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127 results for “Self-assembly”
Experimental data for "Yu-Shiba-Rusinov bands in a self-assembled kagome lattice of magnetic molecules"
<p>Here, we provide all original data used in the manuscript "Yu-Shiba-Rusinov bands in a self-assembled kagome lattice of magnetic molecules"</p> <p>We acknowledge financial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) through projects 277101999 (CRC 183, project C03) and FR2726/10-1.</p>
Geometric Frustration Directs the Self-assembly of Nanoparticles with Crystallized Ligand Bundles
<p>This is the supporting dataset of the publication "Geometric Frustration Directs the Self-assembly of Nanoparticles with Crystallized Ligand Bundles".</p> <p><a href="https://doi.org/10.1021/acs.jpcb.4c04562">https://doi.org/10.1021/acs.jpcb.4c04562</a></p> <p>The description of the dataset can be found in the file README.txt</p>
Dataset for "Self-assembly of dodecagonal and octagonal quasicrystals in hard spheres on a plane"
<p>This dataset contains supplementary data for the publication:<br> <em>Self-assembly of dodecagonal and octagonal quasicrystals in hard spheres on a plane</em><br> E. Fayen, M. Impéror-Clerc, L. Filion, G. Foffi, and F. Smallenburg</p> <p> </p> <p><strong>Contents:</strong><br> The folder Data contains subfolders for each of the simulations performed for the construction of Fig. 3 of the main paper. Each folder name contains the size ratio q, the fraction of large particles x_L, and the packing fraction e in the file name. Note that the fraction of large particles x_L is related to the quantity x_S used in the paper via x_L = 1 - x_S.</p> <p>For simulations that were run for longer times, an additional folder with the same naming convention is included in the subfolder Long.</p> <p>Each simulation subfolder includes:</p> <p>- A coordinate file "last.sph" representing the final configuration of the simulation in plain text format. In this file, the first line specifies the number of particles, the second line the box size and non-additivity parameter Delta, and the remaining lines the coordinates of the particles. Each line containing coordinates consists of a letter indicating particle species (a or b), three spatial coordinates (with the z-coordinate always zero), and the particle radius. All lengths are given in units of the large-particle diameter.</p> <p>- An image of the final particle configuration "snapshot.png".</p> <p>- An image representing the associated scattering pattern, obtained by taking the Fourier transform of the particle coordinates and plotting the result as a function of the 2D wave vector on a logarithmic color scale.</p> <p> </p> <p>Additionally, the main folder contains a set of HTML files ("table_q*.html") that provide an overview of the snapshots and scattering patterns for each size ratio (specified in the file name). The HTML table for each size ratio uses the images from the "Data" and "Data/Long" subfolders as appropriate, and depends on the included "SAtable.css" and "SAtable.js" files. Within each table, clicking on one of the entries will enlarge the associated images.<br> <br> </p>
Research data supporting: "Self-assembly of cyclic peptide monolayers by hydrophobic supramolecular hinges"
<p>This repository contains the set of modelling data shown in the paper:<strong> "Self-assembly of cyclic peptide monolayers by hydrophobic supramolecular hinges"</strong>, published on Chemical Science (DOI: 10.1039/d3sc03930g)</p>
Dataset for "Biocompatible Rhamnolipid Self-Assemblies with pH-Responsive Antimicrobial Activity"
<p>This dataset provides the raw data supporting the paper: Biocompatible Rhamnolipid Self-Assemblies with pH-Responsive Antimicrobial Activity. It comprises SAXS data (Figure 2, Figure 3, Figure 4, Figure 5, Figure S2 and Figure S4), cryo-TEM images (Figure 2D, Figure 4D, Figure 5D, Figure 5E), Zeta-potential measurment (Figure 7), DLS data (Figure 8, Figure S5, Figure S6, Figure S7, Figure S8 and Table S2), Antimicrobial activity data (Figure 9, Table 1, Figure S9, Figure S10, Figure S12, Figure S13, Figure S14, Figure S15, Figure S16 and Table S3), Cytotoxicity data (Figure 10), Colloidal stability images (Figure S1 and Figure S3) and Biofilm inhibition and biofilm eradication assay (Figure S11).</p><p> </p>
Dataset for "CVD growth of self-assembled 2D and 1D WS2 nanomaterials for the ultrasensitive detection of NO2"
<p>This file contains the raw data used in the paper entitled CVD growth of self-assembled 2D and 1D WS2 nanomaterials for the ultrasensitive detection of NO2 published in Sensors and Actuators: B. Chemical 326 (2021) 128813</p> <p>DOI: <a href="https://doi.org/10.1016/j.snb.2020.128813">10.1016/j.snb.2020.128813</a></p>
