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11,506 results for “Dynamics”
Uncertainty-aware molecular dynamics from Bayesian active learning: Phase Transformations and Thermal Transport in SiC
<p>Machine learning interatomic force fields are promising for combining high computational efficiency and accuracy in modeling quantum interactions and simulating atomic level processes. Active learning methods have been recently developed to train force fields efficiently and automatically. Among them, Bayesian active learning utilizes principled uncertainty quantification to make data acquisition decisions. In this work, we present an efficient Bayesian active learning workflow, where the force field is constructed from a sparse Gaussian process regression model based on atomic cluster expansion descriptors. To circumvent the high computational cost of the sparse Gaussian process uncertainty calculation, we formulate a high-performance approximate mapping of the uncertainty and demonstrate a speedup of several orders of magnitude. As an application, we train a model for silicon carbide (SiC), a wide-gap semiconductor with complex polymorphic structure and diverse technological applications in power electronics, nuclear physics and astronomy. We show that the high pressure phase transformation is accurately captured by the autonomous active learning workflow. The trained force field shows excellent agreement with both \textit{ab initio} calculations and experimental measurements, and outperforms existing empirical models on vibrational and thermal properties. The active learning workflow is readily generalized to a wide range of systems, accelerates computational understanding and design.</p>
Figures S1–S10 from: Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN (2022) Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. Pharmacia 69(1): 211-226. https://doi.org/10.3897/pharmacia.69.e77021
Molecular docking and Dynamic simulations study for repurposing of multitarget Coumarins against SARS-CoV-2 main protease, papain like protease and RNA-Dependent RNA polymerase.
Archive data supporting the results in the paper: Long-term soil warming alters fine root dynamics and morphology, and their ectomycorrhizal fungal community in a temperate forest soil"
<p><span>Climate warming is predicted to affect temperate forests severely, but the response of fine roots, key to plant nutrition, water uptake, soil carbon and nutrient cycling is unclear. Understanding how fine roots will respond to increasing temperature is a prerequisite for predicting the functioning of forests in a warmer climate. We studied the response of fine roots and their ectomycorrhizal (EcM) fungal and root-associated bacterial communities to soil warming by 4 °C in a mixed spruce-beech forest in the Austrian Limestone Alps after 8 and 14 years of soil warming, respectively. Fine root biomass (FRB) and fine root production were 17% and 128% higher in the warmed plots, respectively, after 14 years. The increase in FRB (13%) was not significant after 8 years of treatment, whereas specific root length, specific root area, and root tip density were significantly higher in warmed plots at both sampling occasions. Soil warming did not affect EcM exploration types and diversity, but changed their community composition, with an increase in the relative abundance of <em>Cenoccocum</em> at 0 – 10 cm soil depth, a drought-stress tolerant genus, and an increase in short and long-distance exploration types like <em>Sebacina </em>and <em>Boletus </em>at 10 – 20 cm soil depth. Warming increased the root-associated bacterial diversity but did not affect their community composition. Soil warming did not affect nutrient concentrations of fine roots, though we found indications of limited soil phosphorus (P) and potassium (K) availability. </span><span>Our findings suggest that, in the studied ecosystem, global warming could persistently increase soil carbon inputs due to accelerated fine root growth and turnover, and could simultaneously alter fine root morphology and EcM fungal community composition towards improved nutrient foraging. </span></p>
Global analysis of cell behavior and protein localization dynamics reveals region-specific functions for Shroom3 and N-cadherin during neural tube closure
<p>Failures of neural tube closure are common and serious birth defects, yet we have a poor understanding of the interaction of genetics and cell biology during neural tube closure. Additionally, mutations that cause neural tube defects (NTDs) tend to affect anterior or posterior regions of the neural tube but rarely both, indicating a regional specificity to NTD genetics. To better understand the regional specificity of cell behaviors during neural tube closure, we analyzed the dynamic localization of actin and N-cadherin via high-resolution tissue-level time-lapse microscopy during Xenopus neural tube closure. To investigate the regionality of gene function, we generated mosaic mutations in shroom3, a key regulator or neural tube closure This approach elucidates new differences between cell behaviors during cranial/anterior and spinal/posterior neural tube closure, provides mechanistic insight into the function of shroom3 and demonstrates the ability of tissue-level imaging and analysis to generate cell-biological mechanistic insights into neural tube closure.</p>
Molecular Dynamics trajectories of the human PDZ2 domain
<p>Molecular Dynamics trajectories of the human PDZ2 domain. This dataset contains simulations of two systems (PDZ2 apo and PDZ2 bound to the RA-GEF-2 peptide) started from either a crystal or NMR structure.</p>
