Synthetic photobiology for light controllable active matter

Project Information

SYGMA

Grant agreement ID: 834615

DOI

10.3030/834615

Project closed

EC signature date 10 September 2019

Start date 1 November 2019

End date 30 April 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 397 500,00

EU contribution

€ 2 397 500,00

Coordinated by

UNIVERSITA DEGLI STUDI DI ROMA LA SAPIENZA
Italy

Periodic Reporting for period 4 - SYGMA (Synthetic photobiology for light controllable active matter)

Reporting period: 2024-05-01 to 2026-04-30

Summary of the context and overall objectives of the project

The application of physics and engineering principles to the study of living systems is as old as physics itself. What is unprecedented is the range of technical developments that has expanded our possibilities of analysis and manipulation to a degree that was unimaginable 50 years ago. On one side, digital microscopies, fast image processing, micro-fabrication, and micro-manipulation allow tracking of large numbers of cells while actively and precisely shaping the physical world around them. On the other side, molecular biology is constantly providing new tools to edit and reshape the genetic landscape inside cells. In this background, two emerging research fields have seen an explosion of interest in the last twenty years: active matter and synthetic biology.
Active matter is made of active “atoms”, synthetic or biological units that are capable of generating systematic motion using energy that is stored internally or in the local environment. The inherent activity of these systems keeps them away from thermal equilibrium where rectification, self-assembly, flocking and other phenomena of spontaneous organization can be observed. Besides the fundamental questions posed by this new phenomenology, active matter can be thought of as a reservoir of mechanical energy which can be controlled and directed into systematic coherent motions to carry out actuation and transport tasks inside micro-devices. In this respect, while synthetic micro-swimmers may look strikingly similar to swimming bacteria seen from the outside, moving inside a cell, the stable and uniform arrangement of atoms in synthetic microswimmers is replaced by a dynamic orchestra of thousands of biological machines executing a software program written in DNA. After 50 years of extraordinary advances in genetics and molecular biology, we can now read that code, edit it and also write new code from scratch. DNA “cut and paste” has become an indispensable life science tool, but until 20 years ago, also a very technically demanding skill to acquire. Synthetic biology emerged from computer scientists’ desire to apply the principles of engineering and computer science to biology. It aims at building a catalog of modular genetic parts which are reliable, optimized and interchangeable. From a cultural perspective, Synthetic Biology provides a conceptual framework that promotes and facilitates multidisciplinary approaches to biology.

The SYGMA project revolves around the central idea that synthetic biology represents a disruptive technology in the field of active matter. Cells are being reprogrammed to degrade pollutants or to produce drugs, biofuels, and plastics. But there is a hidden potential in synthetic biology that has not been recognized yet: cells can be engineered to execute mechanical tasks, such as actuators in micro machines, or programmable active agents in a new generation of soft materials characterized by dynamical properties that would be inconceivable without biological components. In brief, the aim of the SYGMA project is twofold:
- to provide the building blocks of a light controllable active matter with reliable, reconfigurable and interactively tunable dynamical properties
- to exploit this new generation of active particles to expand our understanding and control of the non-equilibrium dynamics of active microsystems.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The project established a new Synthetic Biology Laboratory within the Department of Physics at Sapienza University of Rome, creating an interdisciplinary research environment combining synthetic biology, optogenetics, advanced microscopy, microfabrication, and active matter physics. By the end of the project, the laboratory was fully operational and provided the infrastructure required to engineer light-responsive microorganisms and investigate their behaviour from the single-cell level to collective dynamics.
Within this framework, we developed a library of genetically engineered Escherichia coli strains whose behaviour can be precisely controlled by light. Starting from basic plasmid systems for inducible expression of heterologous genes, we progressively developed increasingly complex multi-plasmid architectures integrating synthetic genetic circuits and optogenetic sensors. This effort culminated in the demonstration of a synthetic circadian clock in E. coli that can be synchronized and entrained by externally imposed light–dark cycles, establishing a unique platform for the quantitative investigation of biological oscillations and programmable cellular responses.
We expanded the repertoire of light-controlled bacterial behaviours by engineering strains capable of modulating swimming speed, changing swimming direction, altering growth dynamics, undergoing programmed self-lysis for controlled release of molecular cargo, and switching their orientation in response to optical stimuli. These engineered strains provided a versatile toolkit for investigating and manipulating active biological matter.
To quantitatively control and study these systems, we designed and built custom microscopy platforms integrating high-resolution imaging with computer-controlled illumination patterns in space and time. These instruments enabled the generation of programmable optical landscapes and the real-time manipulation of bacterial populations. Using these approaches, we demonstrated that engineered bacteria can be optically confined and accumulated into reconfigurable high-density regions and organized into active fluids capable of transporting passive microscopic objects within microfluidic environments.
By integrating light-responsive bacteria with microfabricated three-dimensional structures, we further explored the realization of biohybrid systems in which living active components operate as remotely controlled functional elements. These studies established a framework for coupling engineered microorganisms with artificial systems for the development of biohybrid microscale robotics.
The results obtained during the project have been disseminated through peer-reviewed publications, presentations at international conferences and invited seminars, and through the training of students and young researchers in interdisciplinary approaches combining physics and synthetic biology. The experimental platforms, biological tools, and conceptual advances generated during the project provide a foundation for future developments in programmable living systems, active matter, and biohybrid technologies.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The project has advanced the state of the art by establishing a new paradigm in which living active matter can be rationally engineered and externally programmed. Prior to this work, bacterial active matter was mainly investigated as a naturally occurring phenomenon, with limited control over the activity, interactions, and collective behaviour of individual microorganisms. By combining synthetic biology with optical engineering, we introduced a framework for the design of programmable active materials in which biological activity becomes an externally controllable physical parameter. A major conceptual advance of the project is the transition from observing active matter to engineering active matter. The ability to genetically encode and optically regulate bacterial motility and collective behaviour provides a new route towards the design of living materials with programmable properties and enables quantitative investigations of non-equilibrium phenomena using biological systems as controllable model platforms.
The project has also provided new insights into the foundations of non-equilibrium statistical physics. By exploiting engineered bacterial populations as controlled active environments, we investigated the meaning and role of thermodynamic-like quantities in systems that operate far from equilibrium. Our results demonstrate that concepts such as temperature and pressure cannot always be described using their equilibrium definitions and require new theoretical approaches adapted to active systems.
We revealed that active biological systems can generate controllable non-equilibrium fluctuations, forces, and transport phenomena. The discovery of mode-dependent effective temperatures in colloidal crystals immersed in bacterial baths challenged the equilibrium concept of a single temperature and provided new insights into energy transfer in active materials. Furthermore, we demonstrated that spatial modulation of bacterial activity generates active pressure gradients that can be harnessed as forces to transport passive suspended objects. Finally, by establishing a framework based on engineered confinement geometries, we showed that boundaries can act as active control parameters to organize and manipulate active particles.
Overall, the project has opened a new research direction at the interface between synthetic biology and statistical physics. It has transformed engineered microorganisms from passive biological systems into programmable active materials and established a foundation for the rational design, control, and understanding of living non-equilibrium matter.