Xanthene[n]arenes: Exceptionally Large, Bowl-Shaped Macrocyclic Building Blocks Suitable for Self-Assembly
<p>Data underlying the figures in the publication “Xanthene[<em>n</em>]arenes: Exceptionally Large, Bowl-Shaped Macrocyclic Building Blocks Suitable for Self-Assembly”, published in <em>J</em><em>ACS Au</em> 2021, 1, 11, 1885–1891. <a href="https://doi.org/10.1021/jacsau.1c00343">https://doi.org/10.1021/jacsau.1c00343</a></p>
Concentration-, Temperature- and Solvent-Dependent Self-Assembly: Merocyanine Dimerization as a Showcase Example for Obtaining Reliable Thermodynamic Data
<p><strong>Abstract:</strong> Mathematical models for the concentration-, temperature- and solvent-dependent analysis of self-assembly equilibria are derived for the most simple case of dimer formation, to highlight the assumptions these models and the thus determined thermodynamic parameters are based on. The three models were applied to UV/Vis absorption data for the dimerization of a highly dipolar merocyanine dye in 1,4-dioxane. Isothermal titration calorimetry (ITC) dilution experiments were performed as an independent reference technique. While the concentration-dependent analysis is according to our studies the most reliable method, also the less time-consuming temperature-dependent evaluation can give accurate results in the present example, despite small thermochromic effects. In contrast, the strong negative solvatochromism of the merocyanine tampers with the results from the solvent-dependent evaluation. Even though the studies presented in this work are limited to the monomer-dimer equilibrium of a dipolar dye, the basic principles can be transferred to other chromophores and different self-assembly models, including those for supramolecular polymerization.</p>
Complex k-Uniform Tilings by a Simple Bitopic Precursor Self-Assembled on Ag(001)_experimental dataset
<p>This experimental dataset contains the raw underlying data for the article "Complex k-Uniform Tilings by a Simple Bitopic Precursor Self-Assembled on Ag(001) Surface" by Lukáš Kormoš, Pavel Procházka, Anton O. Makoveev, and Jan Čechal. </p>
Supporting data for "Influence of an ionic comonomer on polymerization-induced self-assembly of diblock copolymers in non-polar media" (Polymer Chemistry, 2020, doi:10.1039/D0PY00101E)
<p>SAXS data [Q / (1/Å), I(Q) / Arb. unit, Uncertainty I(Q) / Arb. unit] provided as *.txt files</p> <p>DLS histograms [Diameter / nm, Proportion / %] provided as *.csv files</p>
Raw and analyzed data for manuscript: "Superhydrophilic coating of pine wood by plasma functionalization of self-assembled polystyrene spheres"
<p><strong>Abstract: </strong></p> <p>Self-assembling films typically used for colloidal lithography have been applied to pine wood substrates to change the surface wettability. Therefore, monodisperse polystyrene (PS) spheres have been deposited onto a rough pine wood substrate via dip coating. The resulting PS sphere film resembled a polycrystalline FCC-like structure with typical domain sizes of 5 – 15 single spheres. This self-assembled coating was further functionalized via an O<sub>2</sub> plasma. This plasma treatment strongly influenced the particle sizes in the outermost layer, and hydroxyl as well as carbonyl groups were introduced to the PS spheres’ surfaces, thus generating a superhydrophilic behaviour.</p>
Robot Self-Assembly as Adaptive Growth Process: Collective Selection of Seed Position and Self-Organizing Tree-Structures
<p>Autonomous self-assembly allows to create structures and scaffolds on demand and automatically. The desired structure may be predetermined or alternatively it is the result of an artificial growth process that adapts to environmental features and to the intermediate structure itself. In a self-organizing and decentralized control approach the robots interact only locally and form the structure collectively. Designing a complete approach that allows the robot group to collectively decide on where to start the self-assembly, that adapts at runtime to environmental conditions, and that guarantees the structural stability is challenging and does not yet exist. We present an approach to self-assembly inspired by diffusion-limited aggregation that generates an adaptive structure reacting to environmental conditions in an artificial growth process. During a preparatory stage the robots collectively decide where to start the self-assembly also depending on environmental conditions. In the actual self-assembly stage, the robots create tree-like structures that grow towards light. We report the results of robot self-assembly experiments with 50 Kilobots. Our results demonstrate how an adaptive growth process can be implemented in robots. We explain how our approach will be extended to a 3-d growth process and how robot self-assembly as an open-ended adaptive growth process opens up a multiplicity of future opportunities.</p>