Immigration dynamics of tropical and subtropical Southeast Asian limestone karst floras
<p><i>Ex situ </i>origins and dispersal of taxa have played important roles in the assembly of island-like biodiversity hotspots. Insular limestone karsts in Southeast Asia are hotspots of biodiversity and endemism, but the immigration processes of their unique floras are still poorly known. Here, we used Gesneriaceae as a proxy to investigate immigration dynamics of tropical and subtropical Southeast Asian karst floras. We show that immigration into subtropical Southeast Asian karst floras first occurred in the early Miocene, with two peaks in the early to middle Miocene and the Pliocene to early Pleistocene, whereas immigration into tropical Southeast Asian karsts initiated in the late Eocene, with two peaks in the late Oligocene and the late Miocene. The rich geological and ecological diversities of different regions, together with habitat isolation due to climatic changes, might be responsible for the different immigration patterns. We also discover that Southeast Asian karst biodiversity comprises a mix of immigrant pre-adapted lineages and descendants from local acid soil ancestors, although niche shift from acid soil to karst in tropical Southeast Asian islands was lacking. <span>These </span><span>findings</span> <span>provide insights into </span><span>how</span> <span>Southeast </span><span>Asian </span><span>k</span><span>arst</span><span>s</span><span> respond to ongoing climate change and are of particular importance for</span><span> their </span><span>conservation planning</span><span>.</span></p>
Seismogenic process of fluid injection revealed by in situ dynamic CT scanning
<p>In the process of unconventional energy exploitation, large volumes of fluid are injected into low permeability reservoirs for hydraulic transformation to generate a fracture network conducive to fluid migration. Unfortunately, extensive fluid injection can induce earthquakes, endangering human lives and causing serious economic losses. Understanding the seismogenic process of fluid injection within a reservoir helps to minimize the induced earthquakes. To better monitor the deformation changes in reservoirs, we conducted in situ dynamic X-ray computed tomography (CT) during a series of experiments lasting 3 minutes for real-time identification of the location and geometry of hydraulic fractures and found that the seismogenic process of fluid injection with a wide range of frequencies is triggered by water–rock interactions.</p> <p>The data we uploaded can be divided into two main parts. The first part is the confining, axial and water injection pressures recorded during the hydraulic fracturing experiment. The second part is the CT scans of the rock sample during the hydraulic fracturing experiment.</p>
Structural dynamics determine voltage and pH gating in human voltage-gated proton channel
<p>Voltage-gated ion channels are key players of electrical signaling in cells. As a unique subfamily, voltage-gated proton (Hv) channels are standalone voltage sensors without separate ion conductive pores. Hv channels are gated by both voltage and transmembrane proton gradient (i.e ∆pH), serving as acid extruders in most cells. Amongst their many functions, Hv channels are known for regulating the intracellular pH of human spermatozoa and compensating for the charge and pH imbalances caused by NADPH oxidases in phagocytes. Like the canonical voltage sensors, Hv channels are a bundle of 4 helices (named S1 through S4), with the S4 segment carrying 3 positively charged Arg residues. Extensive structural and electrophysiological studies on voltage-gated ion channels, in general, agree on an outwards movement of the S4 segment upon activating voltage, but the real-time conformational transitions are still unattainable. With purified human voltage-gated proton (hHv1) channels reconstituted in liposomes, we have examined its conformational dynamics, including the S4 segment at different voltage and pHs using single-molecule fluorescence resonance energy transfer (smFRET). Here, we provide the first glimpse of real-time conformational trajectories of the hHv1 voltage sensor and show that both voltage and pH gradient shift the conformational dynamics of the S4 segment to control channel gating. Our results indicate that the S4 segment transits among 3 major conformational states and kinetic analysis suggest that only the transitions between the inward and outward conformations are highly dependent on voltage and pH changes. Our smFRET studies uncover the stochastic conformational dynamics of S4 and demonstrate how voltage and pH shift its conformational distributions to regulate channel gating. Altogether, we propose a kinetic model that explains the mechanisms underlying voltage and pH gating in Hv channels, which may also serve as a general framework for understanding the voltage sensing and gating in other voltage-gated ion channels.</p>
"Towards skin-acetone monitors with selective sensitivity: dynamics of PANI-CA films" Raw Videos
<p>These are the original, unedited videos from which all data in the paper "Towards skin-acetone monitors with selective sensitivity: dynamics of PANI-CA films" was extracted by image analysis. This paper was published in <em>PLOS One</em>.</p>
Dynamic deformation calculation of articular cartilage and cells using resonance-driven laser scanning microscopy - Osmotic Challenge and Validation Testing Dataset
