SIST/CITATION.cff at main · CCPBioSim/SIST · GitHub

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# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: SIST
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software

authors:
  - given-names: Craig
    family-names: Benham
    email: 'cjbenham@ucdavis.edu'
    affiliation: 'UC Davis Genome Center and Department of Mathematics, University of California, Davis, CA 95616, USA.'
    affiliation: 'https://orcid.org/0009-0005-4610-2402'
  - given-names: Dina
    family-names: Zhabinskaya
    email: dzhabinskaya@ucdavis.edu
    affiliation: 'UC Davis Genome Center and Department of Mathematics, University of California, Davis, CA 95616, USA.'
  - given-names: Sally
    family-names: Madden
    affiliation: 'UC Davis Genome Center and Department of Mathematics, University of California, Davis, CA 95616, USA.'
  - given-names: Richard M.
    family-names: Fye
  - given-names: Victor
    family-names: Velasco-Berrelleza
    email: v.velascoberrelleza@sheffield.ac.uk
    affiliation: 'School of Mathematical and Physical Sciences, University of Sheffield, United Kingdom'
    orcid: 'https://orcid.org/0000-0002-4809-6254'
  - given-names: Harry
    family-names: Swift
    email: harry.swift@stfc.ac.uk
    affiliation: 'Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, United Kingdom'
    orcid: 'https://orcid.org/0009-0007-3323-753X'
  - given-names: Jas
    family-names: Kalayan
    email: jas.kalayan@stfc.ac.uk
    affiliation: 'Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, United Kingdom'
    orcid: 'https://orcid.org/0000-0002-6833-1864'
  - given-names: Sarah
    family-names: Harris
    email: sarah.harris@sheffield.ac.uk
    affiliation: School of Mathematical and Physical Sciences, University of Sheffield, United Kingdom
    orcid: 'https://orcid.org/0000-0002-2812-1651'
  - given-names: James
    family-names: Gebbie-Rayet
    email: james.gebbie@stfc.ac.uk
    affiliation: 'Scientific Computing Department, STFC Daresbury Laboratory, Warrington WA4 4AD, United Kingdom'
    orcid: 'https://orcid.org/0000-0001-8271-3431'

repository-code: 'https://github.com/CCPBioSim/SIST'
url: 'https://sist.readthedocs.io/en/latest/'

abstract: >-
  SIST (Stress-Induced Structural Transitions) calculates
  stress-induced structural transition probabilities in
  superhelical DNA, including strand separation, Z-DNA
  formation, cruciform extrusion, and competition between
  these transitions.

keywords:
  - DNA
  - superhelical DNA
  - DNA supercoiling
  - strand separation
  - Z-DNA
  - cruciform extrusion
  - structural transitions
  - statistical mechanics
  - biomolecular simulations

license: MIT
version: 1.0.0
date-released: '2026-09-14'