Videos and Images
The movie shows two subdomains of the focal adhesion protein Talin (blue) in search of membrane (grey) interactions. I chose this movie because, even though everything is governed by random motion, the search of the little “arm” looks almost animate. Once first contact is made the protein embraces more contact points, ignoring all Covid-regulation. This is probably something we can all relate to. The simulation vividly showcases how the flexibility of a protein structure can be a great advantage for finding interactions.
Matter, living or non-living, is all around us. Understanding it would be the key to understanding our planet, our lives and ourselves. Polymers are a type of matter or substance consisting of repeating monomers (sub-units), linked together to form extended chains. Due to their wide range of properties, polymers play a crucial and omnipresent role in every aspect of life. In an effort to understand their intrinsic properties, such as the amount of stress a polymer can take before rupturing, we are simulating bulk Polystyrene under a pulling force until breaking. By calculating the force necessary for breaking along with the stress and strain exerted on the polymer we can calculate quantities such as the tensile strength and the toughness of the material.
Integrin-linked Kinase (ILK) and its binding partner parvin, two proteins important for cell attachments, are simulated under mechanical force. Once the interface breaks, mechanical signaling from the extracellular to the intracellular stops.
Force-induced disulfide bond swapping in a protein domain (More info: K Kolsek, C Aponte- Santamaría, and F Gräter. Sci. Rep . 7: 9858, 2017).
Change in flexibility of the von Willebrand factor A2 domain upon reduction of the C1669- C1670 disulfide bond (More info: D Butera, et al. Science Adv. 4: eaaq1477, 2018).
Force-induced dissociation of von Willebrand factor A1 and A2 domains (more info: Biophys. J. 108: 2312-2321, 2015).
PPEs are a class of conjugated, semi flexible polymers, which self-assemble through alignment as opposed to entanglement, as shown in the video. We apply coarse-grained Molecular Dynamics to reduce the atomistic degrees of freedom and understand the large-scale structural organization of a PPEs. So far, we followed the Martini 3 philosophy to obtain a coarse (orange) respresentation for the fine (black) PPE structure., which enables us to simulate larger PPE bulk systems on longer timescales. Stress-induced rupture of a circular graphene sheet
The movies show the rupture of a graphene sheet upon indentation by an atomic force microscope tip.
Shown in both cases are a color-coded representation of stress due to indentation. Green represents low levels of background stress due to thermal fluctuations of the graphene atoms; orange represents high stress, delimiting the area in which the bond breaking will very probably take place.
Rupture seen from the side.
MPG, 11.3 MB, 768×576 pixel
Rupture seen from the bottom
MPG, 13.1 MB, 768×576 pixel