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

Authors: Shillcock, Julian C., Hastings, Janna, Riguet, Nathan, Lashuel, Hilal A.

Source: Computational and Structural Biotechnology Journal. 20:309-321

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190063593.0x000001&indx=1&recIds=ETOCvdc_100190063593.0x000001

Model biomolecular condensates have heterogeneous structure quantitatively dependent on the interaction profile of their constituent macromoleculesElectronic supplementary information (ESI) available: Technical details of the graph theoretic measures used, supporting results for condensed networks of polymers with a range of backbone lengths and endcap affinities; data showing that the dense phase concentration is independent of the system size, and that it is highly solvated. Movies of the networks under different conditions are also provided. Movie M1: Equilibrium fluctuations of 315 polymers of type 6B6 with ε = 0.84. Movie M2: Equilibrium fluctuations of 309 polymers of type 6B10 with ε = 0.84. Movie M3: Equilibrium fluctuations of 315 polymers of type 6B6 with ε = 0.74. Movie M4: Equilibrium fluctuations of 190 polymers of type 6B10 with ε = 0.74. Movie M5: Equilibrium fluctuations of 254 polymers of type 6B6 with ε = 0.68. Movie M6: Fusion of droplets each containing 763 polymers of type 2B8 with ε = 0.76. Movie M7: Single polymer of type 6B6 (left) and 6B10 (right) with ε = 0.84 in solvent. Movie M8: Droplet of 316 polymers of type 6B6 and ε = 0.84 with two coloured to follow their fluctuations in the dense phase. See DOI: https://doi.org/10.1039/d2sm00387b

Authors: Shillcock, Julian C., Lagisquet, Clément, Alexandre, Jérémy, Vuillon, Laurent, Ipsen, John H.

Source: Soft matter. 18(35):6674-6693

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Investigating the morphological transitions in an associative surfactant ternary systemElectronic supplementary information (ESI) available. See DOI: 10.1039/d1sm01668g

Authors: Honaryar, Houman, LaNasa, Jacob A., Hickey, Robert J., Shillcock, Julian C., Niroobakhsh, Zahra

Source: Soft matter. 18(13):2611-2633

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A Versatile Approach to Stabilize Liquid–Liquid Interfaces using Surfactant Self‐Assembly.

Authors: Honaryar, Houman, Amirfattahi, Saba, Nguyen, Duoc, Kim, Kyungtae, Shillcock, Julian C., Niroobakhsh, Zahra

Source: Small; 10/17/2024, Vol. 20 Issue 42, p1-15, 15p

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Clustering on Membranes: Fluctuations and More

Authors: Johannes, Ludger, Pezeshkian, Weria, Ipsen, John H., Shillcock, Julian C.

Source: In Trends in Cell Biology May 2018 28(5):405-415

Shape fluctuations and elastic properties of two-component bilayer membranes

Authors: Imparato, Alberto, Shillcock, Julian C., Lipowsky, Reinhard

Source: Europhys. Lett., 69 (4), 650-656 (2005).

Subject Terms: Condensed Matter - Soft Condensed Matter

Access URL: http://arxiv.org/abs/cond-mat/0412407

Reconstruction and Simulation of Neocortical Microcircuitry

Authors: Markram, Henry, Muller, Eilif, Ramaswamy, Srikanth, Reimann, Michael W., Abdellah, Marwan, Sanchez, Carlos Aguado, Ailamaki, Anastasia, Alonso-Nanclares, Lidia, Antille, Nicolas, Arsever, Selim, Kahou, Guy Antoine Atenekeng, Berger, Thomas K., Bilgili, Ahmet, Buncic, Nenad, Chalimourda, Athanassia, Chindemi, Giuseppe, Courcol, Jean-Denis, Delalondre, Fabien, Delattre, Vincent, Druckmann, Shaul, Dumusc, Raphael, Dynes, James, Eilemann, Stefan, Gal, Eyal, Gevaert, Michael Emiel, Ghobril, Jean-Pierre, Gidon, Albert, Graham, Joe W., Gupta, Anirudh, Haenel, Valentin, Hay, Etay, Heinis, Thomas, Hernando, Juan B., Hines, Michael, Kanari, Lida, Keller, Daniel, Kenyon, John, Khazen, Georges, Kim, Yihwa, King, James G., Kisvarday, Zoltan, Kumbhar, Pramod, Lasserre, Sébastien, Le Bé, Jean-Vincent, Magalhães, Bruno R.C., Merchán-Pérez, Angel, Meystre, Julie, Morrice, Benjamin Roy, Muller, Jeffrey, Muñoz-Céspedes, Alberto, Muralidhar, Shruti, Muthurasa, Keerthan, Nachbaur, Daniel, Newton, Taylor H., Nolte, Max, Ovcharenko, Aleksandr, Palacios, Juan, Pastor, Luis, Perin, Rodrigo, Ranjan, Rajnish, Riachi, Imad, Rodríguez, José-Rodrigo, Riquelme, Juan Luis, Rössert, Christian, Sfyrakis, Konstantinos, Shi, Ying, Shillcock, Julian C., Silberberg, Gilad, Silva, Ricardo, Tauheed, Farhan, Telefont, Martin, Toledo-Rodriguez, Maria, Tränkler, Thomas, Van Geit, Werner, Díaz, Jafet Villafranca, Walker, Richard, Wang, Yun, Zaninetta, Stefano M., DeFelipe, Javier, Hill, Sean L., Segev, Idan, Schürmann, Felix

