Roberto Di Leonardo

Bacterial propulsion is powered by torque generated by the flagellar motor and transmitted to the flagellum through the hook, a short deformable structure acting as a flexible joint. Despite the hook being essential for propulsion, the physical mechanism governing torque transmission remains poorly characterized. Here, we show that the torque consists of two components: one parallel to the flagellum, responsible for rapid spin, and another along the motor axis, which induces precession of the former component. Evidence of such a two-component torque also emerge in bead assay experiments, where the attached bead can exhibit complex trajectories rather than simple circular motion. We introduce a minimal mechanical model that captures both the spin/precession dynamics and the commonly observed circular orbits.

‘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.

The persistent dynamics of active particles makes them explore extended portions of an obstacle’s boundary during collisions. From impact to escape, the net applied forces depend on the curvature of the wall and increase in the presence of concave features. Here we systematically investigate the forces exerted by swimming bacteria on microfabricated structures, where the radii of curvature can be varied parametrically. We find that these microsails are propelled with a speed that scales linearly with curvature and is directed from concave to convex side along the axis of symmetry. By solving the collision problem for microswimmers subject to aligning torques at the wall, we show that, despite bacteria rapidly aligning with the surface plane, the resulting force law reduces to that of spherical active particles, with the wall-induced reorientation rate effectively replacing rotational diffusion.

Unlike gas molecules at equilibrium, the spatial organization of self-propelled particles can be very sensitive to what happens at the boundaries of their container. Understanding the link between boundary phenomena and bulk stationary distributions could enable the design of optimized container shapes for the geometric control of confined active particles. Here, we propose a boundary method based on the flux transfer formalism typical of radiometry problems, where surface elements transmit and receive “rays” of active particles with infinite persistence length. We demonstrate the power of this boundary method in the case of the swimming microalgae Euglena gracilis trapped in light-defined billiard geometries. Quite surprisingly, we found that Euglena scatters with a nearly Lambertian cosine law, resembling the behavior of blackbody radiation and consequently resulting in nearly uniform distributions inside simple cavity geometries. Nevertheless, leveraging our boundary method, we were able to design a stacked multistage billiard geometry, with a connection scheme between subunits that breaks spatial symmetry and achieves an exponential amplification of cell concentration between its two ends. Our method can be applied to confined active matter in contexts ranging from spatial control and sorting of microorganisms to the design of efficient navigation strategies for microscopic and macroscopic robots.

Humanity has long sought inspiration from nature to innovate materials and devices. As science advances, nature-inspired materials are becoming part of our lives. Animate materials, characterized by their activity, adaptability, and autonomy, emulate properties of living systems. While only biological materials fully embody these principles, artificial versions are advancing rapidly, promising transformative impacts in the circular economy, health and climate resilience within a generation. This roadmap presents authoritative perspectives on animate materials across different disciplines and scales, highlighting their interdisciplinary nature and potential applications in diverse fields including nanotechnology, robotics and the built environment. It underscores the need for concerted efforts to address shared challenges such as complexity management, scalability, evolvability, interdisciplinary collaboration, and ethical and environmental considerations. The framework defined by classifying materials based on their level of animacy can guide this emerging field to encourage cooperation and responsible development. By unravelling the mysteries of living matter and leveraging its principles, we can design materials and systems that will transform our world in a more sustainable manner.

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.

Engineered bacteria have the potential to deliver therapeutic payloads directly to tumors, with synthetic biology enabling precise control over therapeutic release in space and time. However, it remains unclear how to optimize therapeutic bacteria for durable colonization and sustained payload release. Here, we characterize nonpathogenic Escherichia coli expressing the bacterial toxin Perfringolysin O (PFO) and dynamic strategies that optimize therapeutic efficacy. While PFO is known for its potent cancer cell cytotoxicity, we present experimental evidence that expression of PFO causes lysis of bacteria in both batch culture and microfluidic systems, facilitating its efficient release. However, prolonged expression of PFO leads to the emergence of a mutant population that limits therapeutic-releasing bacteria in a PFO expression level-dependent manner. We present sequencing data revealing the mutant takeover and employ molecular dynamics to confirm that the observed mutations inhibit the lysis efficiency of PFO. To analyze this further, we developed a mathematical model describing the evolution of therapeutic-releasing and mutant bacteria populations revealing trade-offs between therapeutic load delivered and fraction of mutants that arise. We demonstrate that a dynamic strategy employing short and repeated inductions of the pfo gene better preserves the original population of therapeutic bacteria by mitigating the effects of mutational escape. Altogether, we demonstrate how dynamic modulation of gene expression can address mutant takeovers giving rise to limitations in engineered bacteria for therapeutic applications.

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.