Active matter in an active city

Author: Guest blogger
Posted: 9 Jul 2019 | 13:39

Giuseppe Negro undertook an HPC-Europa3 visit based in Edinburgh from 15/04/19–27/05/19. He gives us a brief overview of his visit and the work he undertook.

Hi everyone! My name is Giuseppe Negro and I am a PhD student at the University of Bari in Italy. I work in computational modelling of soft matter systems with Prof. Giuseppe Gonnella and with my collegue Livio Nicola Carenza, who was also an HPC-Europa3 visitor in Edinburgh, at the Department of Physics in Bari. I visited EPCC under the HPC-Europa3 transnational access programme, and I was hosted by Prof. D. Marenduzzo at the Department of Physics and Astronomy of the University of Edinburgh located at the James Clerk Maxwell Building.

My research involves computational modelling of soft composite materials focusing on biological fluids. 

In many active biological systems, chirality plays a relevant role. Biomolecules such as DNA, actin or microtubules form helical structures which, at sufficiently high density and in the absence of active forces, tend to self-assemble into twisted cholesteric phases. Understanding the outcome of the interplay between chirality and activity is therefore an important and timely question. Studying a droplet of chiral matter in 3D, we have found evidence of a new motility mode, where the rotational motion of surface topological defects, that arrange in a fan-like pattern, is converted into propulsion: see the movie below. This generates regular translatory motion due to the underlying chirality. This is a striking new phenomenon that can be also exploited in practical applications. The use of a parallel (MPI) implementation of lattice Boltzmann models and available HPC resources have been of fundamental importance in conducting the study.

We have also implemented a lattice Boltzmann model able to solve the dynamics of soft deformable droplets immersed in a nematic liquid crystal matrix. The MPI implementation and the huge amount of HPC resources available allowed us to consider big system sizes with high packing fraction. The reological characterisation of such systems that was carried out during my stay constitutes the first step in the study of tissue development and morphogenesis to investigate the physics behind these process.

It has been a highly positive time, and I really enjoyed the city of Edinburgh and its marvellous landscapes during relaxing after-work walks. I strongly recommend the HPC-Europa experience, particularly in EPCC. Working with Prof. D Marenduzzo and relying on the essential support provided by Dr Mario Antonioletti has been a really great experience.