Microbial Active Matter: A Topological Framework

Topology transcends boundaries that conventionally delineate physical, biological and engineering sciences. Our ability to mathematically describe topology, combined with our access to precision tracking and manipulation approaches, has triggered a fresh appreciation of topological ramifications, specifically in mediating key functions in biological systems spanning orders of magnitude in length and time scales. Microbial ecosystems, a frequently encountered example of living matter, offer a rich test bed where the role of topological defects and their mechanics can be explored in the context of microbial composition, structure and functions. Emergent processes, triggered by anisotropy and activity characteristic of such structured, out-of-equilibrium systems, underpin fundamental properties in microbial systems. An inevitable consequence of anisotropy is the long-range orientational (or positional) correlations, which give rise to topological defects nucleating due to spontaneous symmetry breaking. The scene stealer of this emerging cross-disciplinary field is the topological defects: singularities embedded within the material field that elicit novel, if not unexpected, dynamics that are at the heart of active processes underpinning soft and living matter systems. In this short review, I have put together a summary of the key recent advances that highlight the interface of liquid crystal physics and the physical ecology of microbes; and combined it with original experimental data on sessile species as a case to demonstrate how this interface offers a biophysical framework that could help to decode and harness active microbial processes in 'true' ecological settings. Topology and its functional manifestations - a crucial and well-timed topic - offer a rich opportunity for both experimentalists and theoreticians willing to take up an exciting journey across scales and disciplines.Comment: 9 pages, 5 figure

Planktonic Active Matter

Planktonic active matter represents an emergent system spanning different scales: individual, population and community; and complexity arising from sub-cellular and cellular to collective and ecosystem scale dynamics. This cross-scale active matter system responds to a range of abiotic (temperature, fluid flow and light conditions) and biotic factors (nutrients, pH, secondary metabolites) characteristic to the relevant ecosystems they are part of. Active modulation of cell phenotypes, including morphology, motility, and intracellular organization enable planktonic microbes to dynamically interact with other individuals and species; and adapt - often rapidly - to the changes in their environment. In this chapter, I discuss both traditional and contemporary approaches to study the dynamics of this multi-scale active matter system from a mechanistic standpoint, with specific references to their local settings and their ability to actively tune the behaviour and physiology, and the emergent structures and functions they elicit under natural ecological constraints as well as due to the shifting climatic trends.Comment: 29 pages, 14 figures, to be published in "Active Matter" (Editors: Giovanni Volpe, Nuno Ara\'ujo, Giorgio Volpe and Agnese Callegari

Cross-talk between topological defects in different fields revealed by nematic microfluidics

Topological defects are singularities in material fields that play a vital role across a range of systems: from cosmic microwave background polarization to superconductors, and biological materials. Although topological defects and their mutual interactions have been extensively studied, little is known about the interplay between defects in different fields -- especially when they co-evolve -- within the same physical system. Here, using nematic microfluidics, we study the cross-talk of topological defects in two different material fields -- the velocity field and the molecular orientational field. Specifically, we generate hydrodynamic stagnation points of different topological charges at the center of star-shaped microfluidic junctions, which then interact with emergent topological defects in the orientational field of the nematic director. We combine experiments, and analytical and numerical calculations to demonstrate that a hydrodynamic singularity of given topological charge can nucleate a nematic defect of equal topological charge, and corroborate this by creating $-1$, $-2$ and $-3$ topological defects in $4-$, $6-$, and $8-$arm junctions. Our work is an attempt toward understanding materials that are governed by distinctly multi-field topology, where disparate topology-carrying fields are coupled, and concertedly determine the material properties and response.Comment: 18 pages, 9 figure

Geometry and mechanics of microdomains in growing bacterial colonies

Bacterial colonies are abundant on living and nonliving surfaces and are known to mediate a broad range of processes in ecology, medicine, and industry. Although extensively researched, from single cells to demographic scales, a comprehensive biomechanical picture, highlighting the cell-to-colony dynamics, is still lacking. Here, using molecular dynamics simulations and continuous modeling, we investigate the geometrical and mechanical properties of a bacterial colony growing on a substrate with a free boundary and demonstrate that such an expanding colony self-organizes into a "mosaic" of microdomains consisting of highly aligned cells. The emergence of microdomains is mediated by two competing forces: the steric forces between neighboring cells, which favor cell alignment, and the extensile stresses due to cell growth that tend to reduce the local orientational order and thereby distort the system. This interplay results in an exponential distribution of the domain areas and sets a characteristic length scale proportional to the square root of the ratio between the system orientational stiffness and the magnitude of the extensile active stress. Our theoretical predictions are finally compared with experiments with freely growing E. coli microcolonies, finding quantitative agreement.Comment: 10 pages, 7 figure

Mono-to-multilayer transition in growing bacterial colonies

The transition from monolayers to multilayered structures in bacterial colonies is a fundamental step in biofilm development. Observed across different morphotypes and species, this transition is triggered within freely growing bacterial microcolonies comprising a few hundred cells. Using a combination of numerical simulations and analytical modeling, here we demonstrate that this transition originates from the competition between growth-induced in-plane active stresses and vertical restoring forces, due to the cell-substrate interactions. Using a simple chain-like colony of laterally confined cells, we show that the transition is triggered by the mechanical instability of individual cells, thus it is localized and mechanically deterministic. Asynchronous cell division renders the process stochastic, so that all the critical parameters that control the onset of the transition are continuously distributed random variables. Upon modeling cell division as a Poisson process, we can approximately calculate the probability distribution function of the position and time associated with the first extrusion. The rate of such a Poisson process can be identified as the order parameter of the transition, thus highlighting its mixed deterministic/stochastic nature

