Algorithms for designing genetic circuits

Unlike in physics, the biological complexity of cellular processes still pushes mathematical modelling to its limits. Nevertheless, synthetic biology is nowadays able to find quantitative descriptions in the form of computer models for simple, self-contained biomolecular systems and to derive meaningful predictions from them. For a very limited set of well-characterised genetic elements, it is also possible to reliably simulate the interconnection of these elements on the computer. Professor Heinz Koeppl's PLATE project deals with algorithms that can automatically combine elements from a sequence and regulator library in a functional combination and characterise the behaviour of the resulting networks or circuits.

Existing methods for this work with phenomenological models, whose large number of parameters often means that the predictive ability of the models is low. By adding biophysical models and basic principles, PLATE develops new design algorithms that achieve a better fit between model and experimental realisation. The foundations for such models were developed in the ERC Consolidator Grant “CONSYN”, which Koeppl received in 2017.

PLATE aims to create an entire digital design software environment in which genetic circuits can be created, analysed and optimised. As the same type of algorithms can also be found in the field of microelectronics, Koeppl will make use of synergies and is working closely with Professor Christian Hochberger, Head of the Computer Systems research group at the Department of Electrical Engineering and Information Technology.

The PLATE project is another important addition to the project portfolio of the Centre for Synthetic Biology (Profile Topic Synthetic Biology) at TU Darmstadt and strengthens the activities and international visibility of the TU in the field of synthetic biology.