<p>This archive contains 3-D image stacks obtained over time of articular cartilage undergoing osmotic swelling. These were acquired with a resonance scanning protocol, which allows for fast scanning but with decreased image quality. The Python package, resonant_lsm, was developed to segment and analyze the deformation of cells in such images. The archive also contains validation testing data of this software. Included README files document the archive contents and how to reproduce the analyses. </p>
Dynamic sensitivity to resource availability influences population responses to mismatches in a shorebird
<p>Climate change has caused shifts in seasonally recurring biological events leading to the temporal decoupling of consumer-resource pairs – i.e., phenological mismatching. Although mismatches often affect individual fitness, they do not invariably scale up to affect populations, making it difficult to assess the risk they pose. Individual variation may contribute to this inconsistency, with changes in resource availability and consumer needs leading mismatches to have different outcomes over time. Nevertheless, most models estimate a consumer's match from a single timepoint, potentially obscuring when mismatches matter to populations. We analyzed how the effects of mismatches varied over time by studying precocial Hudsonian godwit (Limosa haemastica) chicks and their invertebrate prey from 2009 to 2019. We developed individual and population level models to determine how age-specific variation affect the relationship between godwits and resource availability. We found that periods with abundant resources led to higher growth and survival of godwit chicks, but also that chick survival was increasingly related to the availability of larger prey as chicks aged. At the population level, estimates of mismatches using age-structured consumer demand explained more variation in annual godwit fledging rates than more commonly used alternatives. Our study suggests that modeling the effects of mismatches as the disrupted interaction between dynamic consumer needs and resource availability clarifies when mismatches matter to both individuals and populations.</p>
Forest disturbances and climate constrain carbon allocation dynamics in trees
<p>Forest disturbances such as drought, fire and logging affect the forest carbon dynamics and the terrestrial carbon sink. Forest mortality after disturbances creates uncertainties that need to be accounted for to understand forest dynamics and their associated C-sink. We combined data from permanent resampling plots and biomass oriented dendroecological plots to estimate time series of annual woody biomass growth (ABI) in several forests. ABI time series were used to benchmark a vegetation model to analyze dynamics in forest productivity and carbon allocation forced by environmental variability. The model implements source and sink limitations explicitly by dynamically constraining carbon allocation of assimilated photosynthates as a function of temperature and moisture. Bias in tree-ring reconstructed ABI increased back in time from data collection and with increasing disturbance intensity. ABI bias ranged from zero, in open stands without recorded mortality, to over 100% in stands with major disturbances such as thinning or snowstorms. Stand leaf area was still lower than in control plots decades after heavy thinning. Disturbances, species life-history strategy and climatic variability affected carbon partioning patterns in trees. Resprouting broadleaves reached maximum biomass growth at earlier ages than nonresprouting conifers. Environmental variability and leaf area explained much variability in woody biomass allocation. <span>Effects of </span>stand competition on C-allocation were mediated by changes in stand leaf area except after major disturbances. Divergence between tree-ring estimated and simulated ABI were caused by unaccounted changes in allocation or misrepresentation of some functional process independently of the model calibration approach. Higher disturbance intensity produced greater modifications of the C-allocation pattern, increasing error in reconstructed biomass dynamics. Legacy effects from disturbances decreased model performance and reduce the potential use of ABI as a proxy to net primary productivity. Trait-based dynamics of C-allocation in response to environmental variability need to be refined in vegetation models.</p>
Combined dynamical and morphological characterization of geodynamo simulations
<p>Original scripts and data files for generating Figure 2, 3, 8, and 9.</p>
Temporal dynamics in biotic and functional recovery following mining
<p>1. Human-induced disturbance has substantially influenced the structure and function of terrestrial ecosystems globally. However, the extent to which multiple ecosystem functions (multifunctionality) recover following anthropogenic disturbance (ecosystem recovery) remains poorly understood.