Simple Oritatami simulator
iPad / Education
OS simulator is an iPad app that runs arbitrary Oritatami models efficiently.
The Oritatami model was introduced in 2016 in (IJMS 2019) to study the computational potential of RNA cotranscriptional folding as first shown in wet-lab experiments by (Science 2014).
In Oritatami systems (OS), we consider a finite set of bead types, and a periodic sequence of beads, each of a specific bead type. Beads are attracted to each other according to a fixed symmetric relation. In any folding, a bond is formed between any pair of beads located at adjacent positions and attracting each other. At each step, the δ latest nascent beads in the sequence are allowed to explore all possible positions, and adopt only those positions that minimise the energy, or otherwise put, those positions that maximise the number of bonds in the folding. δ is called the delay. ``Beads'' are a metaphor for domains, i.e. subsequences, in RNA and DNA (and are thus not limited to 4 types only). The Oritatami model has proven to be a fruitful framework to study molecular reconfigurability, one of the most promising directions to reduce error in wetlab molecular implementation as error might be erased by reconfiguration later on.
Oritatami systems have to be loaded into the app as a .os file.
More info at: http://perso.ens-lyon.fr/nicolas.schabanel/OSsimulator/
Quoi de neuf dans la dernière version ?
• New compact seed conformation file format (save time and disk space)
• Files can be sorted by modification dates
