2024-03-28T22:42:20Z
https://zenodo.org/oai2d
oai:zenodo.org:4618025
2022-06-30T09:49:30Z
user-gmpavan-lab
Luigi, Leanza
Giovanni, Pavan
Claudio, Perego
Mattia, Perrone
2020-09-29
<p>The fast dynamics occurring in natural processes increases the difficulty of creating biomaterials capable of mimicking Nature. Within synthetic biomaterials, water-soluble supramolecular polymers show great potential in mimicking the dynamic behavior of these natural processes. In particular, benzene-1,3,5-tricaboxamide (BTA)-based supramolecular polymers have shown to be highly dynamic through the exchange of monomers within and between fibers, but their suitability as biomaterials has not been yet explored. Herein we systematically study the interactions of BTA supramolecular polymers bearing either tetraethylene glycol or mannose units at the periphery with different biological entities. When BTA fibers were incubated with bovine serum albumin (BSA), the protein conformation was only affected by the fibers containing tetraethylene glycol at the periphery (BTA-OEG<sub>4</sub>). Coarse-grained molecular simulations showed that BSA interacted with BTA-OEG<sub>4</sub> fibers rather than with BTA-OEG<sub>4</sub> monomers that are present in solution or that may exchange out of the fibers. Microscopy studies revealed that, in the presence of BSA, BTA-OEG<sub>4</sub> retained their fiber conformation although their length was slightly shortened. When further incubated with fetal bovine serum (FBS), both long and short fibers were visualized in solution. Nevertheless, in the hydrogel state, the rheological properties were remarkably preserved. Further studies on the cellular compatibility of all the BTA assemblies and mixtures thereof were performed in four different cell lines. A low cytotoxic effect at most concentrations was observed, confirming the suitability of utilizing functional BTA supramolecular polymers as dynamic biomaterials.</p>
https://doi.org/10.1021/acs.biomac.0c00904
oai:zenodo.org:4618025
eng
Zenodo
https://doi.org/10.1021/acs.biomac.0c00904
https://doi.org/10.5281/zenodo.6782685
https://zenodo.org/communities/gmpavan-lab
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Fibers
Peptides and proteins
Monomers
Biomaterials
Hydrogels
Data on DOI:10.1021/acs.biomac.0c00904
info:eu-repo/semantics/other
oai:zenodo.org:5517760
2021-10-11T14:09:48Z
openaire_data
user-gmpavan-lab
Lionello, Chiara
Gardin, Andrea
Cardellini, Annalisa
Bochicchio, Davide
Shivrayan, Manisha
Fernandez, Ann
Thayumanavan, S.
Pavan, Giovanni Maria
2021-09-20
<p>This repository contains the set of data shown in the paper "<em>Toward Chemotactic Supramolecular Nanoparticles: From Autonomous Surface Motion Following Specific Chemical Gradients to Multivalency-Controlled Disassembly</em>", published on <em>ACS Nano</em> (DOI: 10.1021/acsnano.1c0500).</p>
<p>All the input data needed to run the simulations and get the results are organized in 5 different folders:</p>
<ul>
<li>
<p><code>1-MinimlisticCGModel/</code></p>
<p>in this folder there are the Gromacs and PLUMED input files for reproducing the minimalistic coarse-grained model shown in the article.</p>
</li>
<li>
<p><code>2-AAandFineCGModels/</code></p>
<p>the folder contains the atomistic (<code>monomerAA/</code>) and the coarse-grained Martini "wet" (<code>monomerGCWet/</code>) input files for modelling the Original monomer with one carboxyl group. The coarse-grained Martini "dry" (<code>monomerCGDry/</code>) model is reported for the Original monomer at the three different charged states.</p>
</li>
<li>
<p><code>3-UnbiasedMD/</code></p>
<p>this folder includes the Gromacs input files needed to reproduce the Unbiased simulations as shown in the article.</p>
</li>
<li>
<p><code>4-MetaD/</code></p>
<p>this folder incorporates the Gromacs and PLUMED input files necessary to reproduce both the Infrequent CG Metadynamics simulations (<code>InfrequentMetaD/</code>) and the Multiple-walker CG Metadynamics simulations (<code>MultipleWalkerMetaD/</code>)</p>
</li>
<li>
<p><code>5-InSilico/</code></p>
<p>in this folder all the files used to run the simulations about the exoliation experiments (<code>Original/</code>, <code>Type-1/</code>, <code>Type-2/</code>, <code>Type-3/</code>, <code>Type-4/</code>) are reported. Every subfolder contains all input files for the three different charged monomers (<code>Olig1-/</code>, <code>Olig2-/</code>, <code>Olig3-/</code>).</p>
</li>
</ul>
https://doi.org/10.5281/zenodo.5517760
oai:zenodo.org:5517760
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.5517759
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting: "Toward Chemotactic Supramolecular Nanoparticles: From Autonomous Surface Motion Following Specific Chemical Gradients to Multivalency-Controlled Disassembly"
info:eu-repo/semantics/other
oai:zenodo.org:7064016
2022-09-09T14:16:23Z
user-gmpavan-lab
Massimo Delle Piane
Luca Pesce
Matteo Cioni
Giovanni Maria Pavan
2022-09-09
<p>his repository contains the set of data shown in the paper <strong>"Reconstructing reactivity in dynamic host–guest systems at atomistic resolution: amide hydrolysis under confinement in the cavity of a coordination cage"</strong>, published on Chemical Science (DOI:<a href="https://doi.org/10.1039/D2SC02000A">10.1039/D2SC02000A</a>).</p>
https://doi.org/10.5281/zenodo.7064016
oai:zenodo.org:7064016
Zenodo
https://doi.org/10.1039/D2SC02000A
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.7064015
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Molecular Dynamics
Amide hydrolysis
Reactivity
Research data supporting: "Reconstructing reactivity in dynamic host–guest systems at atomistic resolution: amide hydrolysis under confinement in the cavity of a coordination cage"
info:eu-repo/semantics/other
oai:zenodo.org:6554610
2022-06-23T13:12:36Z
openaire_data
user-gmpavan-lab
Capelli, Riccardo
Muniz-Miranda, Francesco
Pavan, Giovanni Maria
2022-05-16
<p>This repository contains the set of data shown in the paper <strong>"</strong><em>Ephemeral Ice-Like Local Environments in Classical Rigid Models of Liquid Water</em>", published on the Journal of Chemical Physics (DOI:10.1063/5.0088599).</p>
https://doi.org/10.5281/zenodo.6554610
oai:zenodo.org:6554610
Zenodo
https://doi.org/10.1063/5.0088599
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.6554609
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting "Ephemeral Ice-Like Local Environments in Classical Rigid Models of Liquid Water"
info:eu-repo/semantics/other
oai:zenodo.org:6782685
2022-06-30T09:45:47Z
user-gmpavan-lab
Leanza, Luigi
Pavan, Giovanni
Perego, Claudio
Perrone, Mattia
2020-09-29
