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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

A Versatile Approach to Stabilize Liquid-Liquid Interfaces using Surfactant Self-Assembly

H. HonaryarS. AmirfattahiD. NguyenK. KimJ. C. Shillcock  et al.

Small. 2024-06-14. DOI : 10.1002/smll.202403013.

POETS: An Event-driven Approach to Dissipative Particle Dynamics

A. D. BrownJ. R. BeaumontD. B. ThomasJ. C. ShillcockM. F. Naylor  et al.

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

J. C. ShillcockD. B. ThomasJ. H. IpsenA. D. Brown

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

J. C. ShillcockC. LagisquetJ. AlexandreL. VuillonJ. H. Ipsen

Soft Matter. 2022-08-25. DOI : 10.1039/d2sm00387b.

Computational synthesis of cortical dendritic morphologies

L. KanariH. DictusA. ChalimourdaA. ArnaudonW. Van Geit  et al.

Cell Reports. 2022-04-05. DOI : 10.1016/j.celrep.2022.110586.

Investigating the morphological transitions in an associative surfactant ternary system

H. HonaryarJ. A. LaNasaR. J. HickeyJ. C. ShillcockZ. Niroobakhsh

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

J. C. ShillcockD. B. ThomasJ. R. BeaumontG. M. BraggM. L. Vousden  et al.

Membranes. 2022-01-01. DOI : 10.3390/membranes12010017.

Non-monotonic fibril surface occlusion by GFP tags from coarse-grained molecular simulations

J. C. ShillcockJ. HastingsN. RiguetH. A. Lashuel

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

W. PezeshkianJ. C. ShillcockJ. H. Ipsen

Toxins. 2021-06-28. DOI : 10.3390/toxins13070449.

Phase behaviour and structure of a model biomolecular condensate

J. C. ShillcockM. BrochutE. ChenaisJ. H. Ipsen

Soft Matter. 2020-07-21. DOI : 10.1039/d0sm00813c.

Characterization of Protein-Membrane Interfaces through a Synergistic Computational-Experimental Approach

A. Prunotto

Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7278.

Correction to Mechanism of Shiga Toxin Clustering on Membranes

W. PezeshkianH. GaoS. ArumugamU. BeckenP. Bassereau  et al.

ACS NANO. 2018. DOI : 10.1021/acsnano.8b00537.

A Topological Representation of Branching Neuronal Morphologies

L. KanariP. DlotkoM. ScolamieroR. LeviJ. Shillcock  et al.

NEUROINFORMATICS. 2018. DOI : 10.1007/s12021-017-9341-1.

Clustering on Membranes: Fluctuations and More

L. JohannesW. PezeshkianJ. H. IpsenJ. C. Shillcock

Trends in Cell Biology. 2018. DOI : 10.1016/j.tcb.2018.01.009.

Neuronal morphologies: the shapes of thoughts

L. Kanari

Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8255.

Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation

M. AbdellahA. BilgiliS. EilemannJ. ShillcockH. Markram  et al.

Bmc Bioinformatics. 2017. DOI : 10.1186/s12859-016-1444-4.

Mechanism of Shiga Toxin Clustering on Membranes

W. PezeshkianH. GaoS. ArumugamU. BeckenP. Bassereau  et al.

ACS Nano. 2017. DOI : 10.1021/acsnano.6b05706.

Framework for efficient synthesis of spatially embedded morphologies

L. VanherpeL. KanariG. AtenekengJ. PalaciosJ. Shillcock

Physical Review E. 2016. DOI : 10.1103/PhysRevE.94.023315.

Membrane invagination induced by Shiga toxin B-subunit: from molecular structure to tube formation

W. PezeshkianA. G. HansenL. JohannesH. KhandeliaJ. C. Shillcock  et al.

Soft Matter. 2016. DOI : 10.1039/C6SM00464D.

Reconstructing the brain: from image stacks to neuron synthesis

J. C. ShillcockM. HawrylyczS. HillH. Peng

Brain Informatics. 2016. DOI : 10.1007/s40708-016-0041-7.

In situ synthesis and simulation of polydisperse amphiphilic membranes

L. VanherpeL. KanariG. AtenekengJ. PalaciosJ. Shillcock

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

S. RamaswamyJ.-D. CourcolM. AbdellahS. R. AdaszewskiN. Antille  et al.

Frontiers In Neural Circuits. 2015. DOI : 10.3389/fncir.2015.00044.

Reconstruction and Simulation of Neocortical Microcircuitry

H. MarkramE. MullerS. RamaswamyM. W. ReimannM. Abdellah  et al.

Cell. 2015. DOI : 10.1016/j.cell.2015.09.029.

The effects of globotriaosylceramide tail saturation level on bilayer phases

W. PezeshkianV. V. ChabanL. JohannesJ. ShillcockJ. H. Ipsena  et al.

Soft Matter. 2015. DOI : 10.1039/c4sm02456g.

Vesicles and Vesicle Fusion: Coarse-Grained Simulations

J. C. Shillcock

Biomolecular Simulations; Totowa, NJ: Humana Press, 2013. p. 659-697.

Spontaneous Vesicle Self-Assembly: A Mesoscopic View of Membrane Dynamics

J. C. Shillcock

Langmuir. 2012. DOI : 10.1021/la2033803.

Tension-induced fusion of bilayer membranes and vesicles

J. C. ShillcockR. Lipowsky

Nature Materials. 2005. DOI : 10.1038/nmat1333.

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