.. _our-results:

.. role:: header
   :class: h4


Main studies performed with |pyretis|
-------------------------------------

The *Source Files* link of each study below points to a folder with
ready-to-run inputs: a ``retis.rst`` for |pyretis| 3 and the equivalent
``retis.toml`` for |pyretis| 4, together with a ``README`` describing the
case, its requirements and how to run it. Some studies are large solvated
or *ab initio* systems whose full convergence requires HPC resources.

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      .. image:: /_static/img/examples/thumbnails/dna-400x400.png
         :width: 100%
         :class: img-responsive

      .. container:: caption

         :header:`Predicting the mechanism and rate of H-NS binding to AT-rich DNA.`

         The adsorption of H-NS on DNA is studied at atomistic resolution
         with GROMACS. Local minima have been located by metadynamics
         and the transition rates computed by RETIS.

         `Source Files <https://www.pyretis.org/source_files/H-NS_2019/>`__

         Paper: E. Riccardi, E. C. van Mastbergen, W. W. Navarre and
         J. Vreede, `Predicting the mechanism and rate of H-NS binding
         to AT-rich DNA <https://doi.org/10.1371/journal.pcbi.1006845>`_,
         PLoS Comput. Biol. **15**, e1006845 (2019).


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      .. image:: /_static/img/examples/thumbnails/water-400x400.png
         :width: 100%
         :class: img-responsive

      .. container:: caption

         :header:`Autoionization of water.`

         BO-DFT simulations, via the RETIS approach, were used to study water
         autoionization. The mechanism(s) have been highlighted and their rate(s)
         quantified. Machine learning was applied to test the quality of 
         the order parameters.

         `Source Files <https://www.pyretis.org/source_files/Water_2019/>`__

         Paper: M. Moqadam, A. Lervik, E. Riccardi, V. Venkatraman,
         B. K. Alsberg and T. S. van Erp, `Local initiation conditions
         for water autoionization <https://doi.org/10.1073/pnas.1714070115>`_,
         Proc. Natl. Acad. Sci. U.S.A. **115**, E4569-E4576 (2018).


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      .. image:: /_static/img/examples/thumbnails/cyclophilin-400x400.png
         :width: 100%
         :class: img-responsive

      .. container:: caption

         :header:`Conformational study of Cyclophilin - A.`

         Full atomistic simulations with GROMACS have been performed to sample
         and quantify the rate of the structural rearrangements of CyP-A and
         its muted confomer.
        
         `Source Files <https://www.pyretis.org/source_files/CyP-A_2019/>`__

         Paper in preparation.


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      .. image:: /_static/img/examples/thumbnails/trimer-400x400.png
         :width: 100%
         :class: img-responsive

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         :header:`Proton transfer in a water trimer.`

         A study on the proton transfer reaction with a polarizable potential
         is included. The various features of |pyvisa| can be tested
         on the simulation outputs.
        
         `Source Files <https://www.pyretis.org/source_files/Water_trimer_2020/>`__

         Paper: O. Aarøen, H. Kiær and E. Riccardi, `PyVisA:
         Visualization and Analysis of path sampling trajectories
         <https://doi.org/10.1002/jcc.26467>`_, J. Comput. Chem. **42**,
         435-446 (2021).


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      .. image:: /_static/img/examples/thumbnails/formic-400x400.png
         :width: 100%
         :class: img-responsive

      .. container:: caption

         :header:`Formic acid catalysed formation of sulfuric acid`. 

         A study on the formic acid catalysed conversion of
         sulfur trioxide and water to sulfuric acid.
         The mechanism(s) have been highlighted and their rate(s) estimated
         as a function of the temperature.

         `Source Files <https://www.pyretis.org/source_files/Formic_acid_2020/>`__

         Paper: C. D. Daub, E. Riccardi, V. Hänninen and L. Halonen,
         `Path sampling for atmospheric reactions: formic acid catalysed
         conversion of SO3 + H2O to H2SO4
         <https://doi.org/10.7717/peerj-pchem.7>`_, PeerJ Phys. Chem.
         **2**, e7 (2020).


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      .. image:: /_static/img/pyvisa/chemitree-formic-water.png
         :width: 100%
         :class: img-responsive

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         :header:`ChemiTrees for reaction-path interpretation.`

         Decision-tree analysis was used as a post-processing workflow
         for path-sampling trajectories of proton exchange in formic
         acid-water clusters, identifying geometric descriptors that
         distinguish reactive and unreactive paths.

         Source files: to be recovered and mirrored.

         Paper: S. Roet, C. D. Daub and E. Riccardi, `Chemistrees:
         data driven identification of reaction pathways via machine
         learning <https://doi.org/10.1021/acs.jctc.1c00458>`_,
         J. Chem. Theory Comput. **17**, 6193-6202 (2021).


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      .. image:: /_static/img/examples/thumbnails/repptis-400x400.png
         :width: 100%
         :class: img-responsive

      .. container:: caption

         :header:`Memory reduction using partial path ensembles`.

         A study on how the path ensemble definitions can be changed when
         long-lived metastable states are present in the reaction.

         `Source Files <https://github.com/WouterWV/pathsampling_toymodels>`__

         Paper: W. Vervust, D. T. Zhang, T. S. van Erp and A. Ghysels,
         `Path sampling with memory reduction and replica exchange to
         reach long permeation timescales
         <https://doi.org/10.1016/j.bpj.2023.02.021>`_, Biophys. J.
         **122**, 2960-2972 (2023).


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      .. image:: /_static/img/examples/thumbnails/submoves-hole-400x400.png
         :width: 100%
         :class: img-responsive

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         :header:`Rupture of a thin liquid film.`

         Subtrajectory Monte Carlo moves (Wire Fencing and Stone
         Skipping) applied to the rupture of a dodecane film in water,
         sampled with GROMACS. A large, condensed-phase test of the
         moves introduced in the subtrajectory-moves study.

         `Source Files <https://www.pyretis.org/source_files/Submoves_2022/hole/>`__

         Paper: D. T. Zhang, E. Riccardi and T. S. van Erp, `Enhanced
         path sampling using subtrajectory Monte Carlo moves
         <https://doi.org/10.1063/5.0127249>`_, J. Chem. Phys. **158**,
         024113 (2023).


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      .. image:: /_static/img/examples/thumbnails/submoves-ruru-400x400.png
         :width: 100%
         :class: img-responsive

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         :header:`Redox reaction of a diruthenium complex.`

         The same subtrajectory moves on an *ab initio* (CP2K)
         di-ruthenium aqua complex, where each force evaluation is
         expensive. The companion *ab initio* benchmark of the
         subtrajectory-moves study.

         `Source Files <https://www.pyretis.org/source_files/Submoves_2022/ruru/>`__

         Paper: D. T. Zhang, E. Riccardi and T. S. van Erp, `Enhanced
         path sampling using subtrajectory Monte Carlo moves
         <https://doi.org/10.1063/5.0127249>`_, J. Chem. Phys. **158**,
         024113 (2023).