<p>This repository contains the set of data shown in the paper <strong>"</strong>Exploring the Potential of Benzene-1,3,5-tricarboxamide Supramolecular Polymers as Biomaterials", published on Biomacromolecules (DOI:10.1021/acs.biomac.0c00904).</p>
<p>Abstract:</p>
<p>The fast dynamics occurring in natural processes increases the difficulty of creating biomaterials capable of mimicking Nature. Within synthetic biomaterials, water-soluble supramolecular polymers show great potential in mimicking the dynamic behavior of these natural processes. In particular, benzene-1,3,5-tricaboxamide (BTA)-based supramolecular polymers have shown to be highly dynamic through the exchange of monomers within and between fibers, but their suitability as biomaterials has not been yet explored. Herein we systematically study the interactions of BTA supramolecular polymers bearing either tetraethylene glycol or mannose units at the periphery with different biological entities. When BTA fibers were incubated with bovine serum albumin (BSA), the protein conformation was only affected by the fibers containing tetraethylene glycol at the periphery (BTA-OEG<sub>4</sub>). Coarse-grained molecular simulations showed that BSA interacted with BTA-OEG<sub>4</sub> fibers rather than with BTA-OEG<sub>4</sub> monomers that are present in solution or that may exchange out of the fibers. Microscopy studies revealed that, in the presence of BSA, BTA-OEG<sub>4</sub> retained their fiber conformation although their length was slightly shortened. When further incubated with fetal bovine serum (FBS), both long and short fibers were visualized in solution. Nevertheless, in the hydrogel state, the rheological properties were remarkably preserved. Further studies on the cellular compatibility of all the BTA assemblies and mixtures thereof were performed in four different cell lines. A low cytotoxic effect at most concentrations was observed, confirming the suitability of utilizing functional BTA supramolecular polymers as dynamic biomaterials.</p>
https://doi.org/10.5281/zenodo.6782685
oai:zenodo.org:6782685
eng
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.6782684
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Fibers
Peptides and proteins
Monomers
Biomaterials
Hydrogels
Data on DOI:10.1021/acs.biomac.0c00904
info:eu-repo/semantics/other
oai:zenodo.org:5771836
2021-12-10T13:48:42Z
user-gmpavan-lab
Liu, Hongxu
Lionello, Chiara
Westley, Jenna
Cardellini, Annalisa
Huynh, Uyen
Pavan, Giovanni Maria
Thayumanavan, S.
2021-06-18
<p>This repository contains the set of data shown in the paper "<em>Understanding functional group and assembly dynamics in temperature responsive systems leads to design principles for enzyme responsive assemblies</em>", published on <em>Nanoscale</em> (DOI: 10.1039/D1NR02000E).</p>
<p> </p>
<p>Understanding the molecular rules behind the dynamics of supramolecular assemblies is fundamentally important for the rational design of responsive assemblies with tunable properties. Herein, we report that the dynamics of temperature-sensitive supramolecular assemblies is not only affected by the dehydration of oligoethylene glycol (OEG) motifs, but also by the thermally-promoted molecular motions. These counteracting features set up a dynamics transition point (DTP) that can be modulated with subtle variations in a small hydrophobic patch on the hydrophilic face of the amphiphilic assembly. Understanding the structural factors that control the dynamics of the assemblies leads to rational design of enzyme-responsive assemblies with tunable temperature responsive profiles.</p>
https://doi.org/10.5281/zenodo.5771836
oai:zenodo.org:5771836
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.5771835
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting: "Understanding functional group and assembly dynamics in temperature responsive systems leads to design principles for enzyme responsive assemblies"
info:eu-repo/semantics/article
oai:zenodo.org:7738141
2023-03-16T02:26:43Z
openaire_data
user-gmpavan-lab
Matteo Cioni
Daniela Polino
Daniele Rapetti
Luca Pesce
Massimo Delle Piane
Giovanni Maria Pavan
2023-03-15
<p>This repository contains the set of data shown in the paper <strong>"Innate dynamics and identity crisis of a metal surface unveiled by machine learning of atomic environments"</strong>, published on The Journal of Chemical Physics (DOI:10.1063/5.0139010)</p>
https://doi.org/10.5281/zenodo.7738141
oai:zenodo.org:7738141
Zenodo
https://doi.org/10.1063/5.0139010
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.7738140
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Ab initio Molecular Dynamics
Deep Neural Network Potentials
Metal Surface Dynamics
Unsupervised Machine Learning
Research data supporting: "Innate dynamics and identity crisis of a metal surface unveiled by machine learning of atomic environments"
info:eu-repo/semantics/other
oai:zenodo.org:4818304
2021-10-11T14:05:07Z
user-gmpavan-lab
Luca, Pesce
Giovanni, Pavan
2021-05-27
<p>Photochromic molecules undergo reversible isomerization upon irradiation with light at different wavelengths, a process that can alter their physical and chemical properties. For instance, dihydropyrene (DHP) is a deep-colored compound that isomerizes to light-brown cyclophanediene (CPD) upon irradiation with visible light. CPD can then isomerize back to DHP upon irradiation with UV light or thermally in the dark. Conversion between DHP and CPD is thought to proceed via a biradical intermediate; bimolecular events involving this unstable intermediate thus result in rapid decomposition and poor cycling performance. Here, we show that the reversible isomerization of DHP can be stabilized upon confinement within a PdII6L4 coordination cage. By protecting this reactive intermediate using the cage, each isomerization reaction proceeds to higher yield, which significantly decreases the fatigue experienced by the system upon repeated photocycling. Although molecular confinement is known to help stabilize reactive species, this effect is not typically employed to protect reactive intermediates and thus improve reaction yields. We envisage that performing reactions under confinement will not only improve the cyclic performance of photochromic molecules, but may also increase the amount of product obtainable from traditionally low-yielding organic reactions.</p>
https://doi.org/10.1021/jacs.0c06146
oai:zenodo.org:4818304
Zenodo
https://zenodo.org/communities/gmpavan-lab
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Data on DOI:10.1021/jacs.0c06146
info:eu-repo/semantics/other
oai:zenodo.org:7070651
2022-09-13T10:51:53Z
user-gmpavan-lab
user-m3b
user-eu
Uchida, Noriyuki
Kohata, Ai
Okuro, Kou
Cardellini, Annalisa
Lionello, Chiara
Zizzi, Eric A.
