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96 results for “Dynamic Characterization”
Model for: Characterizing long‐term population conditions of the elusive red tree vole with dynamic individual‐based modeling
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Data from: A pioneering experimental investigation of a novel in-situ dynamic characterization of the tensile/compression stress-strain mechanism on human plantar soft tissue
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An Omni-Mesoscope for multiscale high-throughput quantitative phase imaging of cellular dynamics and high-content molecular characterization
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Combined dynamical and morphological characterization of geodynamo simulations
<p>Original scripts and data files for generating Figure 2, 3, 8, and 9.</p>
Characterizing the Dynamics of Wildland-Urban Interface and the Potential Impacts on Fire Activities in Alaska from 2000 to 2010
<p>The material contains the shapefiles of wildland-urban interface in Alaska in 2000 and 2010, which are derived from census data and National Land Cover Database.</p>
Project files provided as supporting information to the manuscript "Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model"
<pre>README file to the project files provided as supporting information to the manuscript "Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model" <br>October 8, 2024<br> Authors: Giovanni Mattiotti, Manuel Micheloni, Lorenzo Petrolli, Lorenzo Rovigatti, Luca Tubiana, Samuela Pasquali, Raffaello Potestio</pre> <p>==================================</p> <p>Trajectories and obsvervables relative to the scientific paper entitled:<br>"Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with oxRNA"</p> <p>Authors:<br>Giovanni Mattiotti, Manuel Micheloni, Lorenzo Petrolli, Luca Tubiana, Samuela Pasquali, Raffaello Potestio</p> <p>Brief description of the content of this folder:</p> <p><br>|_ oxDNA-CCMV_force.zip: the modified version of the oxDNA software we used to make the simulations with the CCMV-like spherical potential described in the paper<br>|<br>|_ CCMV_RNA2_oxRNA_simulations<br> |_ FOLDING (files of the "freely-folding" simulations)<br> | |_ FIRST_LAST_FRAMES (frames generated by oxDNA software)<br> | | |_ 0.15M (first and last frames of the runs at 0.15M)<br> | | | |_ REP1 (files relative to REP1 / REPI)<br> | | | | |_ first.dat<br> | | | | |_ last.dat <br> | | | |<br> | | | |_ REP2 (files relative to REP2 / REPII)<br> | | | | |_ first.dat<br> | | | | |_ last.dat <br> | | | |<br> | | | |_ REP3 (files relative to REP3 / REPIII)<br> | | | |_ first.dat<br> | | | |_ last.dat <br> | | |<br> | | |_ 0.50M (first and last frames of the runs at 0.50M)<br> | | | |_ [same structure as for 0.15M]<br> | | |<br> | | |_ 0.50M (first and last frames of the runs at 0.50M, T293K)<br> | | | |_ [same structure as for 0.15M]<br> | | |<br> | | |_ 0.50M (first and last frames of the runs at 0.50M, T293K, harmonic constraint to the ends)<br> | | |_ [same structure as for 0.15M]<br> | |<br> | |<br> | |_ HB_FILES (base pairs files generated by oxDNA software)<br> | | |_ hb_015M_I.dat (annotation of base pairs in oxDNA format, corresponding to REP1 at 0.15M salt concentration)<br> | | |_ hb_015M_II.dat (annotation of base pairs in oxDNA format, corresponding to REP2 at 0.15M salt concentration)<br> | | |_ hb_015M_III.dat (annotation of base pairs in oxDNA format, corresponding to REP3 at 0.15M salt concentration)<br> | | |_ hb_050M_I.dat (annotation of base pairs in oxDNA format, corresponding to REP1 at 0.5M salt concentration)<br> | | |_ hb_050M_II.dat (annotation of base pairs in oxDNA format, corresponding to REP2 at 0.5M salt concentration)<br> | | |_ hb_050M_III.dat (annotation of base pairs in oxDNA format, corresponding to REP3 at 0.5M salt concentration)<br> | | |_ hb_050M_293K_I.dat (annotation of base pairs in oxDNA format, corresponding to REP1 at 0.5M salt concentration, T 293K)<br> | | |_ hb_050M_293K_II.dat (annotation of base pairs in oxDNA format, corresponding to REP2 at 0.5M salt concentration, T 293K)<br> | | |_ hb_050M_293K_III.dat (annotation of base pairs in oxDNA format, corresponding to REP3 at 0.5M salt concentration, T 293K)<br> | | |_ hb_050M_293K_harm_I.dat (annotation of base pairs in oxDNA format, corresponding to REP1 at 0.5M salt concentration, T 293K, harmonic constraint to the ends)<br> | | |_ hb_050M_293K_harm_II.dat (annotation of base pairs in oxDNA format, corresponding to REP2 at 0.5M salt concentration, T 293K, harmonic constraint to the ends)<br> | | |_ hb_050M_293K_harm_III.dat (annotation of base pairs in oxDNA format, corresponding to REP3 at 0.5M salt concentration, T 293K, harmonic constraint to the ends)<br> | |<br> | |_ example_input.ox (example of oxDNA input file used to launch simulations and dump observables and trajectories)<br> | |<br> | |_ example_input_harm.ox (example of oxDNA input file used to launch simulations with harmonic constraint to the ends and dump observables and trajectories)<br> | |<br> | |_ harmonic_ends.dat (constraint force file used to run simulations with harmonic constraint to the ends)<br> |<br> |_ PACKED<br> |_ SIM_VTHEO (files of the simulations with the analytic-based external potential, as described in the paper...)<br> | |_ 0.15M (... with a salt concentration of 0.15M)<br> | | |_ REP1 (Replica with id 1, or I)<br> | | | |_ MD_scripts (files required by oxDNA software to launch the simulation for this replica)<br> | | | | |_ input_0.15M_REP1.ox (input file of oxDNA software to launch the simulation)<br> | | | | |_ force_0.15M_REP1.dat (additional file required for the application of an external force in the simulation, containing the relative parameters)<br> | | | |<br> | | | |_ input_structure (structure files in oxDNA format, one of which is used as starting configuration for the specific replica)<br> | | | | |_ PackingRNA2_0.15M_REP1.dat (last structure of simulation with time-dependent external packaging force)<br> | | | | |_ PackingRNA2_0.15M_REP2.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)<br> | | | | |_ PackingRNA2_0.15M_REP3.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)<br> | | | | |_ PackingRNA2_0.5M_REP1.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)<br> | | | | |_ PackingRNA2_0.5M_REP2.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)<br> | | | | |_ PackingRNA2_0.5M_REP3.dat (last structure of simulation with time-dependent external packaging force, not used - see name corresponding to this replica)<br> | | | |<br> | | | |_ data (output data generated by the simulation)<br> | | | |_ 1.E (files of the observables dumped during simulation)<br> | | | | |_ E_RNA2_0.15M_REP1.dat (energies of the system per each time frame: time frame, potential energy U, kinetic energy, total energy)<br> | | | | |_ P_RNA2_0.15M_REP1.dat (internal pressure of the system: time frame, total pressure, stress tensor components xx, yy, zz, xy, xz, yz)<br> | | | | |_ F_RNA2_0.15M_REP1.dat (components of the external force acting on each nucleotide, ordered according to the topology, per each frame)<br> | | | | |_ HB_RNA2_0.15M_REP1.dat (base pairs annotated, per each time frame dumped)<br> | | | |<br> | | | |_ 3.restart (restart/last configuration file dumped during simulation)<br> | | | |_ last_conf_RNA2_0.15M_Yukawa_REP1.dat (last frame dumped in the simulation, in oxDNA format)<br> | | |<br> | | |<br> | | |_ REP2 (Replica with id 2, or II)<br> | | | |_ [same content as REP1, but relative to replica 2 or II]<br> | | |<br> | | |_ REP3 (Replica with id 3, or III)<br> | | |_ [same content as REP1, but relative to replica 3 or III]<br> | |<br> | |_ 0.5M (... with a salt concentration of 0.5M)<br> | | |_ [same content as 0.15M, but for simulations done at 0.5M of salt concentration]<br> | |<br> | |_ 0.5M_293K_harm (... with a salt concentration of 0.5M, Temperature 293K and harmonic constraint to the ends)<br> | |_ [same content as 0.15M, but for simulations done at 0.5M of salt concentration]<br> |<br> |_ SIM_VCCMV (files of the simulations with the structure-based external potential, as described in the paper)<br> |_ [same content as SIM_VTHEO, but for simulations done with the structure-based external potential]</p> <p><br>For any additional file or data not present here, that was used to produce results in the paper, please ask to: giovanni.mattiotti@inserm.fr, manuel.micheloni@unitn.it, lorenzo.petrolli@unitn.it</p>
Spatial and Dynamic Characterization of Brain Activity for Language and Posture (Verticality) During Normal Aging. Magnetoencephalography (MEG) Study (MEG-AGING)
ClinicalTrials.gov study NCT04036162. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Integrated Diagnostics Characterization of Right Ventricular Diastolic Flow Dynamics in Pulmonary Arterial Hypertension
ClinicalTrials.gov study NCT01491646. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Dynamic Full-Field Optical Coherence Tomography for Structural and Microbiological Characterization of Central Venous Catheter-deposited Biofilm in Critically Ill Patients
ClinicalTrials.gov study NCT06216080. IPD Sharing: UNDECIDED. Countries: 1. Publications: 2.