Novel optofluidic concepts enabled by topological microfluidics

The coupling between flow and director orientation of liquid crystals (LCs) has been long utilized to devise wide-ranging applications spanning modern displays, medical and environmental solutions, and bio-inspired designs and applications. LC-based optofluidic platforms offer a non-invasive handle to modulate light and material fields, both locally and dynamically. The flow-driven reorientation of the LC molecules can tailor distinct optical and mechanical responses in microfluidic confinements, and harness the coupling therein. Yet the synergy between traditional optofluidics with isotropic fluids and LC microfluidics remains at its infancy. Here, we discuss emerging optofluidic concepts based on Topological Microfluidics, leveraging microfluidic control of topological defects and defect landscapes. With a specific focus on the role of surface anchoring and microfluidic geometry, we present recent and ongoing works that harness flow-controlled director and defect configurations to modulate optical fields. The flow-induced optical attributes, and the corresponding feedback, is enhanced in the vicinity of the topological defects which geenerate distinct isotropic opto-material properties within an anisotropic matrix. By harnessing the rich interplay of confining geometry, anchoring and micro-scale nematodynamics, topological microfluidics offers a promising platform to ideate the next generation of optofluidic and optomechnical concepts

Anchoring-dependent bifurcation in nematic microflows within cylindrical capillaries

Capillary microflows of liquid crystal phases are central to material, biological and bio-inspired systems. Despite their fundamental and applied significance, a detailed understanding of the stationary behaviour of nematic liquid crystals (NLC-s) in cylindrical capillaries is still lacking. Here, using numerical simulations based on the continuum theory of Leslie, Ericksen and Parodi, we investigate stationary NLC flows within cylindrical capillaries possessing homeotropic (normal) and uniform planar anchoring conditions. By considering the material parameters of the flow-aligning NLC, 5CB, we report that instead of the expected, unique director field monotonically approaching the alignment angle over corresponding Ericksen numbers (dimensionless number capturing viscous v/s elastic effects), a second solution emerges below a threshold flow rate (or applied pressure gradient). We demonstrate that the onset of the second solution, a nematodynamic bifurcation yielding energetically degenerate director tilts at the threshold pressure gradient, can be controlled by the surface anchoring and the flow driving mechanism (pressure-driven or volume-driven). For homeotropic surface anchoring, this alternate director field orients against the alignment angle in the vicinity of the capillary center; while in the uniform planar case, the alternate director field extends throughout the capillary volume, leading to reduction of the flow speed with increasing pressure gradients. While the practical realization and utilization of such nematodynamic bifurcations still await systematic exploration, signatures of the emergent rheology have been reported previously within microfluidic environments, under both homeotropic (Sengupta et al., Phys. Rev. Lett. 110, 048303, 2013) and planar anchoring conditions (Sengupta, Int. J. Mol. Sci. 14, 22826, 2013).Comment: 27 pages, 12 figure

Time dependent lyotropic chromonic textures in PDMS-based microfluidic confinements

Nematic and columnar phases of lyotropic chromonic liquid crystals (LCLCs) have been long studied for their fundamental and applied prospects in material science and medical diagnostics. LCLC phases represent different self-assembled states of disc-shaped molecules, held together by noncovalent interactions that lead to highly sensitive concentration and temperature dependent properties. Yet, microscale insights into confined LCLCs, specifically in the context of confinement geometry and surface properties, are lacking. Here, we report the emergence of time dependent textures in static disodium chromoglycate (DSCG) solutions, confined in PDMS-based microfluidic devices. We use a combination of soft lithography, surface characterization and polarized optical imaging to generate and analyze the confinement-induced LCLC textures, and demonstrate that over time, herringbone and spherulite textures emerge due to spontaneous nematic (N) to columnar M-phase transition, propagating from the LCLC-PDMS interface into the LCLC bulk. By varying the confinement geometry, anchoring conditions and the initial DSCG concentration, we can systematically tune the temporal dynamics of the N to M-phase transition and textural behaviour of the confined LCLC. Since static molecular states register the initial conditions for LC flows, the time dependent boundary and bulk conditions reported here suggest that the local surface-mediated dynamics could be central in understanding LCLC flows, and in turn, the associated transport properties of this versatile material

Microbes in porous environments: From active interactions to emergent feedback

Microbes thrive in diverse porous environments -- from soil and riverbeds to human lungs and cancer tissues -- spanning multiple scales and conditions. Short- to long-term fluctuations in local factors induce spatio-temporal heterogeneities, often leading to physiologically stressful settings. How microbes respond and adapt to such biophysical constraints is an active field of research where considerable insight has been gained over the last decade and a half. With a focus on bacteria, here we review recent advances in microbial self-organization and dispersal in inorganic and organic porous settings, highlighting the role of active interactions and feedback which mediate their survival and fitness. We conclude by discussing open questions and opportunities for leveraging integrative cross-disciplinary approaches to advance our understanding of the biophysical strategies that microbes employ -- at both species and community scales -- to make porous settings habitable. Active and responsive behaviour is key to microbial survival in porous environments, with far-reaching ramifications for developing strategies to mitigate anthropogenic impacts, innovate subsurface storage solutions, and predict future ecological scenarios imposed by current climatic changes.R-AGR-3401 - A17/MS/11572821/MBRACE - part UL (15/05/2018 - 14/05/2023) - SENGUPTA AnupamR-AGR-3692 - C19/MS/13719464/TOPOFLUME (01/09/2020 - 31/08/2023) - SENGUPTA Anupa