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11,506 results for “Dynamics”
Using a real-world network to model the trade-off between stay-at-home restriction, vaccination, social distancing and working hours on COVID-19 dynamics
<p>These datasets have been obtained through thousands of well-carried simulations by using the agent-based model based on a time-dynamic graph with stochastic transmission events. </p> <p>These simulations have been conducted on MATLAB 2019a.</p>
Figure 2 from: Albratty M, Thangavel N, Chandrasekaran B, Meraya AM, Alhazmi HA, Muthumanickam S, Boomi P, Bhagavan NB, Saleh SF (2024) Benchmarking docking, density functional theory and molecular dynamics studies to assess the aldose reductase inhibitory potential of Trigonella foenum-graecum compounds for managing diabetes-associated complications. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e118949
Figure 2 Benchmarking docking binding energy scores distribution: (a) AutoDock, (b) AutoDock Vina.
Variational manifolds for ground states and scarred dynamics of blockade-constrained spin models on two and three dimensional lattices
<p>Abstract: We introduce a variational manifold of simple tensor network states for the study of a family of constrained models that describe spin-<span><span><span><span><span><span><span><span>1/</span></span></span><span><span><span>2</span></span></span></span></span></span></span></span> systems as realized by Rydberg atom arrays. Our manifold permits analytical calculation via perturbative expansion of one- and two-point functions in arbitrary spatial dimensions and allows for efficient computation of the matrix elements required for variational energy minimization and variational time evolution in up to three dimensions. We apply this framework to the PXP model on the hypercubic lattice in one, two, and three dimensions and show that, in each case, it exhibits quantum phase transitions breaking the sublattice symmetry in equilibrium, and hosts quantum many-body scars out of equilibrium. We demonstrate that our variational ansatz qualitatively captures all these phenomena and predicts key quantities with an accuracy that increases with the dimensionality of the lattice, and conclude that our method can be interpreted as a generalization of mean-field theory to constrained spin models.</p> <p>Access will be granted upon reasonable request.</p>
Molecular Mechanism of Substrate Transport and Dynamics of the Cyanobacterial Bicarbonate Transporter BicA
<p>Molecular Mechanism of Substrate Transport and Dynamics of the Cyanobacterial Bicarbonate Transporter BicA</p>
Raw data molecular dynamics and alphafold (Lemaire et al)
<p>Raw data molecular dynamics and alphafold for manuscript NCOMMS-24-29370</p>
Supporting Software Maintenance with Dynamically Generated Document Hierarchies (Supplemental)
<p>Supplemental materials for submission to ICSME 24 titled "<span>Supporting Software Maintenance with </span><span>Dynamically Generated Document Hierarchies"</span></p>
Molecular Dynamics Assessment of Primary Damage Efficiency for Fusion Relevant Elements Dataset
<p>Dataset containing simulation results and example input scripts for the paper "Molecular Dynamics Assessment of Primary Damage Efficiency for Fusion Relevant Elements".</p>
Dynamic Mode Decomposition Data and Code for Atmospheric Chemistry
<p>The files included here contain a matlab code base for executing the optimized dynamic mode decomposition algorithm for evaluating and forecasting atmospheric chemistry dynamics.</p>
Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions
<p>for manuscript "Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions"</p>
Immersion enthalpies of nanomaterials (metals, metal oxides, organic chemistry structures) in water and octanol through molecular dynamics simulations with GROMACS and LAMMPS software
<p>Molecular dynamics simulations (free energy calculations) of water interface properties of spherical and Wulff structures nanoparticles (metals, metal oxides and carbon structures) with GROMACS and LAMMPS software.</p>
Dynamic Nuclear Polarization Pulse Sequence Engineering using Single-Spin Vector Effective Hamiltonians
<p>The repository contains background data for the paper "Dynamic Nuclear Polarization Pulse Sequence Engineering using Single-Spin Vector Effective Hamiltonians". This includeds files for experimental data, and plotting of these (Exp_data folder) and compiled code and input files for evaluation and non-linear optimization of pulse sequences (Non_linear_optimization_compiled_code folder).</p>
Database of "Dynamic Design and Performance Prediction of Tuned Particle Damper Based on Co-simulation"
<p>These data are obtained based on the co-simulation of ADAMS and EDEM. The first 7 columns are inputs and the last column is output.</p>
Data for Cholesterol binding to the sterol-sensing region of NiemannPick C1 protein confines dynamics of its N-terminal domain
<p>Uploaded zip files contain simulations data, input files, parameters and topologies for the work performed in the article <strong>"Cholesterol binding to the sterol-sensing region of Niemann Pick C1 protein confines dynamics of its N-terminal domain</strong>".</p> <p>Data is organized into 2 folders. First 'Input files' contains the starting structure, topologies and input files for the simulations for each studied case (i.e. POPC,POPC-CHOL,POPC-CHOL-bound). The second 'Trajectories' contains the simulation output of these simulations.</p> <p>Additionally, zip file contains <strong>Readme_for_softwares</strong> and <strong>Readme_Input_files_and_Trajectories </strong>describes the tools used and all the input files respecively.</p> <p> </p> <p> </p>
Figure 5 in Genetic structure and population dynamics of the silver pheasant (Lophura nycthemera) in southern China
Figure 5. The test for STRUCTURE analysis.
