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35 results for “time step”
Automatic time step adjustment for shortening the runtime of the simulation of marine ecosystem models
<p><strong>Abstract:</strong></p> <p>In investigating the global carbon cycle, shortening the runtime of the simulation of marine ecosystem models is an important issue. More specifically, steady annual cycles mostly are used to assess and validate the models against<br> observational data and to identify relevant biogeochemical processes. Offline simulations based on the transport matrix method already reduce the high computational effort significantly. Furthermore, they facilitate the application<br> of larger time steps in a simple way. In this paper, we present two different methods that automatically adjust the time step during the simulation of a steady state using transport matrices. The algorithms use either an adaptive<br> step size control or decreasing time steps. Their aim is to apply always the time step as large as possible but without any manual selection. We applied the methods for a variety of ecosystem models of different complexity, using Latin<br> hypercube samples of size 100 for the model parameters of each model. We showed that both methods computed an approximation of the steady annual cycle that was of the same accuracy as solutions obtained with a fixed time step. Both algorithms lowered the runtime of the steady annual cycle computation significantly. The performance gain depended on the complexity of the models. Moreover, the adaptive method has a certain overhead that might lead to higher computational cost in special cases.</p> <p><strong>Content:</strong></p> <ul> <li>Tracer concentrations of a reference solution for all parameter vectors and biogeochemical models</li> <li>SQLite database including the results using the decreasing time steps algorithm</li> <li>Tracer concentrations of the results using the decreasing time steps algorithm</li> <li>SQLite database including the results using the step size control algorithm</li> <li>Tracer concentrations of the results using the step size control algorithm</li> </ul>
Can a knee sleeve influence ground reaction forces and knee joint power during a step-down hop in participants following ACL reconstruction? Discrete and time-continuous datasets
<p>Using a cross-over design, we estimated GRF and knee kinematics and kinetics during a step-down hop for 30 participants (age 26.1 [SD 6.7] years, 14 women) following ACL reconstruction (median 16 months post-surgery) with and without wearing a knee sleeve. In a subsequent randomised clinical trial, participants in the ‘Sleeve Group’ (n=9) then wore the sleeve for 6 weeks at least 1 hour daily, while a ‘Control Group’ (n=9) did not wear the sleeve. Statistical parametric mapping (SPM) was used to compare (1) GRF trajectories in the three planes as well as knee joint power between three conditions at baseline (uninjured side, unsleeved injured and sleeved injured side); (2) within-participant changes for GRF and knee joint power trajectories from baseline to follow-up between groups. We also compared discrete peak GRFs and power, rate of (vertical) force development, and mean knee joint power in the first 5% of stance phase. Time-continuous and discrete data are included in this dataset.</p>
Input files for "Faster Simulations with a 5 fs Time Step for Lipids in the CHARMM Force Field"
<p>The performance of all-atom molecular dynamics simulations is limited by an integration time step of 2 fs, which is needed to resolve the fastest degrees of freedom in the system, namely, the vibration of bonds and angles involving hydrogen atoms. The virtual interaction sites (VIS) method replaces hydrogen atoms by massless virtual interaction sites to eliminate these degrees of freedom while keeping intact nonbonded interactions and the explicit treatment of hydrogen atoms. We have modified the existing VIS algorithm for most lipids in the popular CHARMM36 force field by increasing the hydrogen atom masses at regular intervals in the lipid acyl chains and obtained lipid properties and pore formation free energies in very good agreement with those calculated in simulations without VIS. Our modified VIS scheme enables a 5 fs time step resulting in a significant performance gain for all-atom simulations of membranes. The method has the potential to make longer time and length scales accessible in all-atom simulations of membrane–protein complexes.</p> <p>The file set contains individual lipid topologies for virtual interaction sites for standard CHARMM lipids, as well as a README file with instructions on how to implement the VIS algorithm for membranes or membrane-protein complexes</p> <p>Please Cite: <a href="//pubs.acs.org/doi/10.1021/acs.jctc.8b00267">10.1021/acs.jctc.8b00267</a></p> <p> </p>
Strain Evolution in 2D-Digital Composites-T= 1-15 time steps.
