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Simplified Computational Model for Generating Biological Networks

preprint
submitted on 16.07.2020 and posted on 17.07.2020 by Matthew Bailey, David Ormrod Morley, Mark Wilson

A method to generate and simulate biological networks is discussed. An expanded Wooten-Winer-Weaire bond switching methods

is proposed which allows for

a distribution of node degrees in the network while conserving the mean average node degree.

The networks are characterised in terms of their polygon structure and assortativities (a measure

of local ordering). A wide range of experimental images are analysed and the underlying networks

quantified in an analogous manner. Limitations in obtaining the network structure are discussed.

A "network landscape" of the experimentally observed and simulated networks is constructed from the underlying metrics.

The enhanced bond switching algorithm is able to generate networks spanning the full range of experimental observations.

Funding

EPSRC Centre for Doctoral Training in Theory and Modelling in Chemical Sciences.

Engineering and Physical Sciences Research Council

Find out more...

History

Email Address of Submitting Author

matthew.bailey@chem.ox.ac.uk

Institution

University of Oxford

Country

United Kingdom

ORCID For Submitting Author

0000-0003-2939-742X

Declaration of Conflict of Interest

no conflict of interest

Exports