Deriu, Marco A.
Pavan, Giovanni M.
Tomishige, Michio
Hikima, Takaaki
Aida, Takuzo
2022-09-12
<p>This repository contains the set of data shown in the paper "<em><strong>Reconstitution of microtubule into GTP-responsive nanocapsules</strong></em>", published on <strong><em>Nature Communications</em></strong> (DOI: 10.1038/s41467-022-33156-5).</p>
<p>All the input data needed to run the simulations and get the results are organized in 3 different folders:</p>
<p> * `00-MDPFiles/`</p>
<p> in this folder there are the mdp files for each step for Gromacs-MD simulations: energy minimization, nvt, npt, production with restraints and production without restraints.</p>
<p> * `01-TubulinSystems/`</p>
<p> the folder contains all the necessary files for the tubulin assembly MD simulations with and without glue (`SystemA_Glue/`, `SystemA_noGlue/`, `SystemB_Glue/`, `SystemB_noGlue/`).</p>
<p> * `02-OnlyGlue/` </p>
<p> the folder contains all the files needed for the the atomistic MD simulations of the glue in water.<br>
</p>
https://doi.org/10.5281/zenodo.7070651
oai:zenodo.org:7070651
Zenodo
https://doi.org/10.1038/s41467-022-33156-5
https://zenodo.org/communities/m3b
https://zenodo.org/communities/gmpavan-lab
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.7070650
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data on "Reconstitution of microtubule into GTP-responsive nanocapsules"
info:eu-repo/semantics/article
oai:zenodo.org:6453179
2022-04-20T13:49:23Z
user-gmpavan-lab
Crippa, Martina
Perego, Claudio
de Marco, Anna L.
Pavan, Giovanni M.
2022-04-12
<p>This repository contains the set of data shown in the paper <strong>"Molecular communications in complex systems of dynamic supramolecular polymers</strong>", published on <strong>Nature Communications</strong> (DOI:10.1038/s41467-022-29804-5).</p>
https://doi.org/10.5281/zenodo.6453179
oai:zenodo.org:6453179
eng
Zenodo
https://doi.org/10.1038/s41467-022-29804-5
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.6453178
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting: "Molecular communications in complex systems of dynamic supramolecular polymers"
info:eu-repo/semantics/article
oai:zenodo.org:5763925
2021-12-08T01:48:48Z
openaire_data
user-gmpavan-lab
Bian, Tong
Gardin, Andrea
Gemen, Julius
Houben, Lothar
Perego, Claudio
Lee, Byeongdu
Elad, Nadav
Chu, Zonglin
Pavan, M. Giovanni
Klajn, Rafal
2021-09-06
<p>This repository contains the set of data shown in the paper "<strong>Electrostatic co-assembly of nanoparticles with oppositely charged small molecules into static and dynamic superstructures</strong>", published on <strong>Nature Chemistry </strong>(DOI: 10.1038/s41557-021-00752-9).</p>
<p>The files in the folders are organized as follow:</p>
<p><strong>AA_models/ : </strong>contains all the files needed to run the Atomistic simulations discussed in the paper (including the topologies and starting configurations).</p>
<p><strong>CG_models/ : </strong>contains all the files needed to run the Coarse Grained simulations discussed in the paper (including the topologies and starting configurations).</p>
<p><strong>citrate_analysis/ : </strong>contains all the files needed to reproduce the analysis of the CV and SOAP+PCA+PAMM (including input files and python scripts).</p>
<p>Additional details are available in the methods section and in the Supporting Information of the main paper.</p>
https://doi.org/10.5281/zenodo.5763925
oai:zenodo.org:5763925
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.5763924
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research Data Supporting "Electrostatic co-assembly of nanoparticles with oppositely charged small molecules into static and dynamic superstructures"
info:eu-repo/semantics/other
oai:zenodo.org:5074816
2021-12-14T18:06:26Z
user-gmpavan-lab
Pesce, Luca
Gardin, Andrea
Bochicchio, Davide
Pavan, Giovanni Maria
2021-07-06
<p>Raw research data supporting the publication Shyshov, O., Haridas, S.V., Pesce, L. <em>et al.</em> Living supramolecular polymerization of fluorinated cyclohexanes. <em>Nat Commun</em> <strong>12, </strong>3134 (2021). https://doi.org/10.1038/s41467-021-23370-y</p>
https://doi.org/10.5281/zenodo.5074816
oai:zenodo.org:5074816
Zenodo
https://doi.org/10.1038/s41467-021-23370-y
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.5074815
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting "Living supramolecular polymerization of fluorinated cyclohexanes"
info:eu-repo/semantics/other
oai:zenodo.org:4891864
2021-09-04T01:48:41Z
openaire_data
user-gmpavan-lab
user-eu
Capelli, Riccardo
Gardin, Andrea
Empereur-mot, Charly
Doni, Giovanni
Pavan, Giovanni Maria
2021-09-03
<p>This repository contains the data used in the paper of Capelli <em>et al. </em>"A Data-Driven Dimensionality Reduction Approach to Compare and Classify Lipid Force Fields", published on Journal of Physical Chemistry B (DOI: 0.1021/acs.jpcb.1c02503).<br>
<br>
The archive traj_processed.tar.gz contains the trajectories converted in xyz format with the dimensions of the box.</p>
<p>The archive trajectories_xtc.tar.gz contains the raw trajectories (of the membranes without solvent) in gromacs xtc format with a .tpr binary file. <br>
</p>
https://doi.org/10.5281/zenodo.4891864
oai:zenodo.org:4891864
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.4891863
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting: "A Data-Driven Dimensionality Reduction Approach to Compare and Classify Lipid Force Fields"
info:eu-repo/semantics/other
oai:zenodo.org:10247242
2023-12-04T16:11:59Z
openaire_data
user-gmpavan-lab
Perrone, Mattia
Capelli, Riccardo
Empereur-mot, Charly
Hassanali, Ali
Pavan, Giovanni M.