Molecular Dynamics trajectories and portable binary run input (TPR) files for the dual role of anionic lipids in amyloid aggregation
<h1>About this repository</h1> <p>We conducted Coarse-Grained molecular dynamics simulations to study the aggregation of the amyloid-beta fragment, Aβ16-22 (K16LVFFAE22), on mixed lipid bilayers composed of POPC and POPS. Three bilayer compositions were examined: 0% PS-100% PC, 10% PS-90% PC and 30% PS-70% PC. Simulations were performed using GROMACS 2019.4, employing the WEPROM forcefield for peptide modeling and WEPMEM for lipid modeling. For each POPS percentage, four independent replicas were run for 3000 ns. </p> <h1><strong>Contents</strong></h1> <h3>> Abeta_PCPS.zip </h3> <p>This zip file contains three main folders: 0PS, 10PS, and 30PS. These represent different percentages of PS present in the lipid bilayer.</p> <p>Each folder contains:</p> <p>1. Initial structures:<br> - em1.gro: Lipid bilayer without peptides<br> - eq1.gro: Lipid bilayer at 95 Ų area-per-lipid (APL)<br> - em2.gro: Lipid bilayer at 95 Ų APL with 16 peptides<br> - eq2.gro: Final equilibrated structure with peptides (used for production)</p> <p>2. Supporting files:<br> - index.ndx: Index groups for peptides and lipid bilayer<br> - run.pdf: Structure file for VMD visualization</p> <p>3. Four replica folders (replica1 to replica4), each containing:<br> - red.tpr: Binary input for analysis (peptides and lipid bilayer only)<br> - full_trj_pbc.xtc: Trajectory file (peptides and lipid bilayer only, centered in box)</p> <p>Note: The `.tpr` files were created using the `gmx convert-tpr` tool.</p> <p><strong>To access the source files with which these simulations were set-up, and a brief tutorial, see: </strong><a href="https://github.com/suhasgotla/heparin_amyloid_self-assembly">https://github.com/meenaljainumd/PCPS_amyloid_aggregation</a></p>
Idiosyncratic choice bias and feedback-induced bias differ in their long-term dynamics
<p>Overview<br>-------------------<br>This repository is associated with the paper "Idiosyncratic choice bias and feedback-induced bias differ in their long-term dynamics".</p> <p>All data and analyses required to reproduce our results are available in the stabilityFeedback folder.</p> <p>Data<br>-------------------<br>Response data and inter-session-delays are stored as sorted tables ("sortedTable_") and assign tables ("assignTable_"), respectively, by experiments (stabilityFeedback/stability folder and stabilityFeedback/feedback folder) and delay groups: <br>"stabilityFeedback/[EXPERIMENT_NAME]/[TABLES_TYPE]/[TABLE_TYPE]_[EXPERIMENT_NAME]_[DELAY_NAME].csv"</p> <p>Analysis<br>-------------------<br>The code required to reproduce all analyses and related figures is available in the stabilityFeedback/stabilityFeedbackICB.mlx MATLAB (R2023b) Live Editor file (also available as stabilityFeedbackICB.pdf).</p> <p>All figures are saved in the stabilityFeedback/figures folder in both MATLAB FIG and PDF formats. File names for the vertical task match those used in the paper, while file names for the horizontal task include " - appendix." at the end.</p> <p>For Binomial tests, we use the myBinomTest custom function, reference: Matthew Nelson (2015). https://www.mathworks.com/matlabcentral/fileexchange/24813-mybinomtest-s-n-p-sided MATLAB Central File Exchange. Retrieved February 9, 2016.</p> <p>Cite<br>-------------------<br>If you use code from this repository, please cite it using the Zenodo DOI: 10.5281/zenodo.13388598</p> <p>Contributors<br>-------------------<br>This code was authored by Lior Lebovich, 2024.</p>
Replications Package for "Understanding the Dynamics of License Selection in OSS: A Data-Driven Exploration Across Different Programming Languages"
