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title: Tutorials for Membrane Review
message: >-
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type: software
authors:
  - given-names: Miguel
    family-names: Amaral
    email: miguel.amaral@ista.ac.at
    affiliation: ISTA
  - given-names: Adam
    family-names: Prada
    email: adam.prada@ista.ac.at
    affiliation: ISTA
  - given-names: Maitane
    family-names: Munoz-Basagoiti
    email: maitane.munoz-basagoiti@ista.ac.at
    affiliation: ISTA
  - given-names: Felix
    family-names: Frey
    email: felix.frey@ista.ac.at
    affiliation: ISTA
  - given-names: Billie
    family-names: Meadowcroft
    email: billie.meadowcroft@ista.ac.at
    affiliation: ISTA
  - given-names: Andela
    family-names: Saric
    email: andela.saric@ista.ac.at
    affiliation: ISTA
repository-code: 'https://github.com/Saric-Group/MembraneReviewTutorials'
abstract: >-
  All biological cells are defined by a plasma membrane that
  protects the interior of the cell from the extracellular
  environment. This membrane is frequently deformed across
  different scales in various cellular processes. Due to the
  relevance of the topic, the study of membranes and
  membrane deformations is a long-standing area of research
  in biophysics and soft matter, using both experimental and
  theoretical approaches. Various approaches are used for
  modeling membranes and membrane deformations. Analytical
  and numerical modeling has greatly advanced our knowledge
  of simplified or reconstituted systems. In addition,
  computer simulations with varying degrees of detail are
  used. 

  Such simulations have the advantage that they can also be
  applied to highly complex biological problems. They are
  therefore a suitable tool for investigating membranes that
  interact with passive or active molecular structures.
  While it is undisputed that computational modeling is a
  very powerful approach, in practice it comes with many
  difficulties and complications. In particular, beginners
  and non-experts may struggle with the basic understanding
  of the simulation models, making it difficult to develop
  meaningful models. This is partially due to the extension
  period of time over which this field has developed, but
  also because of the requirement of two very different
  expertise to develop and apply such simulations:
  theoretical statistical physics and programming. With this
  review, we aim to introduce the non-expert reader to
  non-specific-lipid coarse-grained membrane simulations at
  the mesoscale using a three-step protocol. First, we
  provide a short but concise overview of the computational
  approaches to study fluid membranes as a starting point
  from which readers are directed to more specialized
  references. Second, we provide a conceptual guide on how
  to develop coarse-grained membrane simulations. And third,
  we construct a hands on tutorial on how to apply mesoscale
  membrane simulations. Specifically, our focus is on a
  comparison of different models and a pedagogical
  examination of them in terms of what these models can
  achieve and how resource-intensive they are. To ease the
  non-expert reader's venture into the field, we provide a
  GitHub repository with ready-to-run tutorials/code to
  simulate the different models.
keywords:
  - simulation
  - membrane