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
A Versatile Approach to Stabilize Liquid-Liquid Interfaces using Surfactant Self-Assembly
Small. 2024-06-14. DOI : 10.1002/smll.202403013.POETS: An Event-driven Approach to Dissipative Particle Dynamics
Acm Transactions On Parallel Computing. 2023-06-01. DOI : 10.1145/3580372.Macromolecular Crowding Is Surprisingly Unable to Deform the Structure of a Model Biomolecular Condensate
Biology-Basel. 2023-02-01. DOI : 10.3390/biology12020181.Model biomolecular condensates have heterogeneous structure quantitatively dependent on the interaction profile of their constituent macromolecules
Soft Matter. 2022-08-25. DOI : 10.1039/d2sm00387b.Computational synthesis of cortical dendritic morphologies
Cell Reports. 2022-04-05. DOI : 10.1016/j.celrep.2022.110586.Investigating the morphological transitions in an associative surfactant ternary system
Soft Matter. 2022-03-07. DOI : 10.1039/d1sm01668g.Coupling Bulk Phase Separation of Disordered Proteins to Membrane Domain Formation in Molecular Simulations on a Bespoke Compute Fabric
Membranes. 2022-01-01. DOI : 10.3390/membranes12010017.Non-monotonic fibril surface occlusion by GFP tags from coarse-grained molecular simulations
Computational and Structural Biotechnology Journal. 2022. DOI : 10.1016/j.csbj.2021.12.017.Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell
Toxins. 2021-06-28. DOI : 10.3390/toxins13070449.Phase behaviour and structure of a model biomolecular condensate
Soft Matter. 2020-07-21. DOI : 10.1039/d0sm00813c.Characterization of Protein-Membrane Interfaces through a Synergistic Computational-Experimental Approach
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7278.Correction to Mechanism of Shiga Toxin Clustering on Membranes
ACS NANO. 2018. DOI : 10.1021/acsnano.8b00537.A Topological Representation of Branching Neuronal Morphologies
NEUROINFORMATICS. 2018. DOI : 10.1007/s12021-017-9341-1.Clustering on Membranes: Fluctuations and More
Trends in Cell Biology. 2018. DOI : 10.1016/j.tcb.2018.01.009.Neuronal morphologies: the shapes of thoughts
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8255.Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation
Bmc Bioinformatics. 2017. DOI : 10.1186/s12859-016-1444-4.Mechanism of Shiga Toxin Clustering on Membranes
ACS Nano. 2017. DOI : 10.1021/acsnano.6b05706.Framework for efficient synthesis of spatially embedded morphologies
Physical Review E. 2016. DOI : 10.1103/PhysRevE.94.023315.Membrane invagination induced by Shiga toxin B-subunit: from molecular structure to tube formation
Soft Matter. 2016. DOI : 10.1039/C6SM00464D.Reconstructing the brain: from image stacks to neuron synthesis
Brain Informatics. 2016. DOI : 10.1007/s40708-016-0041-7.In situ synthesis and simulation of polydisperse amphiphilic membranes
International Journal of Advances in Engineering Sciences and Applied Mathematics. 2015. DOI : 10.1007/s12572-015-0156-8.The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex
Frontiers In Neural Circuits. 2015. DOI : 10.3389/fncir.2015.00044.Reconstruction and Simulation of Neocortical Microcircuitry
Cell. 2015. DOI : 10.1016/j.cell.2015.09.029.The effects of globotriaosylceramide tail saturation level on bilayer phases
Soft Matter. 2015. DOI : 10.1039/c4sm02456g.Vesicles and Vesicle Fusion: Coarse-Grained Simulations
Biomolecular Simulations; Totowa, NJ: Humana Press, 2013. p. 659-697.Spontaneous Vesicle Self-Assembly: A Mesoscopic View of Membrane Dynamics
Langmuir. 2012. DOI : 10.1021/la2033803.Tension-induced fusion of bilayer membranes and vesicles
Nature Materials. 2005. DOI : 10.1038/nmat1333.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