Living Systems often seem to follow, in addition to external constraints and interactions, an intrinsic predictive model of the world — a defining trait of Anticipatory Systems. Here we study rhythmic behaviour in Caulerpa, a marine green alga, which appears to predict the day/night light cycle. Caulerpa consists of differentiated organs resembling leaves, stems and roots. While an individual can exceed a meter in size, it is a single multinucleated giant cell. Active transport has been hypothesized to play a key role in organismal development. It has been an open question in the literature whether rhythmic transport phenomena in this organism are of autonomous circadian nature. Using Raspberry-Pi cameras, we track over weeks the morphogenesis of tens of samples concurrently, while tracing at resolution of tens of seconds the variation of the green coverage. The latter reveals waves propagating over centimeters within few hours, and is attributed to chloroplast redistribution at whole-organism scale. Our observations of algal segments regenerating under 12-hour light/dark cycles indicate that the initiation of the waves precedes the external light change. Using time-frequency analysis, we find that the temporal spectrum of these green pulses contains a circadian period. The latter persists over days even under constant illumination, indicative of its autonomous nature. We further explore the system under non-circadian periods, to reveal how the spectral content changes in response. Time-keeping and synchronization are recurring themes in biological research at various levels of description — from subcellular components to ecological systems. We present a seemingly primitive living system that exhibits apparent anticipatory behaviour. This research offers quantitative constraints for theoretical frameworks of such systems.

Individual bacteria transported in viscous flows, show complex interactions with flows and bounding surfaces resulting from their complex shape as well as their activity. Understanding these transport dynamics is crucial, as they impact soil contamination, transport in biological conducts or catheters, and constitute thus a serious health threat. Here we investigate the trajectories of individual E-coli bacteria in confined geometries under flow, using microfluidic model systems in bulk flows as well as close to surfaces using a novel Langrangian 3D tracking method. Combining experimental observations and modelling we elucidate the origin of upstream swimming, lateral drift or persistent transport along corners. [1] Junot et al, EPL, 126 (2019) 44003 [2] Mathijssen et al. 10:3 (2019) Nature Comm. [3] Figueroa-Morales et al., Soft Matter, 2015,11, 6284-6293 [4] Darnige et al. Review of Scientific Instruments 88, 055106 (2017) [5] Jing et al, Science Advances, 2020; 6 : eabb2012 [6] Figueroa-Morales et al, Sci. Adv. 2020; 6 : eaay0155, 2020, 10.1126/sciadv.aay0155

While the motion and collective behavior of cells are well-studied on flat surfaces or in unconfined liquid media, in most natural settings, cells thrive in complex 3D environments. Bioprinting processes are capable of structuring cells in 3D and conventional bioprinting approaches address this challenge by embedding cells in bio-degradable polymer networks. However, heterogeneity in network structure and biodegradation often preclude quantitative studies of cell behavior in specified 3D architectures. Here, I will present a new approach to 3D bioprinting of cellular communities that utilizes jammed, granular polyelectrolyte microgels as a support medium. The self-healing nature of this medium allows the creation of highly precise cellular communities and tissue-like structures by direct injection of cells inside the 3D medium. Further, the transparent nature of this medium enables precise characterization of cellular behavior. I will describe two examples of my work using this platform to study the behavior of two different classes of cells in 3D. First, I will describe how we interrogate the growth, viability, and migration of mammalian cells—ranging from epithelial cells, cancer cells, and T cells—in the 3D pore space. Second, I will describe how we interrogate the migration of E. coli bacteria through the 3D pore space. Direct visualization enables us to reveal a new mode of motility exhibited by individual cells, in stark contrast to the paradigm of run-and-tumble motility, in which cells are intermittently and transiently trapped as they navigate the pore space; further, analysis of these dynamics enables prediction of single-cell transport over large length and time scales. Moreover, we show that concentrated populations of E. coli can collectively migrate through a porous medium—despite being strongly confined—by chemotactically “surfing” a self-generated nutrient gradient. Together, these studies highlight how the jammed microgel medium provides a powerful platform to design and interrogate complex cellular communities in 3D—with implications for tissue engineering, microtissue mechanics, studies of cellular interactions, and biophysical studies of active matter.

