VDNA-Lab: A computational simulation platform for DNA multi-strand dynamics

The dynamics of nucleic-acids dynamical systems is intrinsically based on local interaction. The major acting mechanisms are that of Watson-Crick complementarity on one-hand, generating binding events, and thermal energy on the other, generating random motion and un-binding. It is thus predictable that such systems can be successfully captured by computational modeling paradigms based on local interactions, such as the rule-based modeling methodology. In this research we introduce the Virtual DNA Lab (VDNA-Lab) a simulation tool which provides an easy to use graphical interface for creating, running and visualizing synthetic simulations for DNA assembly systems, such as assembly of DNA nanostructures, strand displacement cascades systems, DNA-tile assembly etc. It employs a custom designed model, implemented in the BioNetGen Language (BNGL) formalism, to capture the DNA dynamics, as well as the NFsim computational modeling engine to run simulations and generate outputs. These outputs can be visualized using the VDNA-Lab’s own visualization tool, which allows also for further analysis and filtering. The software is freely available at https://github.com/Frankie-Spencer/virtual dna lab.