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70 results for “mechanical simulation”
Molecular dynamics simulations reveal the selectivity mechanism of structurally similar agonists to TLR7 and TLR8
<p>Trajectory, topology and index files for TLR7 (apo), TLR7-R, TLR7-H, TLR7-G, TLR8 (apo), TLR8-R, TLR8-H, TLR8-G systems. </p>
Raw data for: Simulation of neurotrophin receptor transmembrane helix interactions reveals active states and distinct signaling mechanisms
<p>This repository contains raw data and code related to "Simulation of neurotrophin receptor transmembrane helix interactions reveals active states and distinct signaling mechanisms" by Athanasiou et al.</p> <p>Included are molecular dynamics parameter files, initial structures and structures shown in the figures of the manuscript.</p> <p> </p> <p>Contact information:</p> <p>Name: Rebecca C. Wade<br>Institution: Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS); Heidelberg, Germany<br>Email: Rebecca.wade@h-its.org</p> <p> </p> <p>This research was funded by the European Union’s Horizon 2020 research and innovation programme “Euroneurotrophin” under the Marie Skłodowska-Curie grant agreement No 765704 and the Klaus Tschira Foundation. </p>
Investigating fracture mechanisms in glassy polymers using coupled particle-continuum simulations
<p>This repository contains public data for the publication "Investigating fracture mechanisms in glassy polymers using coupled atomistic-continuum simulations" [1].</p> <p>These scripts, force fields, topologies and other files may be used to reproduce the simulations and calculations that led to the above publication.</p> <p>The folder "md simulations" contains data files for pure MD simulations that were used as a reference for understanding molecular fracture mechanisms in our model.</p> <p>The folder "coupled simulations" contains data files for coupled MD-FE simulations which are the highlight of our publication.</p> <p> </p> <p>Reference:</p> <p>[1] W. Zhao, Y. Jain, F. Müller-Plathe, P. Steinmann, S. Pfaller, "Investigating fracture mechanisms in glassy polymers using coupled particle-continuum simulations", Journal of the Mechanics and Physics of Solids, 2024, 105884. DOI: <a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.jmps.2024.105884" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.jmps.2024.105884</span></span></a></p>
Experimental and Simulation data for the molecular mechanism of temperature-dependent phase separation of HSF1
<p>1. lmp_datatfile</p> <p>The documents contain the LAMMPS input datafiles of initial configuration used to run all simulations, including single chain, trimer(LZ1-3-RD), and RD systems.</p> <p>2.Experimental data.</p> <p>The documents contain original ucsf data</p>
Monte Carlo Simulations results for estimating an offshore structure fatigue life with a Fracture Mechanics based crack growth model, after additional information was considered through Bayesian inference at t=13 years
<p>Monte Carlo Simulations results for estimating an offshore structure fatigue life with a Fracture Mechanics based crack growth model, after additional information was considered through Bayesian inference at t=13 years</p>
Simulation code and results for "Critical behavior and the Kibble-Zurek mechanism in a musical phase transition"
<p>Matlab simulation code and results for "Critical behavior and the Kibble-Zurek mechanism in a musical phase transition."</p> <p>See readme.txt for descriptions of all files.</p>
Convolution, aggregation and attention based deep neural networks for accelerating simulations in mechanics [Dataset]
<p>Supplementary data for 'Convolution, aggregation and attention based deep neural networks for accelerating simulations in mechanics'. </p>
Initial and final MD simulation coordinates for "Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization"
<p>Initial and final coordinates for all MD simulations performed for the manuscript: "Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization."</p> <p>File uploaded is a ZIP folder, containing sub-folders for each capsid construct (wild type and mutants). Additionally, a README file is given in the top-level folder, which contains a description of the file contents.</p>
MD_Simulations_Molecular_mechanisms_of_inorganic-phosphate_release_from_the_core_and_barbed_end_of_actin_filaments
<p>This repository contains the models, protocols, datasets and Jupyter notebooks to reproduce the computational experiments in the paper:</p> <p>"Molecular mechanisms of inorganic-phosphate release from the core and<br> barbed end of actin filaments"</p> <p>by W. Oosterheert, F.E.C Blanc, A. Roy, A. Belyy, M.B. Sanders,, O. Hofnagel, G. Hummer, P. Bieling, S. Raunser</p>
ERCP Mechanical Simulator (EMS) Practice for Training Endoscopic Sphincterotomy
ClinicalTrials.gov study NCT02393638. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Effect of ERCP Mechanical Simulator (EMS) Practice on Endoscopic Retrograde Cholangiopancreatography (ERCP) Training
ClinicalTrials.gov study NCT01080833. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Mother Scented Simulated Hand for Mechanically Ventilated Preterm Neonates During Invasive Procedures?
ClinicalTrials.gov study NCT05080582. IPD Sharing: NO. Countries: 1. Publications: 7.