Ultrasound Characterization of Ovarian Follicle Dynamics in Women With Amenorrhea
ClinicalTrials.gov study NCT01927432. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae)
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Structuran and NMR Characterization of Hexamer and Octamer Foldamers in Chloroform and Water: A Molecular Dynamics and Quantum Mechanics Approach
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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>
Data supporting publication: MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics
<p>MiFoDB (Microbial Foods Database) is a workflow and primary reference database which includes 675 assembled MAGs and RefSeq bacterial, yeast, fungal, and substrate genomes from fermented foods.</p>
LBA-ECO LC-23 Characterization of Vegetation Fire Dynamics for Brazil: 2001-2003
Satellite fire detection was determined from two sensors—the Advanced Very High Resolution Radiometer (AVHRR) on NOAA-12 and the Moderate Resolution Imaging Spectroradiometer (MODIS) on both the Terra and Aqua platforms, for 2001- 2003 to characterize fire activity in Brazil, giving special emphasis to the Amazon region. Active fire data for AVHRR/NOAA-12 was produced using a fixed threshold fire detection technique based on the algorithm developed by the Centro de Previsao do Tempo e Estudos Climaticos (CPTEC/INPE) (Setzer and Pereira, 1991; Setzer et al., 1994; Setzer and Malingreau, 1996). Active fire data for MODIS/Terra and MODIS/Aqua was produced using a contextual fire detection technique based on NASA-University of Maryland algorithm (Justice et al., 2003; Giglio et al.2003).Resulting fire counts were compared for major biomes of Brazil (Figure 1), the nine states of the Legal Amazon (e.g., Tocantins, Figure 2), and two important road corridors in the Amazon region (Figure 3). In evaluating the daily fire counts, there is a dependence on variations in satellite viewing geometry, overpass time, atmospheric conditions, and fire characteristics (Schroeder et al., 2005). The data provided are the coordinates of daily active vegetation fires in Brazil for 2001 through 2003 at 1km resolution for both AVHRR and MODIS sensors. Data are provided in both Arcview (shape file format) and ASCII comma separated file formats. Vector files for the major biomes of Brazil, the nine states of the Legal Amazon, and two important road corridors in the Amazon region are also included.
ABoVE: Characterization of Carbon Dynamics in Burned Forest Plots, NWT, Canada, 2014
This dataset provides field data from boreal forests in the Northwest Territories (NWT), Canada, that were burned by wildfires in 2014. During fieldwork in 2015, 211 burned plots were established. From these plots, thirty-two forest plots were selected that were dominated by black spruce and were representative of the full moisture gradient across the landscape, ranging from xeric to sub-hygric. Plot observations included slope, aspect, and moisture. At each plot, one intact organic soil profile associated with a specific burn depth was selected and analyzed for carbon content and radiocarbon (14C) values at specific profile depth increments to assess legacy carbon presence and combustion. Vegetation observations included tree density. Stand age at the time of the fire was determined from tree-ring counts. Estimates of pre-fire below and aboveground carbon pools were derived. The percent of total NWT wildfire burned area comprising of "young" stands (less than 60 years old at time of fire) was estimated.
Translational characterization of the temporal dynamics of metabolic dysfunctions in liver, adipose tissue and the gut during diet-induced NASH development in Ldlr−/−.Leiden mice
GEO Series GSE209762. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
Characterizing dynamics and lineage of bihormonal cell in mammalian pancreatic islets
GEO Series GSE248196. Mus musculus. 1440 samples. Type: Expression profiling by high throughput sequencing.
Linking cell dynamics with coexpression networks to characterize key events in chronic virus infections
GEO Series GSE123134. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Characterization of the dynamics of lamin A and lamin B LADs in HepG2 cells: impact of cyclosporin A
GEO Series GSE119631. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
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.