<p>Replications Package for "Understanding the Dynamics of License Selection in OSS: A Data-Driven Exploration Across Different Programming Languages"<br><br>Includes datasets and R code.</p>
Data and code for "Human neural dynamics of real-world and imagined navigation"
<ul> <li>Please download the zip file</li> <li>Unzip it on your computer</li> <li>Run the plot_FigureX.m scripts in Matlab</li> <li>The scripts generate the panels for the manuscript's figures</li> <li>Figure panels are saved in subfolders for your review</li> </ul>
Video results of the study "Dynamic Region of Interest Generation for Maritime Horizon Line Detection using Time Series Analysis"
<p># Video Results of the Study "Dynamic Region of Interest Generation for Maritime Horizon Line Detection using Time Series Analysis"</p> <p>This repository contains the result videos from the study titled *"Dynamic Region of Interest Generation for Maritime Horizon Line Detection using Time Series Analysis"*. These videos showcase the performance of the algorithm on two datasets: the **Singapore Maritime Dataset (Onboard Segment)** and the **Buoy Dataset**. Please note that the original datasets are not included in this repository but are publicly available elsewhere.</p> <p>## Contents</p> <p>### 1. Singapore Maritime Dataset (Onboard Segment)<br>The videos labeled with **MVI** belong to the Singapore Maritime Dataset. These result videos demonstrate the performance of the horizon line detection algorithm on onboard maritime footage. For example:<br>- **MVI_0792_VIS_OB.avi** - Original input video (available in the Singapore Maritime Dataset)<br>- **MVI_0792_VIS_OB_R.avi** - The output video showing the results of the algorithm</p> <p>### 2. Buoy Dataset<br>The videos labeled with **buoyGT** belong to the Buoy Dataset. These results show the performance of the algorithm near maritime buoys. For example:<br>- **buoyGT_2_5_3_0.avi** - Original input video (available in the Buoy Dataset)<br>- **buoyGT_2_5_3_0_R.avi** - The output video showing the results of the algorithm</p> <p>## Video Naming Convention<br>Each result video follows a consistent naming convention related to the original input videos:<br>- **Original Video Filename**: [dataset]_[video details].avi<br>- **Result Video Filename**: [original video filename]_R.avi</p> <p>For instance:<br>- **buoyGT_2_5_3_0.avi** corresponds to **buoyGT_2_5_3_0_R.avi**<br>- **MVI_0792_VIS_OB.avi** corresponds to **MVI_0792_VIS_OB_R.avi**</p> <p>The **_R** suffix in the result videos indicates that the video contains the output of the horizon line detection algorithm.</p> <p>## How to Use<br>- To view the results for a specific video, locate the original input video in the corresponding public dataset and find the matching result video in this repository.<br>- For example, the result for the video "buoyGT_2_5_3_0.avi" can be found as "buoyGT_2_5_3_0_R.avi".</p> <p>## Datasets<br>The original datasets used in this study are not included in this repository. They are publicly available from the following sources:<br>1. **Singapore Maritime Dataset** (Onboard Segment)<br>2. **Buoy Dataset**</p> <p>Please refer to the respective dataset repositories for the original video files.</p> <p>## Citation<br>If you use these videos or the method presented in this study in your work, please cite the following:</p> <p>*Dynamic Region of Interest Generation for Maritime Horizon Line Detection using Time Series Analysis*.</p>
Methylation sequencing enhances interpretation of clonal hematopoiesis dynamics
<p><strong>We have developed a cost-effective DNA methylation sequencing assay to improve monitoring of clonal hematopoiesis. By inferring cell-type proportions, this method enhances interpretation of clonal trajectories compared to interpretation based on variant allele fraction only.</strong></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.