Julian Charles Shillcock

Nationality: British

Expertise

Physics
Biophysics
Mesoscale simulations of soft matter
Numerical analysis
Computer simulations
I received my PhD at Simon Fraser University in Canada for work on Monte Carlo simulations of liquid crystal phase transitions and the elastic properties of fluid and polymerized membranes.
Then I moved to the Max Planck Institute of Colloids and Interfaces, Germany, and was a group leader for five years applying coarse-grained simulation techniques - principally Dissipative Particle Dynamics (DPD) and Brownian Dynamics - to equilibrium and dynamic properties of fluid lipid membranes. A major target of this research was to reveal the molecular rearrangements that occur during vesicle fusion. During this time, I developed a parallel DPD code that is still being used by several universities (https://github.com/Osprey-DPD/osprey-dpd)
I was then an Associate Professor at MEMPHYS in the Department of Physics and Chemistry, University of Southern Denmark. In a previous life, I performed mission analysis for communication satellites, designed and wrote software for satellite simulations (British Aerospace, 1986-1990), and developed commercial fluid simulation software (Accelrys, Inc., 1998-1999).
I joined the Blue Brain Project in 2011 to develop mesoscale simulations of cellular dynamics, and am now studying the structure of biomolecular condensates using mesoscale simulations. I teach Master's and PhD courses in computational cell biology and biophysics, and was awarded the Polysphère prize for Best Teacher in Life Sciences in 2021.

Awards

Polysphère SV

Pour l'excellence de son enseignement

2021

Publications

Research

Accelerating Coarse-Grained Molecular Simulations

I have developed and maintain a parallel Dissipative Particle Dynamics (DPD) code to perform complex fluid simulations on length and time scales far beyond those attainable with Molecular Dynamics simulations. The code is used under license from the Max Planck Institute, where part of it was developed. It uses the common Message Passing Interface protocol, and its execution shows excellent weak scaling up to 2000 processors. The code has been used in more than a dozen publications, and is in current use at several universities and research institutes.
I am working with Imperial College London and the University of Southampton to implement the code on a novel computing platform called POETS - Partially-Oriented Event Triggered Systems (www.poets-project.org) which has the potential to speed up DPD simulations by several orders of magnitude. POETS is funded by the UK

Mechanism of Shiga toxin entry into cells

The plasma membrane of cells protects the interior from the environment while permitting signals to be transduced across it and allowing material to be taken in or expelled in a controlled way. Bacteria and viruses have evolved to co-opt signalling and endocytic pathways to invade a cell in order to propagate themselves. Some of these pathways are independent of the cellular endocytic machinery, an example being that used by Ricin, Shiga and Shiga-like bacterial toxins.
Shiga toxin invasion begins when toxin particles in the bulk solution adsorb to the plasma membrane by binding to globotriaosylceramide glyoclipids (Gb3) lipids. They subsequently diffuse around and form clusters. This clustering process takes place over distances much larger than the particle size, and in the absence of direct protein-protein attractive forces. We have used atomistic and mesoscopic simulations to characterise the toxin

Teaching & PhD

Past EPFL PhD Students as codirector

Lida Kanari

Courses

Computational cell biology

BIOENG-455

Computer modeling is used to study dynamic phenomena in cell biology. This course shows how to identify mathematical features of cell biology mechanisms and use numerical algorithms to model their behavior.

Dynamical systems in biology

BIO-341

Life is non-linear. This course introduces dynamical systems as a technique for modelling simple biological processes. The emphasis is on the qualitative and numerical analysis of non-linear dynamical models. Examples are taken from biology and population models.

Symmetry and Conservation in the Cell

BIO-692

This course shows students how the physical principles of conservation, symmetry, and locality influence the dynamics of living organisms at the molecular and cellular level. Computer simulations are used to explore examples of cellular dynamics and phase transitions.