2023-12-02
<p>This repository contains the set of data and the code to reproduce the results shown in "Lessons learned from multi-objective automatic optimizations of classical three-site rigid water models using microscopic and macroscopic target experimental observables" published on Journal of Chemical Engineering and Data (DOI: 10.1021/acs.jced.3c00538).</p>
https://doi.org/10.5281/zenodo.10247242
oai:zenodo.org:10247242
https://doi.org/10.1021/acs.jced.3c00538
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.10247241
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting ""Lessons learned from multi-objective automatic optimizations of classical three-site rigid water models using microscopic and macroscopic target experimental observables""
info:eu-repo/semantics/other
oai:zenodo.org:6701701
2023-06-06T12:55:08Z
software
user-gmpavan-lab
user-eu
Charly Empereur-mot
Riccardo Capelli
Mattia Perrone
Cristina Caruso
Giovanni Doni
Giovanni M. Pavan
2022-01-14
<p>Optimization tool for calibrating CG FFs of lipids, relying on the simultaneous usage of reference AA trajectories (bottom-up) and experimental data (top-down)</p>
https://doi.org/10.5281/zenodo.6701701
oai:zenodo.org:6701701
Zenodo
https://github.com/GMPavanLab/SwarmCGM/tree/v1
https://zenodo.org/communities/gmpavan-lab
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.6701700
info:eu-repo/semantics/openAccess
MIT License
https://opensource.org/licenses/MIT
coarse-graining
molecular modeling
optimization
force field
Research data supporting: "Automatic multi-objective optimization of coarse-grained lipid force fields using SwarmCG"
info:eu-repo/semantics/other
oai:zenodo.org:7696708
2023-03-04T02:26:40Z
openaire_data
user-gmpavan-lab
Annalisa Cardellini
Martina Crippa
Chiara Lionello
Syed Pavel Afrose
Dibyendu Das
Giovanni Maria Pavan
2023-03-03
<p>This repository contains the set of data shown in the paper <strong>"Unsupervised Data-Driven Reconstruction of Molecular Motifs in Simple to Complex Dynamic Micelles"</strong>, published on The Journal of Physical Chemistry B (DOI:10.1021/acs.jpcb.2c08726).</p>
https://doi.org/10.5281/zenodo.7696708
oai:zenodo.org:7696708
Zenodo
https://doi.org/10.1021/acs.jpcb.2c08726
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.7696707
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Coarse-Grained Molecular-Dynamics
Self-Assembled Amphiphiles
Reconstruction of Molecular Motifs
Unsupervised Machine Learning
Research data supporting: "Unsupervised Data-Driven Reconstruction of Molecular Motifs in Simple to Complex Dynamic Micelles"
info:eu-repo/semantics/other
oai:zenodo.org:6822330
2022-07-12T15:08:56Z
user-gmpavan-lab
Gardin, Andrea
Perego, Claudio
Doni, Giovanni
Pavan, Giovanni Maria
2022-07-12
<p>The root folder contains 5 folders:</p>
<ol>
<li> FIBERS</li>
<li> MEMBRANES_and_MICELLES</li>
<li> NANOPARTICLES</li>
<li> COMPARISON</li>
<li> paper_images</li>
</ol>
<p>The folders 1. to 3. contain the data for every soft-matters architecture used to produce the results discussed in the main paper. Each of these folders contain additional sub-fordels: TRAJ, SOAP, PCA, CLUSTERING, containing the files discussed in the main paper.</p>
<p>TRAJ contains the reduced trajectories used to compute the descriptors; SOAP contains the soap descriptors files used in the main manuscript; PCA contains the pca files used in the manuscript; CLUSTERING contains the clustering labels assignment computed in the manuscript.</p>
<p>Folder 4. contains the data of the comparison between different classes of materials (SOAP, PCA, and CLUSTERING sub-folders).</p>
<p>Folder 5. contains the images that are showed in the main paper and in the Supporting Information</p>
https://doi.org/10.5281/zenodo.6822330
oai:zenodo.org:6822330
Zenodo
https://doi.org/10.1038/s42004-022-00699-z
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.6822329
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Supporting data: "Classifying soft self-assembled materials via unsupervised machine learning of defects"
info:eu-repo/semantics/other
oai:zenodo.org:10213827
2023-11-28T15:10:11Z
openaire_data
user-gmpavan-lab
user-eu
Crippa, Martina
Cardellini, Annalisa
Cioni, Matteo
Pavan, Giovanni M.