</p> <p>2. We report on the first study examining the temporal dynamics in recovery of multifunctionality from 3 to 12 years after the commencement of rehabilitation following mining-induced disturbance, and related this information to changes in biota. We examined changes in 57 biotic (plants, microbial) and functional (soil) attributes associated with biodiversity and ecosystem services at four open-cut coal mines in eastern Australia. </p> <p>3. Increasing time since commencement of rehabilitation was associated with increases in overall multifunctionality, soil microbial abundance, plant productivity, plant structure and soil stability, but not nutrient cycling, soil carbon sequestration nor soil nutrients. However, the temporal responses of individual ecosystem properties varied widely, from strongly positive (e.g., litter cover, fine and coarse frass, seed biomass, microbial and fungal biomass) to strongly negative (groundstorey foliage cover). We also show that sites with more developed biota tended to have greater ecosystem multifunctionality. Moreover, recovery of plant litter was closely associated with recovery of most microbial components, soil integrity and soil respiration. Overall, however, rehabilitated sites still differed from reference ecosystems a decade after commencement of rehabilitation.</p> <p>4. Synthesis and applications. The dominant role of plant and soil biota and litter cover in relation to functions associated with soil respiration, microbial function, soil integrity and C and N pools suggests that recovering biodiversity is a critically important priority in rehabilitation programs. Nonetheless, the slow recovery of most functions after a decade indicates that rehabilitation after open-cut mining is likely to protracted.</p>
Temporal dynamics of range-expander and congeneric native plant responses during and after extreme drought events
<p>Current climate change causes range shifts of many species to higher latitudes and altitudes, and enhances their exposure to extreme weather events. It has been shown that range shifting plant species may perform differently in the new soil than related natives, however, little is known about how extreme weather events influence range-shifting plants compared to related natives. Here, we used outdoor mesocosms to study how range-shifting plant species respond to extreme drought in live soil from a habitat in the new range with and without live soil from a habitat in the original range. During summer drought, shoot biomass of the range-expanders was reduced. In spite of this, in the mixed community range-expanders produced more shoot biomass than congeneric natives. In mesocosms with a history of range-expanders in the previous year, native plants produced less biomass. Plant legacy or soil origin effects did not change the response of natives or range-expanders to summer drought. During rewetting, range-expanders had less biomass than congeneric natives, but had higher drought resilience (survival) in soils from the new range where in the previous year native plant species had grown. The biomass patterns of the mixed plant communities were dominated by Centaurea species, however, not all plant species within the groups of natives and of range expanders showed the general pattern. Drought reduced litter decomposition, microbial biomass and abundances of bacterivorous, fungivorous and carnivorous nematodes. Their abundances recovered during rewetting. There was less microbial biomass, fungal biomass and there were fewer fungivorous nematodes in soils from the original range (Hungary) where range-expanders had grown in the previous year. We conclude that in mixed plant communities of range-expanders and congeneric natives, range-expanders performed better, both under ambient and drought conditions, than congeneric natives. However, when considering the responses of individual species, we observed variations among couples of congenerics, so that under the present-mixed community-conditions there was no uniformity in responses to drought of range expanders versus congeneric natives. Range-expanding plant species reduced soil fungal biomass and numbers of soil fungivorous nematodes, suggesting that effects of range-expanding plant species can trickle up in the soil food web.</p>
Hemodynamic data from the Inspired Therapeutics NeoMate Mechanical Circulatory Support System for neonates and infants as tested in static mock circulatory loops, dynamic mock circulatory loops, and acute animal studies
<p>Inspired Therapeutics (Merritt Island, FL) is developing a mechanical circulatory support (MCS) system designed as a single driver with interchangeable, extracorporeal, magnetically levitated pumps. The NeoMate system design features an integrated centrifugal rotary pump, motor, and controller that will be housed in a single compact unit. Conceptually, the primary innovation of this technology will be the combination of disposable, low-cost pumps for use with a single, multi-functional, universal controller to support multiple pediatric cardiopulmonary indications. In response to the paucity of clinically available pediatric devices, Inspired Therapeutics is specifically targeting the underserved neonate and infant heart failure (HF) patient population first. In this article, we present the development of the prototype Inspired Therapeutics NeoMate System for pediatric left ventricular assist device (LVAD) support, and feasibility testing in static mock flow loops (H-Q curves), dynamic mock flow loops (hemodynamics), and in an acute healthy ovine model (hemodynamics and clinical applicability). The resultant hydrodynamic and hemodynamic data demonstrated the ability of this prototype pediatric LVAD and universal controller to function over a range of rotary pump speeds (500-6000 RPM), to provide pump flow rates of up to 2.6 L/min, and to volume unload the left ventricle in acute animals. Key engineering challenges observed and proposed solutions for the next design iteration are also presented.</p>
Molecular Dynamics simulation dataset for : Hypoxia increases the methylated histones to prevent histone clipping and redistribution of heterochromatin during Raf-induced senescence.
