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11,506 results for “Dynamics”
Figure 8 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
Figure 8 (A) surface map (B) 2D poses showing ligand interactions of Coumermycin; docked into the active site of SARS-CoV-2 papain-like protease (PDB: 6wx4).
Figure 10 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
Figure 10 The RMSD plot of Coumermycin complex with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp, at 50 ns simulation.
Figure 13 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
Figure 13 The time frame of evolution against SASA of Coumermycin complexes with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp, during 50 ns simulation.
Figure 14 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
Figure 14 Protein interaction analysis. The green colour = hydrogen bonding, pink color = ionic interaction, grey colour = hydrophobic interaction and blue colour = water bridges showed in Coumermycin complexes with SARS-CoV-2 (A) Mpro (B) PLpro (C) RdRp during 50 ns MD simulations.
Supplementary material 1 from: Gallão J, Bichuette M (2018) Population dynamics of two troglobitic Troglorhopalurus (Scorpiones: Buthidae) scorpions from Brazil. ARPHA Conference Abstracts 1: e30249. https://doi.org/10.3897/aca.1.e30249
Population dynamics of two troglobitic Troglorhopalurus Lourenço Baptista & Giupponi, 2004 (Scorpiones: Buthidae) scorpions from Brazil
Scaling the extinction vortex: Body size as a predictor of population dynamics close to extinction events
<ol> <li class="Body">Mutual reinforcement between abiotic and biotic factors can drive small populations into a catastrophic downward spiral to extinction – a process known as the 'extinction vortex.' However, empirical studies investigating extinction dynamics in relation to species' traits have been lacking.</li> <li class="Body">We assembled a database of 35 vertebrate populations monitored to extirpation over a period of at least ten years, represented by 32 different species, including 25 birds, five mammals and two reptiles. We supplemented these population time series with species-specific mean adult body size to investigate whether this key intrinsic trait affects the dynamics of populations declining towards extinction.</li> <li class="Body">We performed three analyses to quantify the effects of adult body size on three characteristics of population dynamics: time to extinction, population growth rate, and residual variability in population growth rate.</li> <li class="Body">Our results provide support for the existence of extinction vortex dynamics in extirpated populations. We show that populations typically decline non-linearly to extinction, while both the rate of population decline, and variability in population growth rate increase as extinction is approached. Our results also suggest that smaller-bodied species are particularly prone to the extinction vortex, with larger increases in rates of population decline and population growth rate variability when compared to larger-bodied species.</li> <li class="Body">Our results reaffirm and extend our understanding of extinction dynamics in real-life extirpated populations. In particular, we suggest that smaller-bodied species may be at greater risk of rapid collapse to extinction than larger-bodied species, and thus management of smaller-bodied species should focus on maintaining higher population abundances as a priority. </li> </ol>
An Orthogonal Dynamic Covalent Chemistry Tool for Ring-Opening Polymerization of Cyclic Oligochalcogenides on Detachable Helical Peptide Templates
<p>Original data</p>
Fig. 1 in Some Factors Behind Density Dynamics Of Bat Flies (Diptera, Nycteribiidae) - Ectoparasites Of The Boreal Chiropterans: Omitted Predictors And Hurdle Model Identification
Fig. 1. Study area: winter bats colony — Smolinskaya (1) and Barsukovskaya (2) caves, Korliki village — summer settlement (3).
Identifying biotic drivers of population dynamics in a benthic–pelagic community
Benthic species and communities are linked to pelagic zooplankton through life-stages encompassing both benthic and pelagic habitats and through a mutual dependency on primary producers as a food source. Many zooplankton taxa contribute to the sedimentary system as benthic eggs. Our main aim was to investigate the nature of the population level biotic interactions between and within these two seemingly independent communities, both dependent on the pelagic primary production, while simultaneously accounting for environmental drivers (salinity, temperature and oxygen conditions). To this end we applied multivariate autoregressive state-space models to long (1966–2007) time-series of annual abundance data, comparing models with and without interspecific interactions, as well as models with and without environmental variables included. We were not able to detect any direct coupling between sediment-dwelling benthic taxa and pelagic copepods and cladocerans on the annual scale, but the most parsimonious model indicated that interactions within the benthic community are important. There were also positive residual correlations between the copepods and cladocerans potentially reflecting the availability of a shared resource or similar seasonal dependence, whereas both groups tended to correlate negatively with the zoobenthic taxa. The most notable single interaction within the benthic community was a tendency for a negative effect of <i>Limecola balthica</i> on the amphipods <i>Monoporeia affinis</i> and <i>Pontoporeia femorata</i>, which can help explain the observed decrease of amphipods due to increased competitive interference.
