Julian Charles Shillcock

Julian received his 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. He was a Group Leader at the Max Planck Institute of Colloids and Interfaces, Germany 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, he developed a commercially-available, parallel DPD code that is being used by several universities. He was an Associate Professor at MEMPHYS in the Department of Physics and Chemistry, University of Southern Denmark. He has also worked in industry, designing and writing software for communication satellite simulations (British Aerospace, 1986-1990), and fluid simulation software (Accelrys, Inc., 1998-1999). He joined the Blue Brain Project in 2011, and uses mesoscale simulation techniques, together with theoretical analysis and collaborations with experimentalists, to study the dynamics of cellular processes. Current projects include simulating the formation of the post-synaptic density in dendritic spines and developing theoretical models of the supramolecular organisation of synapses. He also teaches Master's and PhD courses in computational cell biology and biophysics. He wrote and maintains an open source dissipative particle dynamics simulation code: https://github.com/Osprey-DPD/osprey-dpd Orcid: orcid.org/0000-0002-7885-735X

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Cell membrane

The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of a

Lipid bilayer

The lipid bilayer (or phospholipid bilayer) is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell

Simulation

A simulation is the imitation of the operation of a real-world process or system over time. Simulations require the use of models; the model represents the key characteristics or behaviors of the se

BIO-692: Symmetry and Conservation in the Cell

This course instructs students in the use of advanced computational models and simulations in cell biology. The importance of dimensionality, symmetry and conservation in models of self-assembly, membranes, and polymer/filament scaling laws reveals how cells exploit these principles in life.

BIOENG-455: Computational cell biology

Computer modelling is increasingly used to study dynamic phenomena in cell biology. This course shows how to identify common mathematical features in cell biological mechanisms, and become proficient in selecting numerical algorithms to model them and predict their behaviour.

Investigating the morphological transitions in an associative surfactant ternary system

Julian Charles Shillcock

Associative surfactants systems involving polar oils have recently been shown to stabilize immiscible liquids by forming nanostructures at the liquid interface and have been used to print soft materials. Although these associating surfactant systems show great promise for creating nanostructured soft materials, a fundamental understanding of the self-assembly process is still unknown. In this study, a ternary phase diagram for a system of cationic surfactant cetylpyridinium chloride monohydrate (CPCl), a polar oil (oleic acid), and water is established using experiment and simulation, to study the equilibrium phase behavior. A combination of visual inspection, small-angle X-ray scattering (SAXS), and rheological measurements was employed to establish the phase behavior and properties of the self-assembled materials. Dissipative particle dynamics (DPD) is used to simulate the formation of the morphologies in this system and support the experimental results. The ternary phase diagram obtained from the simulations agrees with the experimental results, indicating the robustness of the computational simulation as a supplement to the mesoscale experimental systems. We observe that morphological transitions (e.g., micelle-to-bilayer and vesicle-to-lamellar) are in agreement between experiments and simulations across the ternary diagram. DPD simulations correctly predict that associative surfactant systems form new nanoscale phases due to the co-assembly of the components. The established ternary phase diagram and the DPD model pave the way towards predicting and controlling the formation of different mesostructures like lamellar or vesicles, opening new avenues to tailor and synthesize desired morphologies for applications related to liquid-in-liquid 3D printing.

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 form by liquid-liquid phase separation of intrinsically-disordered proteins. They have a wide range of functions and are associated with chronic neurodegenerative diseases in which they become pathologically rigid. However, it remains unclear how their material properties depend on the molecular structure of the proteins. Here we explore the phase behaviour and structure of a model biomolecular condensate composed of semi-flexible polymers with attractive end-caps using coarse-grained simulations. The model contains the minimal molecular features that are sufficient to observe liquid-liquid phase separation of soluble polymers into a porous, three-dimensional network in which their end-caps reversibly bind at junctions. The distance between connected junctions scales with the polymer length as a self-avoiding random walk over a wide range of concentration with a weak affinity-dependent prefactor. By contrast, the average number of polymers that meet at the junctions depends on the end-cap affinity but only weakly on the polymer length. The structured porosity of the condensed phase suggests a mechanism for cells to regulate biomolecular condensates. Protein interaction sites may be turned on or off to modulate the condensate's porosity and therefore the diffusion and interaction of additional proteins.

2020

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 contribute to this clustering, in addition to direct protein–protein interactions. However, these membrane-mediated forces have not all been equally considered, despite their importance. In this review, we describe how line tension, lipid depletion, and membrane curvature contribute to mem- brane-mediated clustering. Additional attractive forces that arise from protein- induced perturbation of a membrane’s fluctuations are also described. This review aims to provide a survey of the current understanding of membrane- mediated clustering and how this supports precise biological functions.

2018