2023-11-28
<p>This repository contains the set of data and the code to reproduce the results shown in "Machine learning of microscopic structure-dynamics relationships in complex molecular systems" published on Machine Learning: Science and Technology (DOI: 10.1088/2632-2153/ad0fa5).</p>
https://doi.org/10.5281/zenodo.10213827
oai:zenodo.org:10213827
Zenodo
https://doi.org/10.1088/2632-2153/ad0fa5
https://zenodo.org/communities/gmpavan-lab
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.10213826
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting: "Machine learning of microscopic structure-dynamics relationships in complex molecular systems"
info:eu-repo/semantics/other
oai:zenodo.org:5763893
2021-12-08T01:48:48Z
openaire_data
user-gmpavan-lab
user-eu
A. Sarkar
R. Sasmal
C. Empereur-mot
D. Bochicchio
S. V. K. Kompella
K. Sharma
S. Dhiman
B. Sundaram
S. S. Agasti
G. M. Pavan
S. J. George
2020-04-01
<p>Raw research data supporting the article:</p>
<p>A. Sarkar, R. Sasmal, C. Empereur-mot, D. Bochicchio, S. V. K. Kompella, K. Sharma, S. Dhiman, B. Sundaram*, S. S. Agasti*, <strong>G. M. Pavan</strong>* and S. J. George*<br>
“Self-Sorted, Random and Block Supramolecular Co-polymers via Sequence Controlled, Multicomponent Self-Assembly”<br>
<a href="https://pubs.acs.org/doi/abs/10.1021/jacs.0c01822"><em>J. Am. Chem. Soc.</em> <strong>2020</strong>, <em>142</em>, 7606-7617</a></p>
<p>Multicomponent supramolecular copolymerization promises to construct complex nanostructures with emergent properties. However, even with two monomeric components, various possible outcomes such as self-sorted supramolecular homopolymers, a random (statistical) supramolecular copolymer, an alternate supramolecular copolymer, or a complex supramolecular block copolymer can occur, determined by their intermolecular interactions and monomer exchange dynamics and hence structural prediction is extremely challenging. Herein, we target this challenge and demonstrate unprecedented two-component sequence controlled supramolecular copolymerization by manipulating thermodynamic and kinetic routes in the pathway complexity of selfassembly of the constitutive monomers. Extensive molecular dynamics simulations provided useful mechanistic insights into the monomer exchange rates and free energy of interactions between the monomers that dictate the self-assembly pathway and sequence. The fluorescent nature of core-substituted naphthalene diimide monomers has been further utilized to characterize the three sequences via Structured Illumination Microscopy (SIM).</p>
https://doi.org/10.5281/zenodo.5763893
oai:zenodo.org:5763893
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.5763892
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
multicomponent self-assembly
co-polymers
sequence control
Research Data supporting "Self-Sorted, Random, and Block Supramolecular Copolymers via Sequence Controlled, Multicomponent Self-Assembly"
info:eu-repo/semantics/other
oai:zenodo.org:10057290
2023-10-31T10:44:37Z
openaire_data
user-gmpavan-lab
user-eu
Cardellini, Annalisa
Capelli, Riccardo
Pavan, Giovanni M.
Cardellini, Annalisa
Capelli, Riccardo
Pavan, Giovanni M.
2023-10-31
<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>
https://doi.org/10.5281/zenodo.10057290
oai:zenodo.org:10057290
https://doi.org/10.5281/zenodo.10057290
Zenodo
https://doi.org/10.1039/d3sc03930g
https://zenodo.org/communities/gmpavan-lab
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.10057289
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting: "Self-assembly of cyclic peptide monolayers by hydrophobic supramolecular hinges"
info:eu-repo/semantics/other
oai:zenodo.org:5046476
2021-10-11T13:51:15Z
user-gmpavan-lab
Luca Pesce
Giovanni M. Pavan
Claudio, Perego
2021-06-30
<p>Photoswitchable molecules are employed for many applications, from the development of active materials to the design of stimuli-responsive molecular systems and light-powered molecular machines. To fully exploit their potential, we must learn ways to control the mechanism and kinetics of their photoinduced isomerization. One possible strategy involves confinement of photoresponsive switches such as azobenzenes or spiropyrans within crowded molecular environments, which may allow control over their light-induced conversion. However, the molecular factors that influence and control the switching process under realistic conditions and within dynamic molecular regimes often remain difficult to ascertain. As a case study, here we have employed molecular models to probe the isomerization of azobenzene guests within a Pd(II)-based coordination cage host in water. Atomistic molecular dynamics and metadynamics simulations allow us to characterize the flexibility of the cage in the solvent, the (rare) guest encapsulation and release events, and the relative probability/kinetics of light-induced isomerization of azobenzene analogues in these host–guest systems. In this way, we can reconstruct the mechanism of azobenzene switching inside the cage cavity and explore key molecular factors that may control this event. We obtain a molecular-level insight on the effects of crowding and host–guest interactions on azobenzene isomerization. The detailed picture elucidated by this study may enable the rational design of photoswitchable systems whose reactivity can be controlled via host–guest interactions.</p>
https://doi.org/10.5281/zenodo.5046476
oai:zenodo.org:5046476
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.5046475
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Data on DOI:10.1021/jacs.0c03444
info:eu-repo/semantics/other
oai:zenodo.org:8340211
2023-09-14T02:26:52Z
user-gmpavan-lab
Antara Reja
Sumit Pal
Kishalay Mahato
Baishakhi Saha
Massimo Delle Piane
Giovanni M. Pavan
Dibyendu Das
2023-09-13
<p>Research data for "Emergence of Photomodulated Protometabolism by Short Peptide-Based Assemblies"</p>
https://doi.org/10.5281/zenodo.8340211
oai:zenodo.org:8340211
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.8340210
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data for "Emergence of Photomodulated Protometabolism by Short Peptide-Based Assemblies"
info:eu-repo/semantics/article
oai:zenodo.org:5802526
2022-01-10T16:48:03Z
user-gmpavan-lab
Luca Pesce
Claudio Perego
Giovanni M. Pavan
2022-01-10
<p>Raw computational data supporting the article G. Moreno-Alcántar, A. Aliprandi, R. Rouquette, L. Pesce, K. Wurst, C. Perego, P. Brüggeller, G. M. Pavan, L. De Cola, Angew. Chem. Int. Ed. 2021, 60, 5407.</p>
https://doi.org/10.5281/zenodo.5802526
oai:zenodo.org:5802526
Zenodo
https://doi.org/10.1002/anie.202013474
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.5802525
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting "Solvent‐Driven Supramolecular Wrapping of Self‐Assembled Structures"
info:eu-repo/semantics/other
oai:zenodo.org:6967170
2022-08-05T13:50:21Z
user-gmpavan-lab
user-eu
Capelli, Riccardo
Pavan, Giovanni Maria
2022-08-05
<p>The archive contains 4 different folders:<br>
<br>
1. mdp_files, that contains all the input files for the minimization, equilibration and molecular dynamics run (in gromacs format);<br>
2. topologies, that contains the equilibrated configurations and topology of the 4 systems studied (in gromacs format);<br>
3. trajectories, that contains the coordinates of the macrocycles during the metadynamics calculations and the relevant metadynamics output files (hills file and energy file);<br>
4. plumed_input, that contains the input file for the metadynamics calculations.</p>
https://doi.org/10.5281/zenodo.6967170
oai:zenodo.org:6967170
Zenodo
https://doi.org/10.1021/acsomega.2c03536
https://zenodo.org/communities/gmpavan-lab
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.6967169
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research Data on "Well-Tempered Metadynamics Simulations Predict the Structural and Dynamic Properties of a Chiral 24-Atom Macrocycle in Solution"
info:eu-repo/semantics/other
oai:zenodo.org:5047177
2021-10-11T14:03:49Z
software
user-gmpavan-lab
Empereur-mot, Charly
Pesce, Luca
Bochicchio, Davide
Capelli, Riccardo
Perego, Claudio
Pavan, Giovanni M.
