Research Groups

Simulating biological processes in complex 3D geometries

Discovering the decision and communication patterns cells execute when arranging into tissues is a reverse-engineering task. In order to see what phenotype and developmental dynamics a cellular “algorithm” produces we need to be able to simulate that “algorithm of tissue formation” in a computer. It is hence our mid-term goal to develop a modular numerical simulation paradigm for biophysical and biological processes in 3D space and time.

We address this by novel hybrid particle-mesh methods that we designed to meet the intricacies of biological systems (i.e., non-linearity, internal activity, complex geometries). Particles are used as collocation points to represent continuous fields. A theory (DC PSE) developed in our group enables consistent approximation of differential operators on any particle function representation. This provides the freedom of distributing the particles arbitrarily, in particular so as to be adapted to the simulated geometries and their temporal dynamics. Further, the particles self-organize according to adjustable interaction potentials, providing unprecedented flexibility to simulate multiple scales of resolution.

So far, we have completed simulation modules for biochemical reaction networks, reaction-diffusion systems, and the first-ever simulation of active biomechanics with the group of Frank Jülicher.

Collaborators:

  • Dr. Rajesh Ramaswamy (MPI-PKS)
  • Prof. Dr. Frank Jülicher (MPI-PKS)
  • Dr. George Bourantas (Institute of Fluid Mechanics, Uni Luxembourg)
  • Prof. Dr. Jens H. Walther (Mechanical Engineering, DTU Copenhagen)
First-ever numerical solution of active polar gels showing that motor protein activity in the cytoskeleton can tune the global orientation of the filaments. Increasing or decreasing the activity, an aster spontaneously transforms to a spiral and vice versa. Such transformations have also been observed experimentally in vitro, modulating the orientation of microtubules by changing the concentration of motor proteins. Image courtesy of Dr. Rajesh Ramaswamy, MPI-PKS.