Source: In Cell 8 October 2015 163(2):456-492

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

Authors: Shillcock, Julian C.¹ (AUTHOR) julian.shillcock@epfl.ch, Thomas, David B.² (AUTHOR), Ipsen, John H.³ (AUTHOR), Brown, Andrew D.² (AUTHOR)

Source: Biology (2079-7737). Feb2023, Vol. 12 Issue 2, p181. 22p.

Subject Terms: *DEFORMATIONS (Mechanics), *CELL compartmentation, *MACROMOLECULAR dynamics, *CELL physiology, *MOLECULAR weights, *PHASE separation, *ARTIFICIAL membranes, *POLYMERIC membranes

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Tension-induced fusion of bilayer membranes and vesicles.

Authors: Shillcock, Julian C.¹, Lipowsky, Reinhard¹ Lipowsky@mpikg.mpg.de

Source: Nature Materials. Mar2005, Vol. 4 Issue 3, p225-228. 4p.

Subject Terms: *CELL membranes, *BIOLOGICAL membranes, *CELLS, *BIOLOGY, *DRUG delivery systems

Equilibrium structure and lateral stress distribution of amphiphilic bilayers from dissipative particle dynamics simulations.

Authors: Shillcock, Julian C., Lipowsky, Reinhard

Source: Journal of Chemical Physics. 9/8/2002, Vol. 117 Issue 10, p5048. 14p. 2 Black and White Photographs, 2 Charts, 9 Graphs.

Subject Terms: *BILAYER lipid membranes, *EQUILIBRIUM, *STRESS concentration

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

Authors: Shillcock, Julian C.¹ (AUTHOR) julian.shillcock@epfl.ch, Thomas, David B.² (AUTHOR) D.B.Thomas@southampton.ac.uk, Beaumont, Jonathan R.³ (AUTHOR) jonathan.r.beaumont@gmail.com, Bragg, Graeme M.² (AUTHOR) gmb@ecs.soton.ac.uk, Vousden, Mark L.² (AUTHOR) M.Vousden@soton.ac.uk, Brown, Andrew D.² (AUTHOR) adb@ecs.soton.ac.uk

Source: Membranes. Jan2022, Vol. 12 Issue 1, p17-N.PAG. 1p.

Computational Approaches to Explore Bacterial Toxin Entry into the Host Cell.

Authors: Pezeshkian, Weria¹ (AUTHOR) weria.pezeshkian@gmail.com, Shillcock, Julian C.² (AUTHOR) julian.shillcock@epfl.ch, Ipsen, John H.³ (AUTHOR) ipsen@memphys.sdu.dk

Source: Toxins. Jul2021, Vol. 13 Issue 7, p449-449. 1p.

Subject Terms: *BACTERIAL toxins, *MOLECULAR dynamics, *TARGETED drug delivery, *DRUG design, *TOXINS, *CHOLERA toxin, *DRUG carriers, *PROTEIN fractionation

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Vesicles and Vesicle Fusion: Coarse-Grained Simulations.

Authors: Shillcock, Julian C.

Source: Biomolecular Simulations; 2013, p659-697, 39p

Understanding Vesicles and Bio-Inspired Systems with Dissipative Particle Dynamics.

Authors: Avouris, Phaedon, Bhushan, Bharat, Bimberg, Dieter, von Klitzing, Klaus, Sakaki, Hiroyuki, Wiesendanger, Roland, Zvelindovsky, Andrei V., Shillcock, Julian C.

Source: Nanostructured Soft Matter; 2007, p529-554, 26p

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