2021-06-30
<p>Software supporting the publication Empereur-mot C. et al., ACS Omega, 2020, DOI: https://dx.doi.org/10.1021/acsomega.0c05469</p>
https://doi.org/10.5281/zenodo.5047177
oai:zenodo.org:5047177
Zenodo
https://doi.org/10.1021/acsomega.0c05469
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.5047176
info:eu-repo/semantics/openAccess
MIT License
https://opensource.org/licenses/MIT
coarse-graining
molecular modeling
optimization
Research data supporting: "Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-Based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization"
info:eu-repo/semantics/other
oai:zenodo.org:5761668
2021-12-07T01:48:45Z
openaire_data
user-gmpavan-lab
de Marco, Anna L.
Bochicchio, Davide
Gardin, Andrea
Doni, Giovanni
Pavan, M. Giovanni
2021-09-02
<p>This repository contains the set of data shown in the paper "<strong>Controlling Exchange Pathways in Dynamic Supramolecular Polymers by Controlling Defects</strong>", published on <strong>ACS Nano</strong> (DOI: 10.1021/acsnano.1c01398).</p>
<p>The data stored in this section is organized as follow:</p>
<p><strong>supervisedClustering/ :</strong> folder containing scripts for carrying out the supervised analysis as discussed in the main paper. Subfolders are divided in <strong><code>kmeans</code></strong><code><strong>/</strong></code> and <strong><code>spectral</code></strong><code>/</code> contain the different analysis as explained in the paper.</p>
<p><strong>unbiasMD/ : </strong>folder containing the Gromacs input files for reproducing the unbias MD trajectories of the 3 types of fiber, as explained in the paper.</p>
<p><strong>biasMD/</strong> <strong>:</strong> folder containing the PLUMED input files for reproducing enhanced sampling dynamics as discussed in the paper.</p>
<p><strong>unsupervisedClustering/ : </strong>folder containing the directions and the original files to reproduce the unsupervised clustering results.</p>
https://doi.org/10.5281/zenodo.5761668
oai:zenodo.org:5761668
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.5761667
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Supramolecular structures and assemblies, Fibers, Monomers, Defects, Polymers
Research Data Supporting "Controlling Exchange Pathways in Dynamic Supramolecular Polymers by Controlling Defects"
info:eu-repo/semantics/other
oai:zenodo.org:7627816
2023-02-11T02:26:37Z
user-gmpavan-lab
Becchi, Matteo
Capelli, Riccardo
Perego, Claudio
Giovanni, Maria Pavan
Micheletti, Cristian
2022-10-04
<p>Data and code for "Becchi et al., Density-tunable pathway complexity in a minimalistic self-assembly model"</p>
<p>The "setup" folders contain the starting configurations and the LAMMPS scripts to run the simulations.</p>
<p>The "data" folders contain the data extracted from the simulations which have been used to obtain the figures.</p>
https://doi.org/10.5281/zenodo.7627816
oai:zenodo.org:7627816
eng
Zenodo
https://doi.org/10.1039/d2sm00968d
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.7627815
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Supramolecular self-assembly, self-limited self-assembly, pathway complexity
Research data on: "Density-tunable pathway complexity in a minimalistic self-assembly model"
info:eu-repo/semantics/article
oai:zenodo.org:5801291
2022-01-10T16:47:30Z
user-gmpavan-lab
Luca Pesce
Andrea Gardin
Claudio Perego
Giovanni M Pavan
2021-12-23
<p>Raw data and analysis results supporting the article "Solvent-driven chirality for luminescent self-assembled structures: experiments and theory"</p>
https://doi.org/10.5281/zenodo.5801291
oai:zenodo.org:5801291
Zenodo
https://doi.org/10.1039/D0NR04524A
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.5801290
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting "Solvent-driven chirality for luminescent self-assembled structures: experiments and theory"
info:eu-repo/semantics/other
oai:zenodo.org:7962820
2023-05-25T02:28:52Z
openaire_data
user-gmpavan-lab
Caruso Cristina
Cardellini Annalisa
Crippa Martina
Rapetti Daniele
Pavan Giovanni M.
