Periodic Reporting for period 3 - SYGMA (Synthetic photobiology for light controllable active matter)
Período documentado: 2022-11-01 hasta 2024-04-30
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.
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.
In the first period, we set up a new Synthetic Biology lab in the Physics Department of Sapienza University. In this lab, we have already engineered many new strains of E.coli bacteria that respond to light by changing their speed, swimming direction, or growth rate. At the same time, we have designed new custom microscopes that are specifically aimed at studying bacterial dynamics under a computer-controlled illumination that can be structured in space and time with a high resolution. Based on these new methodologies, we have demonstrated that computer-generated light patterns can round up bacteria and “herd” them into small, confined areas. These optically controlled clouds of active particles could be used to power micromachines and to perform systematic studies of non-equilibrium phenomena in active systems. We have also shown that light-driven bacteria, swimming under an inhomogeneous light pattern, behave as an active fluid with an internal pressure gradient that can be exploited to transport passive objects within a microfluidic chip.
We have set up a highly interdisciplinary laboratory where it is possible to start with the genetic engineering of photosensitive bacteria and move on to the systematic study of their response, from the individual cell to collective dynamics, and finally to the definition of innovative strategies for the automated optical control of these new active materials. We have shown that this light-controlled active matter can flow in any desired direction, can be confined in reconfigurable regions of high density and high activity, and can be guided by light to transport passive objects within miniaturized environments. Beyond practical applications, each of these results always entails a significant advance in the physical understanding of the statistical mechanics of these out-of-equilibrium systems. Once the way in which individual cells respond to light has been genetically engineered, a whole series of new problems arise to establish the mathematical link between the spatio-temporal structure of light and the resulting statistical behaviour of cell populations moving within it. In the second half of the project, we will further extend the range of dynamic responses to light and study their technological applications and possible insights into new physical behaviour. We expect important results in the field of remote control of biohybrid micro shuttles and the possibility of using light to guide the morphology of growing bacterial colonies.