Steering self-organisation through confinement
Soft Matter Royal Society of Chemistry 19:9 (2023) 1695-1704
Abstract:
Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units’ translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.Publisher Correction: Active matter in space.
NPJ microgravity 9:1 (2023) 18
Non-reciprocal multifarious self-organization.
Nature nanotechnology 18:1 (2023) 79-85
Abstract:
A hallmark of living systems is the ability to employ a common set of building blocks that can self-organize into a multitude of different structures. This capability can only be afforded in non-equilibrium conditions, as evident from the energy-consuming nature of the plethora of such dynamical processes. To achieve automated dynamical control of such self-assembled structures and transitions between them, we need to identify the fundamental aspects of non-equilibrium dynamics that can enable such processes. Here we identify programmable non-reciprocal interactions as a tool to achieve such functionalities. The design rule is composed of reciprocal interactions that lead to the equilibrium assembly of the different structures, through a process denoted as multifarious self-assembly, and non-reciprocal interactions that give rise to non-equilibrium dynamical transitions between the structures. The design of such self-organized shape-shifting structures can be implemented at different scales, from nucleic acids and peptides to proteins and colloids.Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth.
eLife 11 (2022) e82654
Abstract:
Inside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of a bacterial cell is still limited. Here, we investigated the mobility of a large set of proteins in the cytoplasm of Escherichia coli, by employing fluorescence correlation spectroscopy (FCS) combined with simulations and theoretical modeling. We conclude that cytoplasmic protein mobility could be well described by Brownian diffusion in the confined geometry of the bacterial cell and at the high viscosity imposed by macromolecular crowding. We observed similar size dependence of protein diffusion for the majority of tested proteins, whether native or foreign to E. coli. For the faster-diffusing proteins, this size dependence is well consistent with the Stokes-Einstein relation once taking into account the specific dumbbell shape of protein fusions. Pronounced subdiffusion and hindered mobility are only observed for proteins with extensive interactions within the cytoplasm. Finally, while protein diffusion becomes markedly faster in actively growing cells, at high temperature, or upon treatment with rifampicin, and slower at high osmolarity, all of these perturbations affect proteins of different sizes in the same proportions, which could thus be described as changes of a well-defined cytoplasmic viscosity.Efficiency of navigation strategies for active particles in rugged landscapes
Frontiers in Physics Frontiers 10 (2022) 1034267