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    43 repositories

    • dynsight

      Public
      A framework for the analysis of the dynamics of particle trajectories
      dynamicsmolecular-dynamicsatomistic-simulations
      dynamicsmolecular-dynamicsatomistic-simulationsmolecular-modelingsupramolecular
      Python
      •
      MIT License
      •10•5•10•2•Updated Feb 16, 2026Feb 16, 2026

    • onion_clustering

      Public
      Code for unsupervised clustering of time-correlated data.
      Python
      •
      MIT License
      •1•0•0•0•Updated Jan 20, 2026Jan 20, 2026

    • Molecular-Motor-Fibres

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 25, 2025Nov 25, 2025

    • DefectsTracker_METALS

      Public
      Python
      •1•0•0•0•Updated May 28, 2025May 28, 2025

    • DisNuc

      Public
      Python
      •0•1•0•0•Updated Apr 27, 2025Apr 27, 2025

    • MultiSPbind

      Public
      MATLAB
      •0•0•0•0•Updated Mar 18, 2025Mar 18, 2025

    • Optimal-Spatiotemporal-Resolutions

      Public
      It contains all the code used for: "Optimal Spatiotemporal Resolutions"
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

    • 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-r…
      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 no…
      MIT License
      •0•0•0•0•Updated Dec 12, 2024Dec 12, 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 O…
      optimizationmolecular-dynamicsoptimization-tools
      optimizationmolecular-dynamicsoptimization-toolsgromacscoarse-grainedcoarse-grainingmolecular-modelingbonded-termsbonded-parametersswarm-cg
      Python
      •
      MIT License
      •13•48•9•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…
      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
      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…
      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•1•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 Identitie…
      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 experime…
      optimizationforce-fieldscoarse-graining
      optimizationforce-fieldscoarse-grainingmolecular-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
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