<p>Strain Evolution in 2D - Digital Composites for first 15 time steps.</p> <p>Abaqus simulation script can be found <a href="https://github.com/M3RG-IITD/StrainEvolution">here</a></p>
"I was on vacation in Mala, living in a self-catering holiday cottage, together with my girlfriend (we're together for 11 years now), recovering from a heavy workload in the second half of 2008. We were sitting outside, probably sipping a beer, when we heard the sound of bells approaching. Stepping on the stones that enclose the little forecourt of the cottage, we could just see the goat herd being driven by. Idashed for my R09 (recording equipment) to get that impression – but too slowly too late, it seemed, the herd had disappeared and with it the sound. When Iwas about to pack my R09 again the sound appeared to come back, so Idashed down the driveway, just in time to see the herd pass, and then Ifollowed it a couple of hundred meters, walking behind the herd, trying not to breathe or make stepping sounds, eventually, when dogs started barking and a car approached from behind, I stopped and let the goats go on, the car passes, honks ... and Icut the recording and walk back to the cottage." [Peter/ptroxler]13 in Collecting Sounds. Online Sharing of Field Recordings as Cultural Practice
"I was on vacation in Mala, living in a self-catering holiday cottage, together with my girlfriend (we're together for 11 years now), recovering from a heavy workload in the second half of 2008. We were sitting outside, probably sipping a beer, when we heard the sound of bells approaching. Stepping on the stones that enclose the little forecourt of the cottage, we could just see the goat herd being driven by. Idashed for my R09 (recording equipment) to get that impression – but too slowly too late, it seemed, the herd had disappeared and with it the sound. When Iwas about to pack my R09 again the sound appeared to come back, so Idashed down the driveway, just in time to see the herd pass, and then Ifollowed it a couple of hundred meters, walking behind the herd, trying not to breathe or make stepping sounds, eventually, when dogs started barking and a car approached from behind, I stopped and let the goats go on, the car passes, honks ... and Icut the recording and walk back to the cottage." [Peter/ptroxler]13
Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity
<p>Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved the way for cellular differentiation, including differentiation of male and female gametes. A useful model for studying the evolution of multicellularity and cellular differentiation is the volvocine algae, a clade of freshwater green algae whose members range from unicellular to colonial, from undifferentiated to completely differentiated, and whose gamete types can be isogamous, anisogamous, or oogamous. To better understand how multicellularity, differentiation, and gametes evolved in this group, we used comparative genomics and fossil data to establish a geologically calibrated roadmap of when these innovations occurred. Our results, presented as ancestral-state reconstructions, show that multicellularity arose independently twice in this clade. Our chronograms indicate multicellularity evolved during the Carboniferous-Triassic periods in Goniaceae + Volvocaceae, and possibly as early as the Cretaceous in Tetrabaenaceae. Using divergence time estimates we inferred when, and in what order, specific developmental changes occurred that led to differentiated multicellularity and oogamy. We find that in the volvocine algae the temporal sequence of developmental changes leading to differentiated multicellularity is much as proposed by David Kirk, and that multicellularity is correlated with the acquisition of anisogamy and oogamy. Lastly, morphological, molecular, and divergence time data suggest the possibility of cryptic species in Tetrabaenaceae.</p>
Data for "Fully Implicit Time Stepping can be Efficient on Parallel Computers"
<p>Benchmark data and python plotting programs</p>
Cost of step time asymmetry and step length asymmetry in human walking
Open the record for dataset details and reuse information.
Fossil-calibrated inference of divergence times among the Volvocine algae enables reconstruction of the steps that led to differentiated multicellularity
Open the record for dataset details and reuse information.