Supplementary files for "Connection between water's dynamical and structural properties: insights from ab initio simulations"
<p>Examples of input scripts and data files for the simulations.</p>
IN-CELL QUANTIFICATION OF DRUGS BY MAGIC ANGLE SPINNING DYNAMIC NUCLEAR POLARIZATION NMR
<p>Raw data</p>
Data for WarpX milestone ECP-ADSE06.FY21.2: Assessment of dynamic load-balancing strategies on available exascale systems.
<p>This dataset includes the inputs, outputs, job submission scripts, and data analysis scripts used to prepare the WarpX milestone report for "Assessment of dynamic load-balancing strategies on available exascale systems." The code versions of WarpX, AMReX, and PICSAR used are stored in the outputs file for each run. </p>
Young cluster simulation dynamics
<p>Velocity vectors of stars from a simulation with 200 stars: red arrows show unbound stars, blue arrows show bound stars. Gas expulsion happens at 2 Myr. The black dot shows the centre of the cluster.</p> <p>Backtracing: stars from the same simulation are backtracked using velocity vectors at t=10 Myr and assuming a linear relation. Bound stars are portrayed in blue and unbound stars in red.</p>
research data supporting "Revealing the organization of catalytic sequence-defined oligomers via combined molecular dynamics simulations and network analysis"
<p>This repository contains all the data generated and analyzed including the starting structures, the input files, the trajectory files, the output data from cpptraj and network analyses, and in-house scripts used to prepare the network and module files shown in the paper <strong>"Revealing the organization of catalytic sequence-defined oligomers via combined molecular dynamics simulations and network analysis"</strong> published in <strong>Journal of Chemical Information and Modeling</strong> (DOI: 10.1021/acs.jcim.2c00101). </p>
Dynamic melting behavior of volcanic ash subjected to thermal shock relevant to aviation hazards
<p>All data presented in the main article and supplementary materials are available here. </p>
Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations
<p>Raw simulations of the deacylation step by PETase on a PET dimer model substrate, ran with CP2K 6.1 software at the PBE:AMBER level. Details can be found in the original manuscript (<a href="https://doi.org/10.1021/acscatal.1c03700">https://doi.org/10.1021/acscatal.1c03700</a>): Molecular topology in AMBER Parameter Topology format and Trajectories in CHARMM binary coordinate format DCD.</p> <p>QM RESIDUE LIST:<br> GLY57<br> TYR58<br> SEP131<br> MET132<br> TRP156<br> ASP177<br> SER178<br> ILE179<br> ALA180<br> HID208<br> WAT6290<br> WAT6318<br> WAT7630</p> <p>VMD selection:<br> (name CA C O HA2 HA3 and resname GLY and resid 57) or (name N CA CB H HA HB2 HB3 and resname TYR and resid 58) or (name O2 C3 O3 C4 O4 C5 O5 O6 C7 O7 C8 C9 C10 C11 C12 C13 C14 C15 C16 H5 H6 H7 H12 H13 H14 H15 H16 H17 H18 H19 H20 and resname SEP and resid 131) or (name N CA SD CE CB CG H HA HB2 HB3 HG2 HG3 HE1 HE2 HE3 and resname MET and resid 132) or (name CB CG CD1 CD2 CE2 CE3 NE1 CZ2 CZ3 CH2 HB2 HB3 HD1 HE1 HE3 HZ2 HZ3 HH2 and resname TRP and resid 156) or (name CG OD1 OD2 CB HB2 HB3 and