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Julian Charles Shillcock

Cette personne a quitté l’EPFL

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Publications associées (22)

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Model biomolecular condensates have heterogeneous structure quantitatively dependent on the interaction profile of their constituent macromolecules

Julian Charles Shillcock

Biomolecular condensates play numerous roles in cells by selectively concentrating client proteins while excluding others. These functions are likely to be sensitive to the spatial organization of the scaffold proteins forming the condensate. We use coarse ...

2022

Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell

Julian Charles Shillcock

Many bacteria secrete toxic protein complexes that modify and disrupt essential processes in the infected cell that can lead to cell death. To conduct their action, these toxins often need to cross the cell membrane and reach a specific substrate inside th ...

2021

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

Hilal Lashuel, Julian Charles Shillcock, Joanna Kathleen Hastings

The pathological growth of amyloid fibrils in neurons underlies the progression of neurodegenerative diseases including Alzheimer’s and Parkinson’s disease. Fibrils form whensoluble monomers oligomerise in the cytoplasm. Their subsequent growth occurs via ...

2022

Phase behaviour and structure of a model biomolecular condensate

Julian Charles Shillcock

Phase separation of immiscible fluids is a common phenomenon in polymer chemistry, and is recognized as an important mechanism by which cells compartmentalize their biochemical reactions. Biomolecular condensates are condensed fluid droplets in cells that ...

2020

Macromolecular Crowding Is Surprisingly Unable to Deform the Structure of a Model Biomolecular Condensate

Julian Charles Shillcock

Simple Summary The cytoplasm of a living cell is a crowded place, containing hundreds of types of protein and other macromolecules. Cells reliably and continually perform thousands of biochemical reactions to maintain their health. Biomolecular condensates ...

2023

Framework for efficient synthesis of spatially embedded morphologies

Julian Charles Shillcock, Lida Kanari, Liesbeth Maria L Vanherpe

Many problems in science and engineering require the ability to grow tubular or polymeric structures up to large volume fractions within a bounded region of three-dimensional space. Examples range from the construction of fibrous materials and biological c ...

Amer Physical Soc2016

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

Henry Markram, Felix Schürmann, Marwan Muhammad Ahmed Abdellah, Julian Charles Shillcock, Ahmet Bilgili, Stefan Eilemann

Background: We present a visualization pipeline capable of accurate rendering of highly scattering fluorescent neocortical neuronal models. The pipeline is mainly developed to serve the computational neurobiology community. It allows the scientists to visu ...

2017

Can you Teach Cell Biology using Computer Simulations?

Julian Charles Shillcock

Computational modelling is important in the life sciences, but students may not be greatly exposed to it in typical curricula.This paper describes an innovative, one-semester Master's level course in cell biology that uses computer simulations as the prima ...

European Society for Engineering Education (SEFI)2024

In situ synthesis and simulation of polydisperse amphiphilic membranes

Julian Charles Shillcock, Lida Kanari, Liesbeth Maria L Vanherpe

The field of coarse-grained simulations of biopolymers and membranes has grown rapidly in recent years. Industrial groups manufacture and use polymers in fields as diverse as chemicals processing and personal care products, while academic researchers are i ...

Springer India2015

The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex

Henry Markram, Felix Schürmann, James Gonzalo King, Rajnish Ranjan, Srikanth Ramaswamy, Sean Lewis Hill, Juan Bautista Hernando Vieites, Eilif Benjamin Muller, Daniel Keller, Idan Segev, Michael Reimann, Ying Shi, Marwan Muhammad Ahmed Abdellah, Julian Charles Shillcock, Jean-Denis Georges Emile Courcol, Ahmet Bilgili, Werner Alfons Hilda Van Geit, Stefan Eilemann, Jeffrey Christopher Muller, Lida Kanari, Giuseppe Chindemi, Michael Emiel Gevaert, Nicolas Antille

We have established a multi-constraint, data-driven process to digitally reconstruct, and simulate prototypical neocortical microcircuitry, using sparse experimental data. We applied this process to reconstruct the microcircuitry of the somatosensory corte ...

Frontiers Research Foundation2015

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

Julian Charles Shillcock

The bacterial Shiga toxin is composed of an enzymatically active A-subunit, and a receptor-binding homopentameric B-subunit (STxB) that mediates intracellular toxin trafficking. Upon STxB-mediated binding to the glycolipid globotriaosylceramide (Gb3) at th ...

