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8 results for “filed investigation”
Project files provided as supporting information to the manuscript "Ligand-protein interactions in lysozyme investigated through a dual-resolution model"
<p><strong>README file for the project files provided as supporting information to the manuscript "Ligand-protein interactions in lysozyme investigated through a dual-resolution model"</strong></p> <p>February 12, 2020</p> <p>Authors: Raffaele Fiorentini, Kurt Kremer and Raffaello Potestio</p> <p>================================</p> <p>Overview</p> <p>The dataset is organised in three (compressed) subfolders (see the tree diagrams in each section):</p> <p>- annihilation<br> - decoupling<br> - density</p> <p>The figure deltaG_binding_ann_dec_comparison.png shows the results of binding free energy calculations comparing the values obtained both for annihilation and decoupling.</p> <p>The figure deltaG_binding_annih_gromacs_espp.png displays the results for Binding FE, comparing the values obtained in GROMACS and ESPResSo++.</p> <p>The README.pdf file contains detailed information about these folders and their content.</p> <p>================================</p> <p>The "annihilation" folder contains all results concerning the calculation of binding free energy in case of annihilation and it is divided in two parts: </p> <p>- complex<br> - ligand</p> <p>In "complex" are reported the results of Ligand-Protein FE both in ESPResSo++ and GROMACS. All simulations are fully-atomistic. </p> <p>In "ligand" are reported the results of ligand solvation free energy both in ESPResSo++ and GROMACS. All simulations are fully-atomistic. </p> <p>====</p> <p>The "decoupling" folder contains all results concerning the calculation of binding free energy in case of decoupling and it is divided in three parts: </p> <p>- complex-DualRes<br> - complex-FullyAT<br> - ligand</p> <p>In "complex-DualRes" are reported the results of Ligand-Protein FE only in ESPResSo++ (GROMACS cannot do decoupling). The system is simulated in Dual-Resolution. It is possible to find the trajectory files in the sub-directories "lambdaindex-0" and "lambdaindex-30".</p> <p>In "complex-fullyAT" are reported the results of Ligand-Protein FE only in ESPResSo++. The system simulated is fully-atomistic. It is possible to find the trajectory file in the sub-directories "lambdaindex-0" and "lambdaindex-30".</p> <p>In "ligand" are reported the results of ligand solvation free energy only in ESPResSo++. All simulations are fully-atomistic. It is possible to find the trajectory file in the sub-directories "lambdaindex-0" and "lambdaindex-20".</p> <p>====</p> <p>The "density" folder contains the data for the tuning of the c parameter of the steric repulsion among residues. This parameter is tuned so that the water density attains the value computed in all-atom simulations.</p>
Input parameters and output trajectory files for manuscript "Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CLPro: Insights from the Computational and Experimental Investigations"
<p>Input parameters used for molecular dynamics simulations on GROMACS 2022 software and the output trajectory files for calculating binding free energy, in the manuscript with the title: "Inhibitory Activity of Flavonoid Scaffolds on SARS-CoV-2 3CL<sup>Pro</sup>: Insights from the Computational and Experimental Investigations"</p>
Alignment of mitogenome sequences (FASTA file) for a paleogenomic investigation of overharvest implications in an endemic wild reindeer subspecies
<p>Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-Arctic Svalbard reindeer (<em>Rangifer tarandus platyrhynchus</em>), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17–20th centuries. Here we investigate changes in genetic diversity, population structure, and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient and historical nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90), to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation followed by pronounced genetic drift have altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 23%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long-term interplay of past, current, and future stressors in wildlife conservation.</p>
Pedestrian single file movement on stairway: Investigating the impact of stair construct on pedestrian ascent and descent fundamental diagram
<p>Pedestrian single-file movement on stairs</p>
Supplementary files for 'Investigating the use of grinding tools in prehistoric Bulgaria by phytolith analysis'
<p>Supplementary files for 'Investigating the use of grinding tools in prehistoric Bulgaria by phytolith analysis'.</p> <p>ESM 1. Full description of the protocol used to process archaeological samples for phytolith extraction and other files relevant to the methods.</p> <p>ESM 2. Phytolith datasets, including the full counting sheet, the processing weights and the dataset used for multivariate statistics.</p> <p>ESM 3. Description of the methods and the results of the XRF analysis of two grinding tools.</p>
Alignment of mitogenome sequences (FASTA file) for a paleogenomic investigation of overharvest implications in an endemic wild reindeer subspecies
Open the record for dataset details and reuse information.
CONTAM Project Files and Exposure Data for An In Silico Investigation of Activity-Related Physical, Chemical, and Biological Pollutant Exposure in Basements Using CONTAM
Open the record for dataset details and reuse information.
Experimental files for Investigation of low temperature plasmas formed in low density gases surrounding laser produced plasmas
<p>Temporal and spectral investigation of plasmas produced by interaction of laser pulses, with gaseous mixtures, was performed. The interaction took place inside a small portion of dense gas mixture injected temporarily into a chamber filled with the same mixture under low pressure. High-temperature plasmas produced directly by the laser pulse were a source of soft x rays and charged particles, ionizing and exciting the surrounding gas. In this way, low-temperature plasmas were produced. The formation of low-temperature plasmas was studied using optical spectroscopy and streak imaging. The experimental data.zip file contains the experimental data from an optical spectrograph and optical streak camera.</p> <p>Work supported by the National Science Centre, Poland, grant agreement no. 2020/39/B/ST2/00509</p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.