Periodic Reporting for period 1 - DELTAS (The dynamics and rheology of self-assembled empty liquids: from patchy toy models to anisotropic realistic systems)
Reporting period: 2016-04-01 to 2018-03-31
The main objective of my project was to explore the effect of different kind of anisotropies on the thermodynamics and dynamics of these new materials. My contribution has been to investigate the collective behaviour of both toy and realistic models of anisotropic particles. I have found strong connections between the dynamics and thermodynamics of simple spheres decorated with attractive patches, the so-called patchy particles, and the behaviour of more realistic systems such as water and molecular glasses.
In addition, I have also investigated the phase behaviour of systems made entirely of DNA. In fact, the advances in DNA nanotechnology and in the synthesis of DNA-based materials call for the development of numerical and theoretical methods for the evaluation of their macroscopic properties. In my contribution, I helped developing a theoretical approach to predict the thermodynamic behaviour of particles made entirely of DNA, called DNA nanostars. I have also participated in a joint experimental/numerical effort to measure and interpret the inner structure of hydrogels made of DNA. Our results shed light on the dependence of the phase behaviour on temperature and salt concentration, providing guidance for future experimental work.
The multidisciplinary character of the research I have carried out, which pertains to physics, physical chemistry, material science and nanotechnology, will reach different communities. Indeed, the different nature of the systems I studied, which ranges from colloids to DNA, are relevant to many diverse fields.
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."