Data from: ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps
Partial clonality is commonly used in Eukaryotes and has large consequences for their evolution and ecology. Assessing accurately the relative importance of clonal versus sexual reproduction matters for studying and managing such species. Here, we proposed a Bayesian approach, ClonEstiMate, to infer rates of clonality c from populations sampled twice over a short time interval, ideally one generation time. The method relies on the likelihood of the transitions between genotype frequencies of ancestral and descendent populations, using an extended Wright-Fisher model explicitly integrating reproductive modes. Our model provides posterior probability distribution of inferred c, given the assumed rates of mutation, as well as inbreeding and selfing when occurring. Tested under various conditions, this model provided accurate inferences of c, especially when the amount of information was modest, i.e. low sample sizes, few loci, low polymorphism and strong linkage disequilibrium. Inferences remained robust when mutation models and rates were misinformed. However, the method was sensitive to moderate frequencies of null alleles and when the time interval between required samplings exceeding two generations. Misinformed rates on mating modes (inbreeding and selfing) also resulted in biased inferences. Our method was tested on eleven datasets covering five partially clonal species, for which the extent of clonality was formerly deciphered. It delivered highly consistent results with previous information on the biology of those species. ClonEstiMate represents a powerful tool for detecting and inferring clonality in finite populations, genotyped with SNPs or microsatellites. It is freely available at http://https://w">https://w w w 6.rennes.inra.fr / igepp_eng/ Productions/ Software.
Blueprint for modelling time effects in a stepped-wedge, cluster-randomised trial
<div><strong># Project title</strong></div> <div>Blueprint for modelling time effects in a stepped-wedge, cluster-randomised trial</div> <div> </div> <div><strong># Brief project overview</strong></div> <div>This is Data coming out of the IPOS-Dem project, a Stepped-wedge Cluster Randomised Trial (SW-CRT). Please make shure to check out the SW-CRT protocol for more details at <a href="https://www.doi.org/10.1111/jan.14953">https://www.doi.org/10.1111/jan.14953</a>. </div> <div> </div> <div>We are currently working on our main study (SW-CRT) analysis. While we remain dedicated to open science, our priority is to ensure the utmost integrity of our ongoing research.</div> <div> </div> <div><strong># Contributors</strong></div> <div>Frank Spichiger, Andrea Koppitz, André Meichtry</div> <div> </div> <div><strong>## Repository overview</strong></div> <div> </div> <div>|-- readme.md</div> <div>|-- documentation</div> <div> |--readme.md</div> <div> |--Datadictionary.html</div> <div>|-- data</div> <div> |--readme.md</div> <div> |--IPOS-Dem_CH-SW-CRT_PLD_Qualidem.feather</div> <div> |--IPOS-Dem_CH-SW-CRT_PLD_locf_Qualidem.feather</div> <div> |--csv</div> <div> |--IPOS-Dem_CH-SW-CRT_PLD_Qualidem.csv</div> <div> |--IPOS-Dem_CH-SW-CRT_PLD_locf_Qualidem.csv</div> <div>|-- analysis</div> <div> |--readme.md</div> <div> |--240229_Analysis_Main.html</div> <div> |--240229_Analysis_Main.qmd</div> <div> |--grateful-refs.bib</div> <div> |--output</div> <div> |--models-REML.csv</div> <div> |--models.csv</div> <div> |--figures</div> <div> |--Conversions for plotting - 1.png</div> <div> |--Define Model 5-1.png</div> <div> |--Defining Model 4-1.png</div> <div> |--m1predictions.eps</div> <div> |--m1predictions.png</div> <div> |--m2predictions.eps</div> <div> |--m2predictions.png</div> <div> |--m3predictions.eps</div> <div> |--m3predictions.png</div> <div> |--m4predictions.eps</div> <div> |--m4predictions.png</div> <div> |--m5predictions.eps</div> <div> |--m5predictions.png</div> <div> |--Model 1 plot-1.png</div> <div> |--Model 1 plot-2.png</div> <div> |--Model 2 plot-1.png</div> <div> |--Model 2 plot-2.png</div> <div> |--Model 3 plot-1.png</div> <div> |--More plots for Model 1-1.png</div> <div> |--More plots for Model 1-2.png</div> <div> |--More plots for Model 4-1.png</div> <div> |--More plots for Model 5-1.png</div> <div> |--Plots for Model 4-1.png</div> <div> |--Plots for Model 5-1.png</div> <div> |--Plots for the other two models-1.png</div> <div> |--Plots for the other two models-2.png</div> <div> </div> <div> </div> <div># Applicable instructions</div> <div>The R markdown files were generated using R 4.2.2 in RStudio 2023.12.1 for MacOS X you can run them using free software but will need to install R, Rstudio and the packages cited at the end of the quarto or the rendered html we used.