Julian Charles Shillcock
julian.shillcock@epfl.ch +41 21 693 96 79 https://www.epfl.ch/labs/lashuel-lab/computational-modelling-within-lmnn/
Nationality: British
+41 21 693 96 79
EPFL › VPA › VPA-AVP-DLE › AVP-DLE-EDOC › EDNE-ENS
Website: https://go.epfl.ch/edne
+41 21 693 96 79
EPFL › SV › SV-SSV › SSV-ENS
Website: https://sv.epfl.ch/education
+41 21 693 96 79
EPFL › SV › IBI-SV › UPDALPE
Website: https://lbm.epfl.ch/
Expertise
Biophysics
Mesoscale simulations of soft matter
Numerical analysis
Computer simulations
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
the URL provided has not the 'query' parameters
Research
Accelerating Coarse-Grained Molecular Simulations
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
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
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.