"During the 13 months of my project I have authored or co-authored 7 papers, 5 of which have already been published, one has been accepted and one is under review. Two of these publications are review papers which focus on anisotropic particles with internal degrees of freedom, the main topic of DELTAS. Two more papers report on the thermodynamics property of reversible DNA-based hydrogels, a class of system which is becoming more and more popular in the field. One paper provides the first realistic example of a system exhibiting an unexpected thermodynamic behaviour which has been thought to occur in supercooled water, thus strengthening the link between the fields of anisotropic colloids and molecular systems. Finally, a detailed numerical study dealt with the microscopic origin of a peculiar gel-like dynamical behaviour of a system composed of tetravalent colloid. My collaborators and I have observed a very similar behaviour in other soft-matter systems such as DNA-coated nanocolloids, DNA nanostars and other tetravalent molecular systems. We are currently investigating more in depth the microscopic origin of such a peculiar dynamics.
During the course of the project I have also strengthened my connection with the group I was part of, contributing to some of the projects that people in the group were involved in. In particular, I have supervised a student who worked on the structural and mechanical properties of single-stranded DNA. Indeed, quite counterintuitively, the behaviour of the single-stranded form of DNA can be much more complex than the behaviour of its double-stranded counterpart, whose mechanical properties are much better known. Our work demonstrates that, thanks to realistic computer simulations, that many experimental results, which are seemingly at odds with each other, can be rationalized by looking at them from a different viewpoint.
I have been also involved in the tutoring of one Ph.D. student, with whom I have worked on the elastic properties of supercoiled DNA, which is of fundamental importance in the biological context. We have established a close connection with the experimental group of C. Dekker in Delft, and we are developing a realistic model for the simulation of the behaviour of supercoiled DNA under conditions that match their experiments.
Finally, I have started collaborating with the group of Prof. Emmanuel Levy of the Weizmann Institute of Science (Tel Aviv, Israel) on the modelling of a binary mixtures particular proteins. These proteins, which exhibit a fascinating lock-and-key mechanism, are produced by genetically engineered yeast cells and under the right conditions, form physical gels very similar to the ones formed by patchy particles and DNA nanostars.
Even though the project has been officially terminated, I am still working towards completing the objectives laid out in my proposal. In particular, I have been running the long simulations required to extract the dynamical properties, such as the viscosity, of anisotropically-interacting particles (WP1 and WP2). I hope to finalize the work on this topic over the course of the next year.
A graphic summary of the systems investigated throughout the course of the project can be found attached to this document. The figure shows (a) tetrahedral patchy particles of publication n.4 (b) one of the patchy particle models used for publication n. 3, (c) a polymer-based soft anisotropic particle (called telechelic star polymer), (d) a coarse-grained model, based on the ""soft patchy particle"" concept, used to model the mixture of proteins synthesised by the group of Prof. Levy and (e) a trivalent and a tetravalent DNA nanostar bonded together."
