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45 results for “channel dynamics”
Coupled stochastic modelling of hierarchical channel network dynamics and metapopulation persistency - Dataset
<p>Dynamic changes in the active portion of stream networks represent a phenomenon common to diverse climates and geologic settings. However, the ecological implications of river network expansions/retractions remain poorly understood owing to operational difficulties in mechanistically describing these processes at the relevant spatio-temporal scales. Here we present a novel Bayesian framework for the simulation of event-based channel network dynamics capitalizing on the concept of "hierarchical structuring of temporary streams" - a general principle to identify the activation/deactivation order of network nodes. The framework incorporates a dynamic version of a stochastic occupancy metapopulation model, and is used to analyze the impact of pulsing river networks on species persistence in different scenarios. Climate strongly controls temporal variations of the active length, influencing the preferential configuration of the active channels and the speed of network retraction during drying. We also identify a climate-dependent detrimental effect of network dynamics on species spread and persistence. This effect is enhanced by dry climates, where flashy expansions and retractions of the flowing channels induce metapopulation extinction. Survival probabilities are particularly reduced in settings where the spatial heterogeneity of network connectivity is pronounced. The proposed framework provides novel insight on the multi-faced ecological legacies of channel network dynamics.</p>
Investigation on Dynamic Characteristics of Lightning Return Stroke Channel
<p>The dynamic characteristics in lightning discharge plasma channel are of great significance in studying the micro-physical mechanism of the discharge process. This paper established a simplified radiation-hydrodynamic model (SRHM) of the return stroke channel radial expansion based on the fluid dynamics theory and the time evolution characteristics of the light radiation power observed by experiments. The influence of current waveform on the dynamic characteristics of return stroke channel was investigated, and the temporal evolutions of the characteristic parameters, such as temperature, pressure and expansion speed for return stroke channel were analyzed. The results indicated that the current peak value and the risetime are important factors in determining the channel dynamics characteristics. At the initial stage of return stroke, the light radiation loss has a distinct influence on channel temperature, which leads to a transitory drop in temperature forming a bimodal waveform structure. Following the peak current, the channel reaches peak pressure, which leads to a subsequent secondary temperature peak and accelerates the expansion of the channel. Large peak current and the rise time are the indicative parameters of strong discharge and the main factors leading to lightning disaster. This work provides reference data for further research on the radial energy transport of lightning return stroke channel and the formation mechanism of shock waves.</p>
Coupled stochastic modelling of hierarchical channel network dynamics and metapopulation persistency - Dataset
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Data from: Conformational dynamics in TRPV1 channels reported by an encoded coumarin amino acid
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Phonon calculations for "Uncovering design principles for amorphous-like heat conduction using two-channel lattice dynamics"
<p>These are the phonon calculations for</p> <p>R. Hanus, <strong>J. George</strong>, M. Wood, <strong>A. Bonkowski</strong>, Y. Cheng, D. L. Abernathy, M. E. Manley, G. Hautier, G. J. Snyder, R. P. Hermann, “Uncovering design principles for amorphous-like heat conduction using two-channel lattice dynamics”, <em>Materials Today Physics</em>, <strong>2021</strong>, In Press, <a href="https://doi.org/10.1016/j.mtphys.2021.100344">https://doi.org/10.1016/j.mtphys.2021.100344</a></p>
Dynamic Characteristics of Lightning Channel Radial Expansion
<p>The original datas of manuscript entitled“Dynamic Characteristics of Lightning Channel Radial Expansion”.</p>
Data from: Variation across river channels in demographic dynamics of a riparian herb with threatened status: management and conservation implications
PREMISE OF THE STUDY: Gesneria pauciflora is a rare-threatened plant growing in riparian forests. Periodic disturbances, expected in this habitat, could influence demographic dynamics on plant populations, yet their impact may not be the same across watershed. We hypothesize that differences in disturbances between the main-channel and tributaries may lead to spatial dissimilarities in population growth rate (λ), structure, and fecundity. METHODS: 1277 plants were tagged and monitored over a 1.5-years period. Every 6-months we measured plant size, survival and fecundity, in addition to appearance of seedlings. These variables were applied in Integral Projection Models to assess the population status of G. pauciflora. KEY RESULTS: Plants in the main-channel were smaller but were more likely to flower and fruit than those in the tributaries. Overall mortality was greater in the main-channel and more so during the rainy season. At both sites λ ranged from 0.9114-0.9865, and survival/growth of larger plants had a greater effect on lambda (> 0.90) regardless of site. CONCLUSIONS: Lambda values suggest that G. pauciflora is declining across the watershed. Higher mortality rates in the main channel (more-perturbed sites) might driving G. pauciflora to reproduced at smaller sizes, while the tributaries (less-perturbed sites) may benefit growth and lead to larger plant sizes. Extreme climatic events are expected to increase in the Caribbean and might decrease the population if left unmanaged. Management strategies that reduce the time plants require to reach larger sizes might be necessary to increase λ, and reintroduction of cuttings might be a possible solution.