Research data supporting "Sequence-Dependent Self-Assembly and Structural Diversity of Islet Amyloid Polypeptide-Derived β-Sheet Fibrils"
<p>Research data supporting the publication:</p> <p>Wang, S.-T. et al., 2017, Sequence-Dependent Self-Assembly and Structural Diversity of Islet Amyloid Polypeptide-Derived β-Sheet Fibrils, ACS Nano, http://dx.doi.org/10.1021/acsnano.7b02325</p>
Amyloid-motif-dependent tau self-assembly is modulated by isoform sequence context
<p><span>The microtubule-associated protein tau is implicated in neurodegenerative diseases characterized by amyloid formation. Mutations associated with frontotemporal dementia increase tau aggregation propensity and disrupt its endogenous microtubule-binding activity. However, the structural relationship between aggregation propensity and biological activity remains unclear. We employed a multi-disciplinary approach, including computational modeling, NMR, cross-linking mass spectrometry, and cell models to engineer tau sequences that modulate its structural ensemble. Our findings show that substitutions near the conserved 'PGGG' </span><span>β</span><span>-turn motif informed by tau isoform context reduce tau aggregation in vitro and cells and can even counteract aggregation from disease-associated proline-to-serine mutations. Engineered tau sequences maintain microtubule binding and explain why 3R isoforms exhibit reduced pathogenesis compared to 4R. We propose a simple mechanism to reduce the formation of pathogenic tau species while preserving biological function, thus offering insights for therapeutic strategies aimed at reducing tau protein misfolding in neurodegenerative diseases.</span></p> <p><strong>Description of Source Data and Supplementary Data</strong>: All MD, NMR (peptide and tauRD), ThT, XL-MS, MT stabilization, MT:tau modeling, and cell-based aggregation data are available in the Source_Data directory as Data S1, Data S2, Data S3, Data S4, Data S5, Data S6, Data S7, and Data S8, respectively. Supplementary Data for raw MD trajectory files, structure files for MSM modeling and validation file, and tau:MT modeling are available as "Supplementary_Data_MD_Trajectories_Structures", "Supplementary_Data_MSM_models_Structures" and "Supplementary_Data_MT-tau_complex_models", respectively."</p>
Self-Assembled Proteomimetic (SAP) with Antibody-like Binding from Short PNA-Peptide Conjugates
<p><span><span>Affinity proteins </span><span>based on </span><span>a </span><span>three-helix </span><span>bundle</span> <span>(</span><span>affibodies, </span><span>alphabodies</span><span> and computationally </span></span><span><span>de novo</span></span><span> <span>designed</span><span> ones)</span><span> have shown to be a general platform to discover binders with properties reminiscent of </span><span>antibodies</span><span>, combining </span><span>high </span><span>target </span><span>specificity</span><span> with </span><span>affinities reaching well below</span> <span>the </span><span>nanomolar</span><span>.</span> <span>Herein</span><span>,</span><span> we report a new strategy</span><span>, coined self-assembled proteomimetic (SAP)</span><span>,</span><span> to mimic </span><span>such</span><span> three-helix bundle</span><span> architecture with a hybridization-enforced two-helix </span><span>coiled</span> <span>coil</span><span> that is obtained by templated</span> <span>native chemical ligation (</span><span>T-</span><span>NCL) of PNA-peptide conjugates.</span> <span>This SAP </span><span>strategy</span> <span>stands out by</span><span> its</span><span> synthetic accessibility reducing the length on the longest </span><span>synthetic</span><span> peptide to </span><span>less than 30 amino acids, readily attainable by standard SPPS methodologies</span><span>. We show that the </span><span>T</span><span>-NCL dramatically accelerates the </span><span>ligation</span><span>, enabling this chemistry to </span><span>proceed</span> <span>in a combinatorial fashion </span><span>at</span><span> low</span> <span>micromolar</span><span> concentration</span><span>s</span><span>.</span> <span>We </span><span>demonstrate</span> <span>that small </span><span>combinatorial </span><span>libraries of </span><span>SAP</span><span>s</span><span> can be prepared in one operation and used directly in </span><span>affinity selection</span><span>s</span><span> against a target of interest </span><span>with an</span><span> LC-MS </span><span>analysis</span><span> of the fittest binders</span><span>.