High-throughput molecular dynamics (MD) simulations are a computational method consisting of using multiple short trajectories, instead of few long ones, to cover slow biological time scales. ...Compared to long trajectories this method offers the possibility to start the simulations in successive batches, building a knowledgeable model of the available data to inform subsequent new simulations iteratively. Here, we demonstrate an automatic, iterative, on-the-fly method for learning and sampling molecular simulations in the context of ligand binding for the case of trypsin–benzamidine binding. The method uses Markov state models to learn a simplified model of the simulations and decide where best to sample from, achieving a converged binding affinity in approximately one microsecond, 1 order of magnitude faster than classical sampling. This method demonstrates for the first time the potential of adaptive sampling schemes in the case of ligand binding.
Wildfire can lead to considerable hydrological and geomorphological change, both directly by weathering bedrock surfaces and changing soil structure and properties, and indirectly through the effects ...of changes to the soil and vegetation on hydrological and geomorphological processes. This review summarizes current knowledge and identifies research gaps focusing particularly on the contribution of research from the Mediterranean Basin, Australia and South Africa over the last two decades or so to the state of knowledge mostly built on research carried out in the USA.
Wildfire-induced weathering rates have been reported to be high relative to other weathering processes in fire-prone terrain, possibly as much as one or two magnitudes higher than frost action, with important implications for cosmogenic-isotope dating of the length of rock exposure. Wildfire impacts on soil properties have been a major focus of interest over the last two decades. Fire usually reduces soil aggregate stability and can induce, enhance or destroy soil water repellency depending on the temperature reached and its duration. These changes have implications for infiltration, overland flow and rainsplash detachment. A large proportion of publications concerned with fire impacts have focused on post-fire soil erosion by water, particularly at small scales. These have shown elevated, sometimes extremely large post-fire losses before geomorphological stability is re-established. Soil losses per unit area are generally negatively related to measurement scale reflecting increased opportunities for sediment storage at larger scales. Over the last 20 years, there has been much improvement in the understanding of the forms, causes and timing of debris flow and landslide activity on burnt terrain. Advances in previously largely unreported processes (e.g. bio-transfer of sediment and wind erosion) have also been made.
Post-fire hydrological effects have generally also been studied at small rather than large scales, with soil water repellency effects on infiltration and overland flow being a particular focus. At catchment scales, post-fire accentuated peakflow has received more attention than changes in total flow, reflecting easier measurement and the greater hazard posed by the former. Post-fire changes to stream channels occur over both short and long terms with complex feedback mechanisms, though research to date has been limited.
Research gaps identified include the need to: (1) develop a fire severity index relevant to soil changes rather than to degree of biomass destruction; (2) isolate the hydrological and geomorphological impacts of fire-induced soil water repellency changes from other important post-fire changes (e.g. litter and vegetation destruction); (3) improve knowledge of the hydrological and geomorphological impacts of wildfire in a wider range of fire-prone terrain types; (4) solve important problems in the determination and analysis of hillslope and catchment sediment yields including poor knowledge about soil losses other than at small spatial and short temporal scales, the lack of a clear measure of the degradational significance of post-fire soil losses, and confusion arising from errors in and lack of scale context for many quoted post-fire soil erosion rates; and (5) increase the research effort into past and potential future hydrological and geomorphological changes resulting from wildfire.
An important step in structure-based drug design consists in the prediction of druggable binding sites. Several algorithms for detecting binding cavities, those likely to bind to a small drug ...compound, have been developed over the years by clever exploitation of geometric, chemical and evolutionary features of the protein.
Here we present a novel knowledge-based approach that uses state-of-the-art convolutional neural networks, where the algorithm is learned by examples. In total, 7622 proteins from the scPDB database of binding sites have been evaluated using both a distance and a volumetric overlap approach. Our machine-learning based method demonstrates superior performance to two other competitive algorithmic strategies.