<p>Files are Initial structures of Cathepsin L(CTSL) with histone H3 peptides (naive and K23me3) and their Molecular Dynamics simulation trajectories. AutoDock Vina and Charmm were used in H3 peptide docking. </p> <p>Wild type CTSL was modeled with apo-Cathepsin L C25A mutant(PDB ID : 3K24) using Charmm-GUI. Trimethylated histone H3 peptide was generated with PyMol. H3 peptide Molecular Dynamics simulations were performed with GPU-accelerated OpenMM.</p>
Appendix to Combinatorial Methods for Dynamic Gray-Box SQL Injection Testing
<p>This appendix contains the detailed results of our case study performed in the context of our article "Combinatorial Methods for Dynamic Gray-Box SQL Injection Testing", published in the Journal of Software Testing, Verification and Reliability.</p> <p><br> For each web application investigated, one table exists, provided as a separate PDF file.<br> In each of these tables, the results are grouped by endpoint. For each investigated approach, we list the total number of submitted vectors, the number of injected vectors and the injection rate, the amount of executed vectors and the execution rate, and the total time required to submit the attack vectors and evaluate the responses.</p> <p>Please note that no false positive endpoints are listed for WAVSEP. Furthermore, some entries for the execution rate may be displayed as 0.00 despite some vectors having been executed; this is merely a consequence of rounding.</p>
Dynamical topological phase realized in a trapped-ion quantum simulator
<p>Experimental and simulation data as presented.</p>
Ancient geological dynamics impact neutral biodiversity accumulation and are detectable in phylogenetic reconstructions
<p><strong>Aim</strong> Landmasses have been continuously modified by tectonic activity, the breakup and collision of landmasses is thought to have generated or suppressed ecological opportunities, altering the rates of speciation, dispersal and extinction. However, the extent to which the signatures of past geologic events are retained in modern biodiversity patterns - or obliterated by recent ecological dynamics - remains unresolved. We aim to identify the fingerprint of different scenarios of geological activity on phylogenetic trees and geographic range size distributions.<br> <strong>Location</strong> Global.<br> <strong>Time period</strong> Geological time.<br> <strong>Major taxa studied</strong> Theoretical predictions for any taxa.<br> <strong>Methods </strong>We conducted spatially explicit simulations under a neutral model of range evolution, speciation and extinction for three different geological scenarios that differed in their geological histories. We set a limit in the number of populations that locally can coexist which along with the geographic boundaries of landmasses, influences the rate of range expansion.<br> <strong>Results</strong> Our results demonstrate regions of similar size, age and ecological limits will differ in richness and macroevolutionary patterns based solely on the geological history of landmass breakup-collision even in the absence of species' ecological differences i.e., neutrality. When landmasses collide, regional richness is higher, lineages exhibit more similar rates of speciation and phylogenetic trees are more balanced than in the geologically static scenario. Stringent local limits to coexistence yield lower regional diversity but in general do not affect our ability to distinguish geological scenarios.<br> <strong>Main conclusions</strong> These findings provide an alternative explanation for existence of some hotspots of diversity in areas of high geological activity. Although a limit in the number of coexisting species largely influences regional diversity, its contribution to phylogenetic patterns is lower than variation in per-capita rates of speciation and extirpation. Importantly, these findings demonstrate the potential for inferring past geological history from distributions of phylogenies and range sizes.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.