METHODS. Bovine ilia were used in the simulations because their histological structure (a fibrolamellar cortex overlying cancellous bone26) was found to match that of the Triceratops ilium. Bone sections 10 x 50 x 縠 3.0 cm with cortices ranging from 0.5 to 5.5 mm in depth (the range of initial cortical-thickness estimates based on gross morphology) were mounted on a servohydraulic mechanical loading frame (MTS Bionix, Minneapolis) and penetrated with an aluminium-bronze T. rex tooth replica. The replica was cast from an actual adult T. rex maxillary tooth, after casts made from some ofthe deeper bite marks revealed the size and shape of the teeth that had impacted the pelvis8 • The replica was penetrated into the ilia sections at 1 mm s-1 to a depth of 11.5 mm, equivalent to the maximum depth of the deepest ilium bite mark8 • Forces were measured with an MTS 25 N strain-gauge-based axial load cell accurate to 0.2%. The forces increased with increasing penetration depth even after the cortical layer had been perforated and the underlying cancellous bone was being crushed. The increase in force with penetration depth is attributed to a greater cortical surface area coming into contact with the semi-conical penetrator tooth as it descended through the ilia. in Bite-force estimation for Tyrannosaurus rex from tooth-marked bones
METHODS. Bovine ilia were used in the simulations because their histological structure (a fibrolamellar cortex overlying cancellous bone26) was found to match that of the Triceratops ilium. Bone sections 10 x 50 x 縠 3.0 cm with cortices ranging from 0.5 to 5.5 mm in depth (the range of initial cortical-thickness estimates based on gross morphology) were mounted on a servohydraulic mechanical loading frame (MTS Bionix, Minneapolis) and penetrated with an aluminium-bronze T. rex tooth replica. The replica was cast from an actual adult T. rex maxillary tooth, after casts made from some ofthe deeper bite marks revealed the size and shape of the teeth that had impacted the pelvis8 • The replica was penetrated into the ilia sections at 1 mm s-1 to a depth of 11.5 mm, equivalent to the maximum depth of the deepest ilium bite mark8 • Forces were measured with an MTS 25 N strain-gauge-based axial load cell accurate to 0.2%. The forces increased with increasing penetration depth even after the cortical layer had been perforated and the underlying cancellous bone was being crushed. The increase in force with penetration depth is attributed to a greater cortical surface area coming into contact with the semi-conical penetrator tooth as it descended through the ilia.
Data from: Sexual size dimorphism, prey morphology, and catch success in relation to flight mechanics in the Peregrine Falcon: a simulation study
In common with many other raptors, female Peregrine Falcons Falco peregrinus are about 50% heavier than males. Their sexual dimorphism is thought to allow breeding pairs to exploit a wider range of prey through a division of labor: the male being able to catch more maneuverable prey species; the female capable of carrying larger ones. Given the difficulty of assessing the catch success and load carrying capacity of both sexes of falcon in the field, we here adopt a novel approach to test the division‐of‐labor theory by using a detailed physics‐based flight simulator of birds. We study attacks by male and female Peregrine Falcons on prey species ranging from small passerines to large ducks, testing how catch success relates to the flight performance of predator and prey. Males prove to be better than females at catching highly maneuverable prey in level flight, but the catch success of both sexes improves and becomes more similar when diving, because of the higher aerodynamic forces that are available to both sexes for maneuvering in high‐speed flight. The higher maximum roll acceleration of the male Peregrine Falcon explains its edge over the female in catching maneuverable prey in level flight. Overall, catch success is more strongly influenced by the differences in maneuverability that exist between different species of prey than between the different sexes of falcon. On the other hand, the female can carry up to 50% greater loads than the male. More generally, our detailed simulation approach highlights the importance of several previously overlooked features of attack and escape. In particular, we find that it is not the prey's instantaneous maximum centripetal acceleration but the prey's ability to sustain a high centripetal acceleration for an extended period of time that is the primary driver of the variation in catch success across species.
Datasets associated with the manuscript "Discovering SARS-CoV-2 neoepitopes and the associated TCR-pMHC recognition mechanisms by combining single-cell sequencing, deep learning, and molecular dynamics simulation techniques"
<p>meta_data_TCR-pMHC_from_STCRDab.tsv, TCR-pMHC structures used for contacts analysis.</p><p>tcr_gliph_input_sars2.tsv, input files (TCR sequences and related information) used for clustering TCRs targeting SARS-CoV-2 epitopes and epitope-unknown TCRs.</p><p>tcr_gliph_input_non-sars2.tsv, input files used for clustering TCRs targeting non-SARS-CoV-2 epitopes and epitope-unknown TCRs.</p><p>tcr_gliph_output*, output files from the GLIPH software, including the recognized TCR clusters by GLIPH (convergence-group.txt), the linkage information of TCR clusters (clone-network.txt), and the recognized motif in TCR clusters (kmer.txt).</p><p>md_trajs.tar, structures and MD simulation trajectories of TCR-614-pMHC and TCR-204-pMHC complexes.</p>
Exploring Conformational Landscapes and Binding Mechanisms of Convergent Evolition for the SARS-CoV-2 Spike Omicron Variant Complexes with the ACE2 Receptor Using AlphaFold2-Based Structural Ensembles and Molecular Dynamics Simulations
Open the record for dataset details and reuse information.
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>
DATA for Evaluating Scale-Aware Boundary Layer Similarity Functions and Their Mechanisms in Tropical Cyclone Modeling Using Idealized Large-Eddy Simulations
<p>data.xlsx has the data to make Figs.1-4</p> <p> </p>
Simulation Data for "A formation mechanism for "Wrong Way" Radio Relics"
<p>Data for the relevant simulation domain used in <a href="https://ui.adsabs.harvard.edu/abs/2023arXiv230900046B/abstract">Böss et. al. (2023a)</a>.</p> <p>Analysis scripts can be found at <a href="https://zenodo.org/record/8391369">here</a>.</p>
Research on the Optimization of Treatment for Spinal Metastases With Radioactive Particle Implantation Using TPS and Mechanical Dual Simulation
ClinicalTrials.gov study NCT07171996. IPD Sharing: YES. Countries: 1. Publications: 0.
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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.