multi-View Stereo algorithms, yielded results that improved stand mapping and the estimation of stand attributes. Automated tree detection and quantification were limited by the presence of overlapping crowns but compensated by the novel stand density mapping and estimates of crown attributes. Height estimation was in line with expectations (R2 = 0.91, RMSE = 0.36) and is therefore a useful parameter with which to complement forest inventories. The diverse spectral indices applied yielded differential results regarding the potential vegetation activity present and were found to be complementary to each other. However, seasonal monitoring and careful estimation of photosynthetic activity are recommended in order to determine the seasonality of plant response. This research contributes to the monitoring of natural forest stands and, coupled with accurate in situ measurements, could refine forest productivity parameters as a strategy for the validity of results. The metrics are reliable and rapid and could serve as model inputs in modern inventories. Nevertheless, increased efforts in the configuration of new technologies and algorithms are required, including full consideration of the costs implied by their adoption
Advances in free-energy-based simulations of protein folding and ligand binding
Free-energy-based simulations are increasingly providing the narratives about the structures, dynamics and biological mechanisms that constitute the fabric of protein science. Here, we review two recent successes. It is becoming practical: (i) to fold small proteins with free-energy methods without knowing substructures, and (ii) to compute ligand-protein binding affinities, not just their binding poses. Over the past 40 years, the timescales that can be simulated by atomistic MD are doubling every 1.3 years – which is faster than Moore's law. Thus, these advances are not simply due to the availability of faster computers. Force fields, solvation models and simulation methodology have kept pace with computing advancements, and are now quite good. At the tip of the spear recently are GPU-based computing, improved fast-solvation methods, continued advances in force fields, and conformational sampling methods that harness external information