DeepSite is freely available at www.playmolecule.org. Users can submit either a PDB ID or PDB file for pocket detection to our NVIDIA GPU-equipped servers through a WebGL graphical interface.
gianni.defabritiis@upf.edu.
Supplementary data are available at Bioinformatics online.
Recent advances in molecular simulations have allowed scientists to investigate slower biological processes than ever before. Together with these advances came an explosion of data that has ...transformed a traditionally computing-bound into a data-bound problem. Here, we present HTMD, a programmable, extensible platform written in Python that aims to solve the data generation and analysis problem as well as increase reproducibility by providing a complete workspace for simulation-based discovery. So far, HTMD includes system building for CHARMM and AMBER force fields, projection methods, clustering, molecular simulation production, adaptive sampling, an Amazon cloud interface, Markov state models, and visualization. As a result, a single, short HTMD script can lead from a PDB structure to useful quantities such as relaxation time scales, equilibrium populations, metastable conformations, and kinetic rates. In this paper, we focus on the adaptive sampling and Markov state modeling features.
Fire-induced or enhanced soil water repellency is often viewed as a key cause of the substantial increases in runoff and erosion following severe wildfires. In this study, the effects of different ...fire severities on soil water repellency are examined in eucalypt forest catchments in the Sandstone Tablelands near Sydney, burnt in 2001 and 2003. At sites affected by different fire severities and in long-unburnt control sites, repellency persistence was determined in situ and in the laboratory for surface and subsurface soil samples (
n=846) using the Water Drop Penetration Time (WDPT) test. All long-unburnt samples were found to be water repellent, with severe to extreme persistence (>900
s) being dominant for surface (0–2.5
cm) and slight to moderate persistence (10–900
s) for subsurface (2.5–5
cm) soil, indicating naturally very high ‘background’ levels of repellency. In contrast to the generation or enhancement of repellency usually reported following forest fires of similar severity in previous studies, burning caused widespread destruction of repellency. The mineral soil depth to which repellency was destroyed (0.5–5
cm) was found to increase with burn severity. Below this charred wettable layer, persistence of pre-existing water repellency increased. Two years after the fire, the frequency of extreme repellency persistence was reduced in the surface and subsurface. However, recovery to pre-fire repellency levels had not been achieved.
The associated hydrological impacts of these fire effects are more complex than simply the enhancement of overland flow, runoff and soil erosion with increasing fire severity. For forest fires sufficiently severe to remove foliage and ground litter above already repellent soil, a more severe burn, in which there is destruction of surface soil repellency, would result in lower runoff response compared to a burn insufficiently severe to destroy surface repellency. During storms intense enough to saturate the wettable surface rapidly, this layer may, however, be removed by overland flow, with potentially severe implications for soil fertility and seedbed survival, post-fire ecosystem recovery, and downstream sedimentation and water quality.
The results demonstrate that existing fire severity classifications are not well suited to predicting fire impacts on soil hydrological responses and highlight the need for a new fire severity evaluation scheme. A scheme encompassing not only foliage and ground cover status, but also changes to surface and subsurface soil hydrological properties, would provide a better prediction of the immediate hydrological effects of wildfires on catchments such as flash flooding and erosion, and also of their time-to-recovery than current classifications allow. Such a scheme could prove invaluable given the future increase in fire frequency and severity predicted for many regions.
