PIMMS (0.24 pre-beta)

PIMMS (Polymer Interactions in Multi-components MixtureS) is a lattice-based Monte Carlo simulation engine.

This version of PIMMS represents the original implementation used in the paper "Valence and patterning of aromatic residues determine the phase behavior of prion-like domains" by Martin, Holehouse, Peran et al. [1].

This version (PIMMS 0.24 rc1) should NOT be used for new science. It is provided to ensure a DOI-stamped version of the code used in the associated paper is available. HOWEVER, a much more modern implementation of PIMMS is actively being developed and finalized.

PIMMS was originally developed between 2015-2017, and was then used to construct sticker-and-spacer simulations for this manuscript during 2017 and 2018. Over the course of 2019, while the paper was undergoing reviewer, we re-structured PIMMS as a Python 3.7 application and as a fully packaged software tool, that includes unit tests, software documentation, much improved code documentation,  additional features, many bug fixes (none of which impact functionality used in the Valence and patterning... paper).

I cannot emphasize strongly enough that there are many features that remain incomplete in version 0.24 PIMMS that were not used for the stickers and spacers simulations. As a result, trying to use this as a stand alone package will likely result in disaster (or at least inconvenience). It can, of course, be used to reproduce the work done in this paper, as is shown in the /demo directory.

If you are interested in using PIMMS for new science, please know we are finalizing this modern implementation for a release in early 2020. We would be happy to share early versions of the code if this is of interest. Please contact me at alex.holehouse@wustl.edu for more information.

[1] Valence and patterning of aromatic residues determine the phase behavior of prion-like domains
Erik W. Martin¹†, Alex S. Holehouse^2,3†, Ivan Peran¹†, Mina Farag^2,3, J. Jeremias Incicco⁴, Anne Bremer¹, Christy R. Grace¹, Andrea Soranno^3,4, Rohit V. Pappu^2,3§, Tanja Mittag¹§

1 Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
2 Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
3 Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO 63130, USA
4 Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA

† These authors contributed equally
§ These authors are co-corresponding authors