</span> <span>Moreover, we </span><span>show</span><span> that </span><span>the underlying</span> <span>design</span><span> paradigm</span><span> is functional for</span><span> SAPs based on structurally distinct three-helix peptides </span><span>aimed at</span><span> different </span><span>therapeutic </span><span>targets, namely</span> <span>HER2 </span><span>and</span><span> spike’s RBD</span><span>,</span></span> <span><span>reaching picomolar </span><span>affinities</span></span><span><span>. We further </span><span>illustrate </span><span>that the</span> <span>affinity </span><span>of the </span><span>S</span><span>AP</span><span> can be allosterically regulated using a toehold displacement</span><span> of the hybridizing PNAs</span><span> to disrupt the </span><span>coiled coil</span><span> stabilization.</span> <span>Finally, w</span><span>e show that </span><span>an RBD-targeting </span><span>SAP effectively inhibits viral </span><span>entry </span><span>of SARS-CoV-2</span> <span>with an IC</span></span><span><span>50</span></span><span><span> of </span><span>2.8</span> <span>nM</span><span>.</span></span><span> </span></p>
In vivo metallophilic self-assembly of a light-activated anticancer drug
<p>This data set contains all data of our submitted manuscript with the same title.</p> <p> </p>
Research data supporting "Self-assembled 2D free-standing Janus nanosheets with single-layer thickness"
<p>Raw research data supporting the publication Lin Y. et al., JACS, 2017, DOI: http://dx.doi.org/10.1021/jacs.7b06591</p>
Robust and Adaptive Robot Self-Assembly Based on Vascular Morphogenesis
<p>Self-assembly is the aggregation of simple parts into complex patterns as frequently observed in nature. Following this inspiration, creating programmable systems of self-assembly that achieve similar complexity and robustness with robots is challenging. As role model we pick the growth of natural plants that adapts to environmental conditions and is robust to disturbances, such as changes due to dynamic environments and cut parts. We program a robot swarm to self-assemble into tree-like shapes and to efficiently adapt to the environment. Our approach is inspired by the vascular morphogenesis of plants, that is the patterned formation of vascular tissue to transport fluids and nutrients internally. The aggregated robots establish an internal network of resource sharing, allowing them to make rational decisions collectively about where to add and where to remove robots. As an effect, the growth is adaptive to an environmental feature (here, light) and robust to changes in a dynamic environment. The robot swarm is able to self-repair by regrowing lost parts. We successfully validate and benchmark our approach in a number of robot swarm experiments showing adaptivity, robustness, and self-repair.</p>
Adaptive Path Formation in Self-Assembling Robot Swarms by Tree-like Vascular Morphogenesis
<p>For self-assembly, robot swarms can be programmed to form predefined shapes. <br> However, if the swarm is required to adapt the assembled shapes to dynamic features of the environment at runtime, then the shapes' structures need to be dynamic, too. <br> Prerequisite for adaptation is exploration and detection of changes followed by appropriate rearrangements of the assembled structure. <br> We study a self-assembling robot swarm forming trees to explore its environment and searching for bright areas. <br> The tree-formation process is inspired by the vascular morphogenesis of natural plants. <br> Detecting light produces a virtual resource shared within the tree, helping to drop useless branches while reinforcing efficient paths between bright areas and the tree root.<br> We successfully verify our self-assembly approach in several swarm robot experiments in a dynamic environment showing that the robot swarm can collectively discriminate between light sources at different distances and of different qualities.</p>
Data For New Methods for Understanding and Controlling the Self-Assembly of Reacting Systems Using Coarse-Grained Molecular Dynamics
<p>Data necessary to reproduce results in the dissertation : Thomas, Stephen, "New Methods for Understanding and Controlling the Self-Assembly of Reacting Systems Using Coarse-Grained Molecular Dynamics" (2018). <em>Boise State University Theses and Dissertations</em>. 1448.</p> <p>10.18122/td/1448/boisestate</p>
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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)
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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.