■ Designing adaptable matter with DNA-coated colloidal particles

Description of the PhD project

Functionalities we expect from future advanced matter seem like those that already exist in biological systems, where functionality comes from highly specific interactions on a microscopic level that are transferred to macroscopic behavior through coupled reactions and feedback mechanisms. Therefore biology-inspired design is a powerful paradigm for synthesizing advanced matter through tailoring the interactions of building blocks. The building blocks self-assemble, i.e., without external driving, into functional matter.
Biology-inspired self-assembly was introduced in a physical model of spherical colloids, and confirmed in numerical simulations and in experiments on micron-sized colloids with specific interactions realized through DNA-coating. Using theory and numerics, it has been demonstrated how the model can exhibit three fundamental properties of bio matter: spontaneous assembly of complex structures, self-replication and emergence of complex catalytic reactions reminiscent of a metabolism.
This project will focus on adding the function of adaptability. ``Adaptability’’ here means that some quantity recovers its original value after another quantity has changed. In a system with metabolism-like catalytic reactions among many assembled structures, we want to stabilize the concentrations of desired structures, i.e. achieve adaptability.
For a colloidal system with a metabolism (fixed by the choice of interactions and catalysis rules), we will study how an arbitrary structure can suppress the presence of another one. We will study two mechanisms: (i) Disassembly of a structure having a weak bond, which is efficiently broken by the other structure. (ii) Geometrical transformation into a different structure. For both mechanisms we will algorithmically search and compare all allowed structure geometries. This combinatorial analysis will reveal candidates for weak bonds. Using tools of statistical and condensed matter physics we will explore the breaking of weak bonds through three-particle interactions inspired by biology and chemistry.
Next we will systematically compare different metabolisms starting from simplest systems (few building block types). Promising systems will be simulated using Dissipative Particle Dynamics, where we will explore the physical realization of structure transformations and dissassembly under thermal fluctuations.
The key novelty of our system is that we can study the entire hierarchy from the particle interactions to the emergent catalytic cycles. The model also represents an actual physical system and will be calibrated to experiments. Our questions lie predominantly at the interface of physics, biology and chemistry. As we aim at understanding the ingredients necessary to achieve adaptability by modifying the particle interactions, the uncovered design principles will have an immediate impact on artificial materials (metamaterials, artificial cells) and biological DNA/RNA assemblies.


self-assembly, self-organization, adaptation, catalysis, design principles, DNA-coated colloids,in- and out-of-equilibrium statistical physics

Research unit

UMR7083 Gulliver

Description of the research Unit/subunit

The PhD candidate will be hosted at Gulliver lab, supervised by Zorana Zeravcic and David Lacoste from the Physical Chemistry Theory (PCT) group.
Gulliver is a multidisciplinary lab, with research interest covering diversity of scales, from millimeter-scale capillary gravity waves to micrometer-scale colloidal objects, and ranges of fields, from molecular and colloidal systems, interfaces in soft matter, to active and topological matter, and stochastic dynamics and information theory. The PCT group uses tools of statistical physics together with numerical methods, to work on problems inspired from experiments in physical chemistry and soft matter, from the interfaces between physics and biology and between physics and computational sciences.
Gullliver lab is a very dynamic and active place providing thriving environment for work and interactions between researchers.

Name of the supervisor
Zorana Zeravcic (Zorana.Zeravcic@espci.fr)

Name of the co-supervisor
David Lacoste (David.Lacoste@espci.fr)

3i Aspects of the proposal

The proposed project asks fundamental questions and aims at uncovering general design principles for adaptable matter having building blocks with short-ranged interactions. Such design principles can be immediatelly applied in various experimental systems. The proposed project is at the interface between physics, biology and chemistry. It uses tools of equilibrium and non-equilibrium statistical physics, condensed matter physics, chemical kinetics, as well as algorithms of computer science and discrete mathematics. The types of particle interactions and correspinding models come directly from various biological systems. Self-assembly is a popular field with leading groups spanning the world and with a strong presence in international conferences. The PhD student will directly benefit from multiple international close collaborations of the supervisors with theoretical, computational, and experimental groups in Europe, UK, India and the USA. The student will be required to present and communicate in international meetings and workshops.

Expected Profile of the candidate

The potential candidate should have physics background. This project is theoretically and numerically oriented, therefore strong skills in programming are preferred. In addition, knowledge of statistical physics will be required.

Important dates

Call for applications : from February 1st to March 31st 2019
Eligibility check results : Mid April
3i Committee evaluation results : Mid May
Interviews from the shortlisted candidates with the Selection Committee : Late June-Early July
Final results : Mid July