Molecular dynamics simulation of a pentameric ligand-gated ion channel DeCLIC
<p>Molecular dynamics simulation trajectories, parameter files for a bacterial pentameric ligand-gated ion channel DeCLIC, in the system with 150mM CaCl2 or NaCl2.</p>
Dynamic conformational changes of acid-sensing ion channels in different desensitizing conditions
<p>Peer-reviewed manuscript, supplemental file, and source data related to the article 'Dynamic conformational changes of acid-sensing ion channels in different desensitizing conditions'.</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>
Experimental data for: Long-term memory and synapse-like dynamics in two-dimensional nanofluidic channels
<p>Experimental data set for: Long-term memory and synapse-like dynamics in two-dimensional nanofluidic channels. Provides all raw data needed to reproduce experimental graphs presented within the paper.</p>
Inlists for "An Alternative Channel to Black Hole Low-Mass X-ray Binaries: Dynamical Friction of Dark Matter? "
<p>In this work, we employ MESA code to diagnose whether the dynamical friction between dark matter and the companion stars can drive BH binaries to evolve toward the observed BH LMXBs and alleviate the effective temperature problem. Assuming that there exists a density spike of dark matter around BH, the dynamical friction can produce an efficient angular momentum loss, driving BH binaries with an intermediate-mass companion star to evolve into BH LMXBs for a spike index higher than $\gamma = 1.58$.</p> <p>MESA version: r12115; SDK compiler: mesasdk-x86_64-linux-20190830</p> <p> </p>
Tidal channel formation in a rapidly invaded micro-tidal marsh: the role of dynamic vegetation pattern and concurrent channel deepening
<p>The channel formation during the spartina alterniflora invasion influenced by vegetation pattern dynamic and concurrent channel deepening.</p>
Data from: Variation across river channels in demographic dynamics of a riparian herb with threatened status: management and conservation implications
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Structural dynamics determine voltage and pH gating in human voltage-gated proton channel
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DATA of 'Quantification of seasonal and diurnal dynamics of subglacial channels using seismic observations on an Alpine Glacier.' from Nanni et al. 2020,
<p>This dataset belongs to the study of <strong>Nanni et al., 2020</strong> "Quantification of seasonal and diurnal dynamics of subglacial channels using seismic observations on an Alpine Glacier." accepted for publication in The Cryosphere on March 9th 2020.</p> <p>You can find additional information on the "<strong>README_data_NANNI_2020_glacier</strong>"</p>
Data from: Force and torque on spherical particles in micro-channel flows using computational fluid dynamics
To delineate the influence of hemodynamic force on cell adhesion processes, model in vitro fluidic assays that mimic physiological conditions are commonly employed. Herein, we offer a framework for solution of the three-dimensional Navier–Stokes equations using computational fluid dynamics (CFD) to estimate the forces resulting from fluid flow near a plane acting on a sphere that is either stationary or in free flow, and we compare these results to a widely used theoretical model that assumes Stokes flow with a constant shear rate. We find that while the full three-dimensional solutions using a parabolic velocity profile in CFD simulations yield similar translational velocities to those predicted by the theoretical method, the CFD approach results in approximately 50% larger rotational velocities over the wall shear stress range of 0.1–5.0 dynes cm−2. This leads to an approximately 25% difference in force and torque calculations between the two methods. When compared with experimental measurements of translational and rotational velocities of microspheres or cells perfused in microfluidic channels, the CFD simulations yield significantly less error. We propose that CFD modelling can provide better estimations of hemodynamic force levels acting on perfused microspheres and cells in flow fields through microfluidic devices used for cell adhesion dynamics analysis.
Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel
<p><strong>Molecular dynamics simulations</strong></p> <p>Trajectories and related files.</p>
Dynamics of seal bomb use in Channel Islands and Monterey Bay National Marine Sanctuaries
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Data from: Force and torque on spherical particles in micro-channel flows using computational fluid dynamics
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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.