Repositories list

• Optimal-Spatiotemporal-Resolutions

  Public
  It contains all the code used for: "Optimal Spatiotemporal Resolutions"

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

• Descriptors

  Public
  It contains all the code used for: "A data-driven approach to classify descriptors based on their efficiency in translating noisy trajectories into physically-relevant information"

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

• HiddenInformation

  Public
  Contains all the data used in the paper "Relevant, hidden, and frustrated information in high-dimensional analyses of complex dynamical systems with internal noise"

  MIT License

  •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

• dynsight

  Public
  A framework for the analysis of the dynamics of particle trajectories

  dynamicsmolecular-dynamicsatomistic-simulations+ 2molecular-modelingsupramolecular

  Python

  •

  MIT License

  •6•1•8•0•Updated Dec 11, 2024Dec 11, 2024

• DefectsTracker_METALS

  Public
  Python

  •1•0•0•0•Updated Oct 23, 2024Oct 23, 2024

• timeseries_analysis

  Public
  Code for unsupervised clustering of time-correlated data.

  Python

  •

  MIT License

  •1•0•0•0•Updated Oct 1, 2024Oct 1, 2024

• LEAP

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

• Swarm-CG

  Public
  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

  optimizationmolecular-dynamicsoptimization-tools+ 8gromacscoarse-grainedcoarse-grainingmolecular-modelingbonded-termsbonded-parametersswarm-cg+ 1

  Python

  •

  MIT License

  •12•43•8•0•Updated Aug 19, 2024Aug 19, 2024

• Porphyrin-SPcapping

  Public
  Structures and topologies of submitted paper "Controlling the length of porphyrin-based supramolecular polymers via coupled equilibria and dilution induced self-assembly"

  0•0•0•0•Updated May 30, 2024May 30, 2024

• Wateropti

  Public
  Supporting data for wateropti paper

  Python

  •0•0•0•0•Updated Dec 6, 2023Dec 6, 2023

• cpctools

  Public
  System analysis with soap fingerprints

  pythonmolecular-dynamics

  Python

  •

  MIT License

  •6•4•3•0•Updated Nov 16, 2023Nov 16, 2023

• LENS

  Public
  Supporting data of submitted paper "Detecting dynamic domains and local fluctuations in complex molecular systems via timelapse neighbors shuffling".

  Jupyter Notebook

  •2•3•0•0•Updated Nov 16, 2023Nov 16, 2023

• StrDynRel

  Public
  Supporting data of submitted paper "Machine learning of microscopic structure-dynamics relationships in complex molecular systems".

  Jupyter Notebook

  •1•0•0•0•Updated Nov 8, 2023Nov 8, 2023

• Macrocycles3

  Public
  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 26, 2023Oct 26, 2023

• C14-Catenane

  Public
  Input files for the paper "Synthesis of C60/[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition". The folder contains the input files for reproducing the figure 4 of the main paper and supplementary information (mdp, topologies, plumed files, residence times, ...)

  0•0•0•0•Updated Oct 24, 2023Oct 24, 2023

• CGExplore

  Public
  A general tool set for working with coarse-grained stk models

  Python

  •

  MIT License

  •1•0•0•0•Updated Oct 13, 2023Oct 13, 2023

• AuNP

  Public
  Python

  •0•0•0•0•Updated Oct 7, 2023Oct 7, 2023

• CyclicPeptideNTs

  Public
  Supporting data and molecular dynamics input data for the paper: "Self-assembly Mechanism of Cyclic Peptide Monolayers by a Supramolecular Hinge ".

  MATLAB

  •0•0•0•0•Updated Jul 21, 2023Jul 21, 2023

• dynNP

  Public
  Repository for the code used to reproduce the analysis and the simulations for the paper "Machine Learning of Atomic Dynamics and Statistical Surface Identities in Gold Nanoparticles"

  Python

  •1•1•0•0•Updated Jul 10, 2023Jul 10, 2023

• SwarmCGM

  Public
  Optimization tool for calibrating coarse-grained force fields of lipids, relying on the simultaneous usage of reference AA trajectories (bottom-up) and experimental data (top-down)

  optimizationforce-fieldscoarse-graining+ 2molecular-modelinglipids

  Python

  •

  MIT License

  •0•10•1•0•Updated Jun 6, 2023Jun 6, 2023

• MIMs

  Public
  0•0•0•0•Updated May 31, 2023May 31, 2023

• TimeSOAP

  Public
  Python

  •0•1•0•0•Updated Mar 1, 2023Mar 1, 2023

• Azo_Peptides

  Public
  This repository contains the set of data shown in the paper "Emergence of Photomodulated Protometabolism by Short Peptide-based Assemblies"

  0•0•0•0•Updated Feb 14, 2023Feb 14, 2023

• NPsuperlattices

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Dec 14, 2022Dec 14, 2022

• Macrocycles2

  Public
  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 15, 2022Nov 15, 2022

• CageReact

  Public
  Tcl

  •1•0•0•0•Updated Aug 29, 2022Aug 29, 2022

• MicellesML

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Aug 5, 2022Aug 5, 2022

• DynMetSurf

  Public
  Repo containing the files for "Innate Dynamics and Identity Crisis of a Metal Surface Unveiled by Machine Learning of Atomic Environments"

  Jupyter Notebook

  •0•0•0•0•Updated Aug 2, 2022Aug 2, 2022

• mbare_ucl

  Public
  mbare_ucl

  Python

  •0•0•0•0•Updated Jun 9, 2022Jun 9, 2022

• Water_SOAP

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 31, 2022Mar 31, 2022