Periodic Reporting for period 1 - DELTAS (The dynamics and rheology of self-assembled empty liquids: from patchy toy models to anisotropic realistic systems)
Okres sprawozdawczy: 2016-04-01 do 2018-03-31
The fabrication of versatile building blocks that reliably self-assemble into desired ordered and disordered phases is amongst the hottest topics in contemporary materials science. The possibility of fine-tuning the structure of these materials by changing the microscopic details of the building blocks lend themselves well to many applications, ranging from medicine to material science. The problem of how the microscopic details of the building blocks affect the behaviour of the resulting macroscopic material particularly complex. The last years have seen a growing interest into non-spherical particles, which have shown to exhibit very interesting properties that has been linked to countless technological applications. As a result, several new sophisticated techniques for particle synthesis have been developed and refined. These recent advances allow for the creation of an immense variety of non-spherical building particles. Anisotropy can arise from shape, surface patterning, inter-particle interactions or a combination thereof. Huge theoretical and numerical efforts have only scratched the surface of the possible phenomena that can occur in systems composed of these exotic building blocks, let alone established the link between microscopic anisotropy and macroscopic phase behaviour.
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.
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 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."
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."
The advances in the understanding of the thermodynamics and dynamics of anisotropic particles during the course of the project has already led to progress beyond the state of the art, as demonstrated by the large number of published (and soon-to-be-published) papers linked to DELTAS. In particular, the work on anisotropic, patchy-like particles with internal degrees of freedom is pushing forward the field of self-assembly. Indeed, the observed behaviour of such soft patchy particles has been linked with several protein, polymer and tetravalent molecular systems (such as water, silica or silicon), thus demonstrating the existence of a common framework able to reproduce many of the interesting phenomena occurring in these systems, as I originally foresaw in the DELTAS proposal.