Giacomo Frangipane

‘Light-mills’ are optically driven microstructures that can exchange orbital angular momentum with light and thus rotate around a central axis with a controlled applied torque. Although many studies have explored the employment of light momentum for torque generation, only a few convincing applications in cellular and molecular biology have been demonstrated. Here, we design a 3D chiral structure that can be selectively coupled to a target nanometric flagellar motor in a live E. coli cell, functioning as an external, tunable torque clamp. We optimize our 3D microstructures for torque conversion efficiency and mechanical stability, and propose a calibration protocol that enables absolute quantification of the torque generated by the flagellar motor during rotation in both its natural and reverse directions. Our results demonstrate that microfabricated light-mills expand the optical toolbox for biomechanical study of individual rotary motors by enabling controlled torque application and measurement at the nanoscale.

Activity and autonomous motion are fundamental aspects of many living and engineering systems. Here, the scale of biological agents covers a wide range, from nanomotors, cytoskeleton, and cells, to insects, fish, birds, and people. Inspired by biological active systems, various types of autonomous synthetic nano- and micromachines have been designed, which provide the basis for multifunctional, highly responsive, intelligent active materials. A major challenge for understanding and designing active matter is their inherent non-equilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Furthermore, interactions in ensembles of active agents are often non-additive and non-reciprocal. An important aspect of biological agents is their ability to sense the environment, process this information, and adjust their motion accordingly. It is an important goal for the engineering of micro-robotic systems to achieve similar functionality. Many fundamental properties of motile active matter are by now reasonably well understood and under control. Thus, the ground is now prepared for the study of physical aspects and mechanisms of motion in complex environments, the behavior of systems with new physical features like chirality, the development of novel micromachines and microbots, the emergent collective behavior and swarming of intelligent self-propelled particles, and particular features of microbial systems. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter poses major challenges, which can only be addressed by a truly interdisciplinary effort involving scientists from biology, chemistry, ecology, engineering, mathematics, and physics. The 2025 motile active matter roadmap of Journal of Physics: Condensed Matter reviews the current state of the art of the field and provides guidance for further progress in this fascinating research area.

Synthetic genetic oscillators can serve as internal clocks within engineered cells to program periodic expression. However, cell-to-cell variability introduces a dispersion in the characteristics of these clocks that drives the population to complete desynchronization. Here, we introduce the optorepressilator, an optically controllable genetic clock that combines the repressilator, a three-node synthetic network in E. coli, with an optogenetic module enabling to reset, delay, or advance its phase using optical inputs. We demonstrate that a population of optorepressilators can be synchronized by transient green light exposure or entrained to oscillate indefinitely by a train of short pulses, through a mechanism reminiscent of natural circadian clocks. Furthermore, we investigate the system’s response to detuned external stimuli observing multiple regimes of global synchronization. Integrating experiments and mathematical modeling, we show that the entrainment mechanism is robust and can be understood quantitatively from single cell to population level.

Synthetic genetic oscillators can serve as internal clocks within engineered cells to program periodic expression. However, cell-to-cell variability introduces a dispersion in the characteristics of these clocks that drives the population to complete desynchronization. Here we introduce the optorepressilator, an optically controllable genetic clock that combines the repressilator, a three-node synthetic network in E. coli, with an optogenetic module enabling to reset, delay, or advance its phase using optical inputs. We demonstrate that a population of optorepressilators can be synchronized by transient green light exposure or entrained to oscillate indefinitely by a train of short pulses, through a mechanism reminiscent of natural circadian clocks. Furthermore, we investigate the system’s response to detuned external stimuli observing multiple regimes of global synchronization. Integrating experiments and mathematical modeling, we show that the entrainment mechanism is robust and can be understood quantitatively from single cell to population level.

Thermal fluctuations constantly excite all relaxation modes in an equilibrium crystal. As the temperature rises, these fluctuations promote the formation of defects and eventually melting. In active solids, the self-propulsion of “atomic” units provides an additional source of non-equilibrium fluctuations whose effect on the melting scenario is still largely unexplored. Here we show that when a colloidal crystal is activated by a bath of swimming bacteria, solvent temperature and active temperature cooperate to define dynamic and thermodynamic properties. Our system consists of repulsive paramagnetic particles confined in two dimensions and immersed in a bath of light-driven E. coli. The relative balance between fluctuations and interactions can be adjusted in two ways: by changing the strength of the magnetic field and by tuning activity with light. When the persistence time of active fluctuations is short, a single effective temperature controls both the amplitudes of relaxation modes and the melting transition. For more persistent active noise, energy equipartition is broken and multiple temperatures emerge, whereas melting occurs before the Lindemann parameter reaches its equilibrium critical value. We show that this phenomenology is fully confirmed by numerical simulations and framed within a minimal model of a single active particle in a periodic potential.