2023-05-23
<p>This repository contains the set of data shown in the paper <strong>"<em>Time</em>SOAP: Tracking high-dimensional fluctuations in complex molecular systems via time variations of SOAP spectra"</strong>, published on The Journal of Chemical Physics (DOI: 10.1063/5.0147025).</p>
https://doi.org/10.5281/zenodo.7962820
oai:zenodo.org:7962820
Zenodo
https://doi.org/10.1063/5.0147025
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.7962819
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting: "TimeSOAP: Tracking high-dimensional fluctuations in complex molecular systems via time variations of SOAP spectra"
info:eu-repo/semantics/other
oai:zenodo.org:10257206
2023-12-04T16:40:24Z
openaire_data
user-gmpavan-lab
user-eu
Perrone, Mattia
Capelli, Riccardo
Empereur-mot, Charly
Hassanali, Ali
Pavan, Giovanni M.
2023-12-04
<p>This repository contains the set of data and the code to reproduce the results shown in "Lessons learned from multi-objective automatic optimizations of classical three-site rigid water models using microscopic and macroscopic target experimental observables" published on Journal of Chemical Engineering and Data (DOI: 10.1021/acs.jced.3c00538).</p>
https://doi.org/10.5281/zenodo.10257206
oai:zenodo.org:10257206
https://doi.org/10.1021/acs.jced.3c00538
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.10257205
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Data supporting "Lessons learned from multi-objective automatic optimizations of classical three-site rigid water models using microscopic and macroscopic target experimental observables"
info:eu-repo/semantics/other
oai:zenodo.org:5052751
2021-10-14T01:48:37Z
openaire_data
user-gmpavan-lab
Claudio Perego
Luca Pesce
Riccardo Capelli
Subi J. George
Giovanni M. Pavan
2021-07-01
<p>Raw research data supporting the publication Perego C. et al., <em>ChemSystemsChem</em> <strong>2021</strong>, DOI: <a href="https://doi.org/10.1002/syst.202000038">https://doi.org/10.1002/syst.202000038</a></p>
https://doi.org/10.5281/zenodo.5052751
oai:zenodo.org:5052751
Zenodo
https://doi.org/10.1002/syst.202000038
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.5052750
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
fuel-regulated self-assembly
Research data supporting "Multiscale Molecular Modelling of ATP-Fueled Supramolecular Polymerisation and Depolymerisation"
info:eu-repo/semantics/other
oai:zenodo.org:7350671
2023-01-10T14:26:49Z
user-gmpavan-lab
Luca Pesce
Giovanni M. Pavan
2022-11-23
<p>This repository contains the set of data shown in the paper <strong>"Subtle Stereochemical Effects Influence Binding and Purification Abilities of an FeII4L4 Cage"</strong>, soon to be submitted.</p>
https://doi.org/10.5281/zenodo.7350671
oai:zenodo.org:7350671
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.7350670
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Computational data supporting: "Subtle Stereochemical Effects Influence Binding and Purification Abilities of an FeII4L4 Cage"
info:eu-repo/semantics/other
oai:zenodo.org:8010318
2023-06-07T02:27:03Z
software
user-gmpavan-lab
user-eu
CharlyEmpereurmot
2023-06-06
<p>Some cleaning of the code towards creating a versatile tool for more use cases, while testing what SwarmCG-lipids could yield in the context of lipids + for gaining insights on the relevance of different CG representations for further improving the Martini lipid models</p>
https://doi.org/10.5281/zenodo.8010318
oai:zenodo.org:8010318
Zenodo
https://github.com/GMPavanLab/SwarmCGM/tree/v1.1
https://zenodo.org/communities/gmpavan-lab
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.6701700
info:eu-repo/semantics/openAccess
Other (Open)
GMPavanLab/SwarmCGM: martini300-testing
info:eu-repo/semantics/other
oai:zenodo.org:8013279
2023-06-28T02:26:48Z
openaire_data
user-gmpavan-lab
Martina Crippa
Annalisa Cardellini
Cristina Caruso
Giovanni M. Pavan
2023-06-27
<p>This repository contains the set of data shown in the paper "Detecting dynamic domains and local fluctuations in complex molecular systems via timelapse neighbors shuffling" published on PNAS (DOI: 10.1073/pnas.2300565120).</p>
https://doi.org/10.5281/zenodo.8013279
oai:zenodo.org:8013279
eng
Zenodo
https://doi.org/10.1073/pnas.2300565120
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.8013278
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting: "Detecting dynamic domains and local fluctuations in complex molecular systems via timelapse neighbors shuffling"
info:eu-repo/semantics/other
oai:zenodo.org:8108900
2023-07-04T02:26:47Z
user-gmpavan-lab
Rapetti, Daniele
Delle Piane, Massimo
Cioni, Matteo
Polino, Daniela
Ferrando, Riccardo
Pavan, Giovanni M.