resname ASP and resid 177) or (name C O and resname SER and resid 178) or (name N CA C O CG2 CD1 CB CG1 H HA HB HG12 HG13 HG21 HG22 HG23 HD11 HD12 HD13 and resname ILE and resid 179) or (name N CA CB H HA HB1 HB2 HB3 and resname ALA and resid 180) or (name CB CG CD2 ND1 CE1 NE2 HB2 HB3 HD1 HD2 HE1 and resname HID and resid 208) or (name O H1 H2 and resname WAT and resid 6290) or (name O H1 H2 and resname WAT and resid 6318) or (name O H1 H2 and resname WAT and resid 7630)</p> <p>PYMOL selection:<br> (name CA+C+O+HA2+HA3 & resn GLY & resi 57) | (name N+CA+CB+H+HA+HB2+HB3 & resn TYR & resi 58) | (name O2+C3+O3+C4+O4+C5+O5+O6+C7+O7+C8+C9+C10+C11+C12+C13+C14+C15+C16+H5+H6+H7+H12+H13+H14+H15+H16+H17+H18+H19+H20 & resn SEP & resi 131) | (name N+CA+SD+CE+CB+CG+H+HA+HB2+HB3+HG2+HG3+HE1+HE2+HE3 & resn MET & resi 132) | (name CB+CG+CD1+CD2+CE2+CE3+NE1+CZ2+CZ3+CH2+HB2+HB3+HD1+HE1+HE3+HZ2+HZ3+HH2 & resn TRP & resi 156) | (name CG+OD1+OD2+CB+HB2+HB3 & resn ASP & resi 177) | (name C+O & resn SER & resi 178) | (name N+CA+C+O+CG2+CD1+CB+CG1+H+HA+HB+HG12+HG13+HG21+HG22+HG23+HD11+HD12+HD13 & resn ILE & resi 179) | (name N+CA+CB+H+HA+HB1+HB2+HB3 & resn ALA & resi 180) | (name CB+CG+CD2+ND1+CE1+NE2+HB2+HB3+HD1+HD2+HE1 & resn HID & resi 208) | (name O+H1+H2 & resn WAT & resi 6290) | (name O+H1+H2 & resn WAT & resi 6318) | (name O+H1+H2 & resn WAT & resi 7630)</p>
Dynamic Uncertainty Lot Sizing Model: Formulation, Solution Methods, and Potential over the Static-Dynamic Uncertainty Model
<p>Test data used in Section 6</p>
Data Archive for Phosphorylation of SAMHD1 Thr592 increases C-terminal domain dynamics, tetramer dissociation, and ssDNA binding kinetics
<p>This archive contains all data communicated in the indicated publication.</p>
Supplementary material 1 from: Zhao M, Tian Y, Dong N, Hu Y, Tian G, Lei Y (2022) Spatial and temporal dynamics of habitat quality in response to socioeconomic and landscape patterns in the context of urbanization: A case in Zhengzhou City, China. Nature Conservation 48: 185-212. https://doi.org/10.3897/natureconservation.48.85179
Notes on the data
Comprehensive analysis of locomotion dynamics in the protochordate Ciona intestinalis reveals how neuromodulators flexibly shape its behavioral repertoire.
<p>This record contains (as of 2022-06-27) datasets corresponding to the study of behavior in swimming <em>Ciona intestinalis</em> larvae (controls and drug treated animals) that were recorded in our behavioural setups. In particular, it contains:</p> <ol> <li>multi-point tracking data of the larvae obtained using the Tierpsy Tracker (developed by Andre Brown's lab, MRC LMS).</li> <li>features like curvature, speed etc calculated from the tracking data</li> <li>results of time-series analyses (matrix-profiling, hidden markov modelling, spatio-temporal clustering) performed on the feature dataset</li> <li>Hidden Markov Models trained for inferences</li> </ol>
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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)
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DANDI Archive for NWB datasets
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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.