Understanding the properties of active matter is a challenge which is currently driving a rapid growth in soft- and bio-physics. Some of the most important examples of active matter are at the microscale, and include active colloids and suspensions of microorganisms, both as a simple active fluid (single species) and as mixed suspensions of active and passive elements. In this last class of systems, recent experimental and theoretical work has started to provide a window into new phenomena including activity-induced depletion interactions, phase separation, and the possibility to extract net work from active suspensions. Here I will present our work on a paradigmatic example of mixed active-passive system, where the activity is provided by swimming microalgae. Macro- and micro-scopic experiments reveal that microorganism-colloid interactions are dominated by rare close encounters leading to large displacements through direct entrainment. Simulations and theoretical modelling show that the ensuing particle dynamics can be understood in terms of a simple jump-diffusion process, combining standard diffusion with Poisson-distributed jumps. Entrainment length can be understood within the framework of Taylor dispersion as a competition between advection by the no-slip surface of the cell body and microparticle diffusion. Building on these results, we then ask how external control of the dynamics of the active component (e.g. induced microswimmer anisotropy/inhomogeneity) can be used to alter the transport of passive cargo. As a first step in this direction, we study the behaviour of mixed active-passive systems in confinement. The resulting spatial inhomogeneity in swimmers’ distribution and orientation has a dramatic effect on the spatial distribution of passive particles, with the colloids accumulating either towards the boundaries or towards the bulk of the sample depending on the size of the container. We show that this can be used to induce the system to de-mix spontaneously.

A key challenge in modern soft matter is to identify the principles that govern the organisation and functionality in non-equilibrium systems. Current research efforts largely focus on non-equilibrium processes that occur either at the single-molecule scale (e.g. protein and DNA conformations under driving forces), or at the scale of whole tissues, organisms, and active colloidal and microscopic objects. However, the range of the scales in-between — from molecules to large-scaled molecular assemblies that consume energy and perform work — remains under-explored. This is, nevertheless, the scale that is crucial for the function of a living cell, where molecular self-assembly driven far from equilibrium produces mechanical work needed for cell reshaping, transport, motility, division, and healing. Today I will discuss physical modelling of active elastic filaments, called ESCRT-III filaments, that dynamically assemble and disassemble on cell membranes. This dynamic assembly changes the filaments’ shape and mechanical properties and leads to the remodelling and cutting of cells. I will present a range of experimental comparisons of our simulation results: from ESCRT-III-driven trafficking in eukaryotes to division of evolutionary simple archaeal cells.

The way single colloidal objects behave in presence of active forces arising from within the bulk of the system is crucial to many situations, notably biological and ecological (e.g. intra-cellular transport, predation), and potential medical or environmental applications (e.g. targeted delivery of cargoes, depollution of waters and soils). In this talk I will present experimental findings that my collaborators and I have obtained over the past years on the dynamics of single Brownian colloids in suspensions of biological micro-swimmers, especially the green alga Chlamydomonas reinhardtii. I'll show notably that spatial heterogeneities and anisotropies in the active particles statistics can control the preferential localisation of their passive counterparts. The results will be rationalized using theoretical approaches from hydrodynamics and stochastic processes.

I shall present two recent piece of work investigating how shape effects the transport of active particles in shear. Firstly we will consider the sedimentation of particles in 2D laminar flow fields of increasing complexity; and how insights from this can help explain why turbulence can enhance the sedimentation of negatively buoyant diatoms [1]. Secondly, we will consider the 3D transport of elongated active particles under the action of an aligning force (e.g. gyrotactic swimmers) in some simple flow fields; and will see how shape can influence the vertical distribution, for example changing the structure of thin layers [2]. [1] Enhanced sedimentation of elongated plankton in simple flows (2018). IMA Journal of Applied Mathematics W Clifton, RN Bearon, & MA Bees. [2] Elongation enhances migration through hydrodynamic shear (in Prep), RN Bearon & WM Durham.

