Julian Charles Shillcock
Nationality: British
+41 21 693 96 79
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Website: https://go.epfl.ch/edne
+41 21 693 96 79
EPFL › SV › SV-SSV › SSV-ENS
Website: https://sv.epfl.ch/education
Expertise
Physics
Biophysics
Mesoscale simulations of soft matter
Numerical analysis
Computer simulations
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.
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
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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
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
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