Royal Society of Chemistry2016

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

Julian Charles Shillcock

Stabilizing liquid-liquid interfaces, whether between miscible or immiscible liquids, is crucial for a wide range of applications, including energy storage, microreactors, and biomimetic structures. In this study, a versatile approach for stabilizing the w ...

Wiley-V C H Verlag Gmbh2024

The effects of globotriaosylceramide tail saturation level on bilayer phases

Julian Charles Shillcock

Globotriaosylceramide (Gb(3)) is a glycosphingolipid present in the plasma membrane that is the natural receptor of the bacterial Shiga toxin. The unsaturation level of Gb(3) acyl chains has a drastic impact on lipid bilayer properties and phase behaviour, ...

Royal Soc Chemistry2015

POETS: An Event-driven Approach to Dissipative Particle Dynamics

Julian Charles Shillcock

HPC clusters have become ever more expensive, both in terms of capital cost and energy consumption; some estimates suggest that competitive installations at the end of the next decade will require their own power station. One way around this looming proble ...

2023

Reconstructing the brain: from image stacks to neuron synthesis

Sean Lewis Hill, Julian Charles Shillcock

Large-scale brain initiatives such as the US BRAIN initiative and the European Human Brain Project aim to marshall a vast amount of data and tools for the purpose of furthering our understanding of brains. Fundamental to this goal is that neuronal morpholo ...

2016

Clustering on Membranes: Fluctuations and More

Julian Charles Shillcock

Clustering of extracellular ligands and proteins on the plasma membrane is required to perform specific cellular functions, such as signaling and endocy- tosis. Attractive forces that originate in perturbations of the membrane’s phys- ical properties contr ...

2018

Reconstruction and Simulation of Neocortical Microcircuitry

Jean-Vincent Le Bé, Henry Markram, Gilad Silberberg, Sébastien Lasserre, Vincent Delattre, Rodrigo de Campos Perin, Felix Schürmann, James Gonzalo King, Rajnish Ranjan, Srikanth Ramaswamy, Sean Lewis Hill, Juan Bautista Hernando Vieites, Georges Khazen, Shruti Muralidhar, Anastasia Ailamaki, Eilif Benjamin Muller, Farhan Tauheed, Jean Pierre Ghobril, Julie Meystre, Daniel Keller, Idan Segev, Michael Reimann, Thomas Heinis, Ying Shi, Marwan Muhammad Ahmed Abdellah, Julian Charles Shillcock, Jean-Denis Georges Emile Courcol, Ahmet Bilgili, Werner Alfons Hilda Van Geit, Stefan Eilemann, Jeffrey Christopher Muller, Daniel Nachbaur, Lida Kanari, Giuseppe Chindemi, Aleksandr Ovcharenko, Michael Emiel Gevaert, Pramod Shivaji Kumbhar, Max Christian Nolte, Nicolas Antille, Taylor Howard Newton

We present a first-draft digital reconstruction of the microcircuitry of somatosensory cortex of juvenile rat. The reconstruction uses cellular and synaptic organizing principles to algorithmically reconstruct detailed anatomy and physiology from sparse ex ...

Elsevier2015

Coupling Bulk Phase Separation of Disordered Proteins to Membrane Domain Formation in Molecular Simulations on a Bespoke Compute Fabric

Julian Charles Shillcock

Phospholipid membranes surround the cell and its internal organelles, and their multicomponent nature allows the formation of domains that are important in cellular signalling, the immune system, and bacterial infection. Cytoplasmic compartments are also c ...

2022

Computational synthesis of cortical dendritic morphologies

Kathryn Hess Bellwald, Henry Markram, Alexis Arnaudon, Julian Charles Shillcock, Werner Alfons Hilda Van Geit, Lida Kanari, Benoît Jean-Albert Coste, Hugo Thabo Dictus

Neuronal morphologies provide the foundation for the electrical behavior of neurons, the connectomes they form, and the dynamical properties of the brain. Comprehensive neuron models are essential for defining cell types, discerning their functional roles, ...

CELL PRESS2022

Mechanism of Shiga Toxin Clustering on Membranes

Julian Charles Shillcock

The bacterial Shiga toxin interacts with its cellular receptor, the glycosphingolipid globotriaosylceramide (Gb3 or CD77), as a first step to entering target cells. Previous studies have shown that toxin molecules cluster on the plasma membrane, despite th ...

2017