Particulate emissions from wildfires impact human health and have a large but uncertain effect on climate. Modelling schemes depend on information about emission factors, emitted particle ...microphysical and optical properties and ageing effects, while satellite retrieval algorithms make use of characteristic aerosol models to improve retrieval. Ground-based remote sensing provides detailed aerosol characterisation, but does not contain information on source. Here, a method is presented to estimate plume origin land cover type and age for AERONET aerosol observations, employing trajectory modelling using the HYSPLIT model, and satellite active fire and aerosol optical thickness (AOT) observations from Moderate Resolution Imaging Spectroradiometer (MODIS) and Along Track Scanning Radiometer (AATSR). It is applied to AERONET stations located in or near northern temperate and boreal forests for the period 2002-2013. The results from 629 fire attributions indicate significant differences in size distributions and particle optical properties between different land cover types and plume age. Smallest fine mode median radius (Rfv) are attributed to plumes from cropland and/or natural vegetation mosaic (0.143 mu m) and grassland (0.157 mu m) fires. North American evergreen needleleaf forest emissions show a significantly smaller Rfv (0.164 mu m) than plumes from Eurasian mixed forests (0.193 mu m) and plumes attributed to the land cover types with sparse tree cover - open shrubland (0.185 mu m) and woody savannas (0.184 mu m). The differences in size distributions are related to inferred variability in plume concentrations between the land cover types. Significant differences are observed between day and night emissions, with daytime emissions showing larger particle sizes. Smoke is predominantly scattering for all of the classes with median single scattering albedo at 440 nm (SSA(440)) values close to 0.95 except the cropland emissions which have an SSA(440) value of 0.9. Plumes aged for 4 days or older have median Rfv larger by ~0.02 mu m compared to young smoke. Differences in size were consistent with a decrease in the Aangstrom Exponent and increase in the asymmetry parameter. Only an insignificant increase in SSA( lambda ) with ageing was found.
Can higher technological capacity help firms to recover quicker from recessions? Analysing the effects of the Covid-19 pandemic on firm revenues in several countries, we find that firms headquartered ...in jurisdictions with better digital infrastructure generated relatively higher revenue during the shock period. Improving a country’s technological capability by one standard deviation is associated with a relative increase in revenues of the average firm by around 4%. The positive effect of technology is more pronounced among smaller firms, suggesting that it could have helped the recovery of SMEs.
•We examine whether technological capacity helps firms recover from the Covid shock.•A better digital infrastructure leads to higher firm revenue during the shock period.•The positive effect of technological capacity is more pronounced among smaller firms.
Soil heating, as for example experienced during vegetation fires, often increases soil water repellency; however, no detailed analysis of the soil chemical changes associated with this increase has ...been conducted to date. Here we characterize the changes in organic compound composition associated with heat‐induced increases in water repellency for three Australian eucalypt‐forest soils (one sandy loam, two sands). Laboratory heating (300°C) strongly increased water drop penetration times (WDPTs) in all soils. Soils were extracted by accelerated solvent extraction (ASE) with an iso‐propanol/ammonia mixture (IPA/NH3 95:5) and pure iso‐propanol (IPA). Extracts were fractionated into less and more polar fractions and analysed by GC‐MS. Water repellency was eliminated in unheated and heated soils by IPA/NH3, but not by pure IPA. Before heating, total solvent extracts were dominated by n‐alkanols, terpenoids, C16 acid, C29 alkane, β‐sitosterol and polar compounds. After heating, dominant compounds were aromatic acids, aldehydes, levoglucosan, simple sugars and glycosides. Heating resulted in a sharp absolute decrease of homologous aliphatic series of alkanols and alkanes, a shift of fatty acid signature to members <C20 and an increase in total content of aromatic compounds. Heating also caused the formation of complex high‐molecular‐weight compounds detected in the more polar fractionated extracts and low‐molecular‐weight oxo‐ and hydroxyacids and aromatics in the IPA/NH3 solvent. We speculate that these compounds in conjunction with fatty acids of <C12 interact with organic and mineral soil surfaces and cause the observed strong increases in soil water repellency following heating.