Understanding the transport of microorganisms and self-propelled particles in porous media has important consequences in human health as well as for microbial ecology. In this work, we explore models for the dispersion of active particles in both periodic and random porous media. In a first problem, we analyze the long-time transport properties in a dilute system of active Brownian particles swimming in a periodic lattice in the presence of an external flow. Using generalized Taylor dispersion theory, we calculate the mean transport velocity and dispersion dyadic and explain their dependence on flow strength, swimming activity and geometry. In a second approach, we address the case of run-and-tumble particles swimming through unstructured porous media composed of randomly distributed circular pillars. There, we show that the long-time dispersion is described by a universal hindrance function that depends on the medium porosity and ratio of the swimmer run length to the pillar size. An asymptotic expression for the hindrance function is derived in dilute media, and its extension to semi-dilute and dense media is obtained using stochastic simulations. We conclude by discussing the role of hydrodynamic interactions and swimmer concentration effects.

Proteins and membranes form remarkably complex structures that are key to intracellular compartmentalization, cargo transport, and cell morphology. Despite this wealth of examples in living systems, we still lack design principles for controlling membrane morphology in synthetic systems. With experiments and simulations, we show that even the simple case of spherical or rod-shaped nanoparticles binding to lipid-bilayer membrane vesicles results in a remarkably rich set of morphologies that can be reliably controlled via the particle binding energy. When the binding energy is weak relative to a characteristic membrane-bending energy, vesicles adhere to one another and form a soft solid gel, which is a useful platform for controlled release. With larger binding energy, a transition from partial to complete wrapping of the nanoparticles causes a remarkable vesicle destruction process culminating in rupture, nanoparticle-membrane tubules, and vesicle inversion. We have explored the behavior across a wide range of parameter space. These findings help unify the wide range of effects observed when vesicles or cells are exposed to nanoparticles. They also show how they open the door to a new class of vesicle-based, closed-cell gels that are more than 99% water and can encapsulate and release on demand. I will discuss how triggering membrane remodeling could lead to shape-responsive systems in the future.

Understanding individual and macroscopic transport properties of motile micro-organisms in complex environments is a timely question, relevant to many ecological, medical and technological situations. At the fundamental level, this question is also receiving a lot of attention as fluids loaded with swimming micro-organisms has become a rich domain of applications and a conceptual playground for the statistical physics of “active matter”. The existence of microscopic sources of energy borne by the motile character of these micro-swimmers is driving self-organization processes at the origin of original emergent phases and unconventional macroscopic properties leading to revisit many standard concepts in the physics of suspensions. In this presentation, I will report on a recent exploration on the question of spontaneous formation of large scale collective motion in relation with the rheological response of active suspensions. I will also present new experiments showing how the motility of bacteria can be controlled such as to extract work macroscopically.

The Smoluchowski equation has often been used as the starting point of many continuum models of active suspensions. However, its six-dimensional nature depending on time, space and orientation requires a huge computational cost, fundamentally limiting its use for large-scale problems, such as mixing and transport of active fluids in turbulent flows. Despite the singular nature in strain-dominant flows, the generalised Taylor dispersion (GTD) theory (Frankel & Brenner 1991, J. Fluid Mech. 230:147-181) has been understood to be one of the most promising ways to reduce the Smoluchowski equation into an advection-diffusion equation, the mean drift and diffusion tensor of which rely on ‘local’ flow information only. In this talk, we will introduce an exact transformation of the Smoluchowski equation into such an advection-diffusion equation requiring only local flow information. Based on this transformation, a new advection-diffusion equation will subsequently be proposed by taking an asymptotic analysis in the limit of small particle velocity. With several examples, it will be demonstrated that the new advection-diffusion model, non-singular in strain-dominant flows, outperforms the GTD theory.