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4 results for “free energy landscape”
Extended ensemble molecular dynamics study of ammonia–cellulose I complex crystal models: free-energy landscape and atomistic pictures of ammonia diffusion in the crystalline phase.
<p>The data deposited here accompany the manuscript "Extended ensemble molecular dynamics study of ammonia–cellulose I complex crystal models: free-energy landscape and atomistic pictures of ammonia diffusion in the crystalline phase" and include the molecular dynamics trajectories and the AMBER topology (parm) files. Detailed file contents are summarized in the README file.</p>
Data and code for "Revealing the free energy landscape of halide perovskites: Metastability and transition characters in CsPbBr3 and MAPbI3"
<p>This record contains a neuroevolution potential (NEP) model (<code>nep-MAPI-SCAN.txt</code> ) for MAPbI3 used in the linked publication. The model can be used in conjunction with the <a href="https://gpumd.org">GPUMD package</a>. The <a href="https://calorine.materialsmodeling.org">calorine package</a> provides a Python interface to GPUMD.<br> Several primitive structures in extended xyz format can be found in the <code>*.xyz</code> files. These structures have been relaxed using the NEP model included here. The <code>demo-for-using-structures-and-model.py</code> script illustrates how to access the structures and model.</p>
Membrane free-energy landscapes derived from atomistic dynamics explain nonuniversal cholesterol-induced stiffening - Sample files
<p><strong>Initial and final snapshots of atomistic simulations of curved lipid bilayers</strong></p> <p>Each PDB file is named according to lipid composition and number of lipid molecules per leaflet.</p> <p>To reduce file size, solvent molecules were excluded and multiple snapshots of the same system zipped together.</p> <p>Reference: <a href="https://doi.org/10.1101/2023.02.02.525347">https://doi.org/10.1101/2023.02.02.525347</a></p>
Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes
<p>Input scripts for the simulations</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.