Soil hydrophobicity is known to enhance runoff responses to rainstorms and to increase soil aggregate stability (AS). It has been widely reported for acidic soils particularly under burnt, but also ...unburnt pine forests following dry periods. Few studies have reported hydrophobicity from alkaline soils, but they have not established whether hydrophobicity also occurs in burnt or unburnt pine forests on alkaline soil. This study examines the wettability and stability of air-dry aggregates and their size fractions (<0.25, 0.25–0.5, 0.5–1 and 1–2 mm) taken from surface layers (0–2.5 and 2.5–5 cm depth) of alkaline, calcareous loamy soils. Four sites in southeastern Spain were sampled with comparable vegetation (>30-year-old Aleppo pine {
Pinus halepensis} and associated shrub community), geology (limestone), soil type (Lithic Xerorthents), slope angle and aspect (5–8°SW). Included were three sites (A, B, C) burned, respectively, in 1998, 1999 and 2000, and one unburnt for >30 years (D). Hydrophobicity was detected in samples from all sites. Both spatial frequency and persistence of hydrophobicity (Water Drop Penetration Times (WDPT) ranged from 10 to 600 s), however, was lower than reported from studies of acidic soils under pine. This might be associated with a lower susceptibility of alkaline soils to hydrophobicity development and/or the comparatively low biomass production in the region. Probably because it had been most recently affected by severe fire, spatial frequency of hydrophobicity was higher at site B (53% of samples), compared to A, C and D (6%, 33% and 10% of samples, respectively). In contrast to some previous studies, the finest size fraction of the samples consistently had the highest degree of hydrophobicity. Degree of hydrophobicity was positively correlated with organic matter (OM) content (
r=0.714). It is speculated that fine, interstitial hydrophobic organic matter accumulating in the finest sieve fraction contributes to this enhanced hydrophobicity. As shown in previous studies on acidic soils, aggregate stability increased with hydrophobicity (
r=0.897 in the fraction 0.25–2 mm) for the samples investigated here. This elevated stability occurs despite an already relatively high level of aggregate stability amongst all samples investigated. Hydrophobicity observed at the study sites was not spatially contiguous and it may therefore enhance overland flow and slope wash over only short distances for most, except the very high intensity rainstorms that occur in the region. The increased stability of hydrophobic soil aggregates against slaking, however, may counter an otherwise enhanced susceptibility to erosion.
Summary
Knowledge of soil water repellency distribution, of factors affecting its occurrence and of its hydrological effects stems primarily from regions with a distinct dry season, whereas ...comparatively little is known about its occurrence in humid temperate regions such as typified by the UK. To address this research gap, we have examined: (i) water repellency persistence (determined by the water drop penetration time method, WDPT) and degree (determined by the critical surface tension method, CST) for soil samples (0–5, 10–15 and 20–25 cm depth) taken from 41 common soil and land‐use types in the humid temperate climate of the UK; (ii) the supposed relationship of soil moisture, textural composition and organic matter content with sample repellency; and (iii) the bulk wetting behaviour of undisturbed surface core samples (0–5 cm depth) over a period of up to 1 week. Repellency was found in surface samples of all major soil textural types amongst most permanently vegetated sites, whereas tilled sites were virtually unaffected. Repellency levels reached those of the most severely affected areas elsewhere in the world, decreased in persistence and degree with depth and showed no consistent relationship with soil textural characteristics, organic matter or soil moisture contents, except that above a water content of c. 28% by volume, repellency was absent. Wetting rate assessments of 100 cm3 intact soil cores using continuous water contact (–20 mm pressure head) over a period of up to 7 days showed that across the whole sample range and irrespective of texture, severe to extreme repellency persistence consistently reduced the maximum water content at any given time to well below that of wettable soils. For slightly to moderately repellent soils the results were more variable and thus hydrological effects of such repellency levels are more difficult to predict. The results imply that: (i) repellency is common for many land‐use types with permanent vegetation cover in humid temperate climates irrespective of soil texture; (ii) supposedly influential parameters (texture, organic matter, specific water content) are poor general predictors of water repellency, whereas land use and the moisture content below which repellency can occur seem more reliable; and (iii) infiltration and water storage capacity of very repellent soils are considerably less than for comparable wettable soils.
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