2023-06-19
<p>Data and analysis setup for "Machine Learning of Atomic Dynamics and Statistical Surface Identities in Gold Nanoparticles".</p>
<p>The files in this repository are tailored to reproduce precisely the results obtained in our simulations (starting from the data that are present in the zenodo link), so if you want to apply the analysis to your data, you will need to modify the scripts.</p>
https://doi.org/10.5281/zenodo.8108900
oai:zenodo.org:8108900
Zenodo
https://doi.org/10.1038/s42004-023-00936-z
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.8108899
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Communications Chemistry, (2023-06-19)
Research data supporting: "Machine Learning of Atomic Dynamics and Statistical Surface Identities in Gold Nanoparticles"
info:eu-repo/semantics/article
oai:zenodo.org:5717968
2021-11-30T09:37:27Z
openaire_data
user-gmpavan-lab
user-eu
Luigi Leanza
Riccardo Capelli
Giovanni Maria Pavan
2021-11-22
<p>Raw research data supporting the article E. Weyandt, L. Leanza, R. Capelli, G. M. Pavan, G. Vantomme, and E.W. Meijer, "Controlling the length of porphyrin supramolecular polymers via coupled equilibria and dilution-induced supramolecular polymerization".</p>
https://doi.org/10.5281/zenodo.5717968
oai:zenodo.org:5717968
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.5717967
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research Data supporting "Controlling the length of porphyrin supramolecular polymers via coupled equilibria and dilution-induced supramolecular polymerization"
info:eu-repo/semantics/other
oai:zenodo.org:7575450
2023-02-02T02:27:16Z
openaire_data
user-gmpavan-lab
Capelli, Riccardo
2023-01-27
<p>The archive contains 5 different folders:<br>
<br>
1. mdp_files, that contains all the input files for the minimization, equilibration and molecular dynamics run (in gromacs format);<br>
2. topologies, that contains the equilibrated configurations and topology of the 4 systems studied (in gromacs format);<br>
3. trajectories, that contains the coordinates of the macrocycles during the metadynamics calculations and the relevant metadynamics output files (hills file and energy file);<br>
4. plumed_input, that contains the input file for the metadynamics calculations.<br>
5. gaussian, that contains input and output for the single-point charge calculations.</p>
https://doi.org/10.5281/zenodo.7575450
oai:zenodo.org:7575450
Zenodo
https://doi.org/10.1021/acs.joc.2c01984
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.7575449
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Computational data on "A Model for the Rapid Assessment of Solution-Structures for 24-Atom Macrocycles: The Impact of β-Branched Amino Acids on Conformation"
info:eu-repo/semantics/other
oai:zenodo.org:5807343
2022-01-10T16:48:50Z
user-gmpavan-lab
Luca Pesce
Claudio Perego
Giovanni M. Pavan
2021-12-27
<p>Raw research data supporting the published article of S. Datta et al., "Self-assembled poly-catenanes from supramolecular toroidal building blocks", Nature volume 583, pages400–405 (2020)</p>
https://doi.org/10.5281/zenodo.5807343
oai:zenodo.org:5807343
Zenodo
https://doi.org/10.1038/s41586-020-2445-z
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.5807342
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data supporting: "Self-assembled poly-catenanes from supramolecular toroidal building blocks"
info:eu-repo/semantics/other
oai:zenodo.org:5025104
2021-12-28T09:44:11Z
openaire_data
user-gmpavan-lab
Pesce, Luca
Pavan, Giovanni Maria
2021-07-30
<p>Raw research data supporting the article K. Tashiro, K. Katayama, K. Tamaki, L. Pesce, N. Shimizu, H. Takagi, R. Haruki, R. Heenan, M. J. Hollamby, G. M. Pavan, S. Yagai, "Non-uniform Photoinduced Unfolding of Supramolecular Polymers Leading to Topological Block Nanofibers".</p>
https://doi.org/10.5281/zenodo.5025104
oai:zenodo.org:5025104
Zenodo
https://doi.org/10.1002/anie.202110224
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.5025103
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
supramolecular polymer
azobenzene
barbituric acid
molecular dynamics simulation
Research data supporting: K. Tashiro, K. Katayama, K. Tamaki, L. Pesce, N. Shimizu, H. Takagi, R. Haruki, R. Heenan, M. J. Hollamby, G. M. Pavan, S. Yagai, "Non-uniform Photoinduced Unfolding of Supramolecular Polymers Leading to Topological Block Nanofibers"
info:eu-repo/semantics/other
oai:zenodo.org:4896475
2021-11-23T01:48:56Z
openaire_data
user-gmpavan-lab
user-eu
Capelli, Riccardo
Empereur-Mot, Charly
Pavan, Giovanni Maria
2021-06-03
<p>Raw research data supporting the article A. Sarkar, T. Behera, R. Sasmal, R. Capelli, C. Empereur-mot, J. Mahato, S. S. Agasti, G. M. Pavan, A. Chowdhury, S. J. George "Cooperative Supramolecular Block Copolymerization for the Synthesis of Functional Axial Organic Heterostructures".</p>
https://doi.org/10.5281/zenodo.4896475
oai:zenodo.org:4896475
Zenodo
https://zenodo.org/communities/gmpavan-lab
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.4896474
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Supramolecular assembly
Kinetics
Research Data supporting "Cooperative Supramolecular Block Copolymerization for the Synthesis of Functional Axial Organic Heterostructures"
info:eu-repo/semantics/other
oai:zenodo.org:7437648
2022-12-14T14:26:39Z
user-gmpavan-lab
Lionello, Chiara
Perego, Claudio
Gardin, Andrea
Klajn, Rafal
Pavan, Giovanni M.
2022-12-14
<p>This repository contains the set of data shown in the paper "<em><strong>Supramolecular Semiconductivity through Emerging Ionic Gates in Ion−Nanoparticle Superlattices</strong></em>", published on <strong><em>ACS Nano</em></strong> (DOI: 10.1021/acsnano.2c07558).</p>
<p>All the input data needed to run the simulations and get the results are organized in 2 different folders:</p>
<p> * `1 - CoarseGrainedSimulations/`</p>
<p> in this folder there are all the Gromacs input files necessary to reproduce the coarse-grained simulations shown in the article.<br>
<br>
* `2 - SOAP&PAMM-Analysis/`</p>
<p> this folder contains an example case and the scripts to reproduce the SOAP and PAMM analysis discussed in this work. In particular, the example (`ExampleCase-300K-E=0.05/`) is referred to the simulation at T = 300 K and E = 0.05 V/nm, and contains the reduced trajectory - necessary for the further analysis. From the Jupyter script `get_soap.ipynb` it is possible to implement the SOAP analysis, from the script `get_pca.ipynb` it is possible to value the PCA analysis, and from the script `pamm_clustering.ipynb` it is possible to perform the PAMM clustering analysis. </p>
https://doi.org/10.5281/zenodo.7437648
oai:zenodo.org:7437648
Zenodo
https://doi.org/10.1021/acsnano.2c07558
https://zenodo.org/communities/gmpavan-lab
https://doi.org/10.5281/zenodo.7437647
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Research data on: "Supramolecular Semiconductivity through Emerging Ionic Gates in Ion−Nanoparticle Superlattices"
info:eu-repo/semantics/article