Synthetic genetic oscillators can serve as internal clocks within engineered cells to program periodic expression. However, cell-to-cell variability introduces a dispersion in the characteristics of these clocks that drives the population to complete desynchronization. Here we introduce the optorepressilator, an optically controllable genetic clock that combines the repressilator, a three-node synthetic network in E. coli, with an optogenetic module enabling to reset, delay, or advance its phase using optical inputs. We demonstrate that a population of optorepressilators can be synchronized by transient green light exposure or entrained to oscillate indefinitely by a train of short pulses, through a mechanism reminiscent of natural circadian clocks. Furthermore, we investigate the system's response to detuned external stimuli observing multiple regimes of global synchronization. Integrating experiments and mathematical modeling, we show that the entrainment mechanism is robust and can be understood quantitatively from single cell to population level.

Many motile bacteria, such as Escherichia coli, swim by rotating multiple flagella. These semiflexible helical filaments are independently actuated by flagellar motors randomly distributed on the surface of the cell body. When all the motors rotate in the same direction, within a fraction of a second, this complex elastohydrodynamic system transforms into a straight swimmer in which all the flagella form a tight bundle propelling the cell forward. Underlying this bundling phenomenon, there are several physical factors, most of which have been analyzed in isolation using theoretical or macroscopic models. Here we report a direct study of bundling dynamics in bacterial cells whose flagellar motors can be switched on and off by light, while fluorescently labeled flagella are observed. Using optical tweezers and microfabrication to constrain cell body kinematics, we found that although translations are not essential for bundling, wobbling plays an important role in achieving a stable configuration of the bundle and body complex. We find that the curved shape of the hook, a flexible joint that transmits motor torque to flagella, strongly affects the vectorial nature of the exchanged torques and must be taken into account to correctly reproduce experimental observations. Finally, we show that once the flagella are aligned, further tightening of the bundle does not lead to an increase in the swimming speed.

Active fluids, like all other fluids, exert mechanical pressure on confining walls. Unlike equilibrium, this pressure is generally not a function of the fluid state in the bulk and displays some peculiar properties. For example, when activity is not uniform, fluid regions with different activity may exert different pressures on the container walls but they can coexist side by side in mechanical equilibrium. Here we show that by spatially modulating bacterial motility with light, we can generate active pressure gradients capable of transporting passive probe particles in controlled directions. Although bacteria swim faster in the brighter side, we find that bacteria in the dark side apply a stronger pressure resulting in a net drift motion that points away from the low activity region. Using a combination of experiments and numerical simulations, we show that this drift originates mainly from an interaction pressure term that builds up due to the compression exerted by a layer of polarized cells surrounding the slow region. In addition to providing new insights into the generalization of pressure for interacting systems with non-uniform activity, our results demonstrate the possibility of exploiting active pressure for the controlled transport of microscopic objects.

Biohybrid microbots integrate biological actuators and sensors into synthetic chassis with the aim of providing the building blocks of next‐generation micro‐robotics. One of the main challenges is the development of self‐assembled systems with consistent behavior and such that they can be controlled independently to perform complex tasks. Herein, it is shown that, using light‐driven bacteria as propellers, 3D printed microbots can be steered by unbalancing light intensity over different microbot parts. An optimal feedback loop is designed in which a central computer projects onto each microbot a tailor‐made light pattern, calculated from its position and orientation. In this way, multiple microbots can be independently guided through a series of spatially distributed checkpoints. By exploiting a natural light‐driven proton pump, these bio‐hybrid microbots are able to extract mechanical energy from light with such high efficiency that, in principle, hundreds of these systems can be controlled simultaneously with a total optical power of just a few milliwatts.

In peritrichous bacteria, such as E. coli, flagella join into a compact bundle that is usually assumed to be rigidly connected to the cell body allowing only counter-rotations around a common axis. This simple microswimmer model has been very successful in providing quantitative predictions on swimming behavior in bulk fluids and in the proximity of different kinds of interfaces and confinement. Here, we show that, when bacteria colonize a water-air interface, capillary forces can strongly deform the body-bundle complex, giving rise to unusual and heterogeneous swimming modes. We find that all trajectories can be classified into four main modes, with cells tracing either clockwise or counterclockwise circles while the cell body can be locked to the swimming direction or spin freely. All the observed phenomenology can be reproduced by simply allowing elastic bending of the bundle axis, where stiffness is the main factor in selecting the swimming mode. Our results allow us to experimentally test flexible models of microswimmers in highly perturbed contexts and provide physical insights into the early stages of bacterial pellicles.