</div> <div> </div> <div># Additional resources</div> <div>- Main study protocol: <a href="https://www.doi.org/10.1111/jan.14953">https://www.doi.org/10.1111/jan.14953</a></div> <div>- QUALIDEM measure used: <a href="https://doi.org/10.1186/1477-7525-11-91">https://doi.org/10.1186/1477-7525-11-91</a> </div> <div>- Pos-Pal consortium with more information on the measure: <a href="https://www.pos-pal.org">https://www.pos-pal.org</a></div> <div>- IPOS-Dem translation and adaption: <a href="https://www.doi.org/10.1186/s41687-022-00420-7">https://www.doi.org/10.1186/s41687-022-00420-7</a></div> <div>- IPOS-Dem inter-rating reliability: <a href="https://doi.org/10.1371/journal.pone.0286557">https://doi.org/10.1371/journal.pone.0286557 </a></div>
Shortening the runtime using larger time steps for the simulation of marine ecosystem models
<p><strong>Abstract:</strong></p> <p>The reduction of computational costs for marine ecosystem models is important for the investigation and detection of the relevant biogeochemical processes because such models are computationally expensive. In order to lower these computational costs by means of larger time steps we investigated the accuracy of steady annual cycles (i.e., an annual periodic solution) calculated with different time steps. We compared the accuracy for a hierarchy of biogeochemical models showing an increasing complexity and computed the steady annual cycles with offline simulations that are based on the transport matrix approach. For each of these biogeochemical models, we obtained practically the same solution even though larger time steps. This indicates that larger time steps shortened the runtime with an acceptable loss of accuracy.</p> <p><strong>Content:</strong></p> <ul> <li>SQLite database including the obtained results</li> <li>Tracer concentrations obtained with different time steps for all used models and parameter vectors</li> </ul>
Simulation input files and analysis scripts for "Small ionic radii limit time step in Martini 3molecular dynamics simulations"
<p>Simulation input files and analysis scripts for "Small ionic radii limit time step in Martini 3molecular dynamics simulations".</p> <p>See <a href="https://aip.scitation.org/doi/10.1063/5.0095523">https://aip.scitation.org/doi/10.1063/5.0095523</a> for details.</p> <p>NOTE: some combinations of settings result in simulations that crash!<br> </p>
Data for 'Storm Surge Modeling as an Application of Local Time-stepping in MPAS-Ocean'
<p>Data for 'Storm Surge Modeling as an Application of Local Time-stepping in MPAS-Ocean', submitted to the Journal for Advances in Modeling Earth Systems (JAMES).</p> <p>The repository consists of three main parts:</p> <ol> <li>The `run` directory contains a pre-built run directory as an example.</li> <li>The `scripts` directory contains the scripts that were used to generate important plots.</li> <li>The `data` directory contains model output from performance and accuracy experiments.</li> </ol>
Data and supplementary information for "A multiple time step algorithm for trajectory surface hopping simulations"
<p>This repository contains the supplementary information as well as the data necessary to reproduce the content of the article "A multiple time step algorithm for trajectory surface hopping simulations".</p>
Numerical experimental data about mixing time step of tracer-aided model
<p>This is the numerical experimental data about mixing time step of tracer-aided model related to the response letter of manuscript HYDROL49160 in Journal of Hydrology</p>
Walking Away From Back Pain, One Step at a Time
ClinicalTrials.gov study NCT02284958. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps
Open the record for dataset details and reuse information.
Impact of horizontal resolution and model time step on European precipitation extremes in the OpenIFS 43r3 atmosphere model
<p>Python scripts used for GMD paper</p>
Impact of horizontal resolution and model time step on European precipitation extremes in the OpenIFS 43r3 atmosphere model
<p>Python scripts used for GMD paper</p>
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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.