arXiv subjects

Marco G. Mazza

Publications and source records attributed to Marco G. Mazza.

At least 19 recordsLinked to original sources

arXiv2025

Form and function in biological filaments: A physicist's review

Nature uses elongated shapes and filaments to build stable structures, generate motion, and allow complex geometric interactions. In this Review, we examine the role of biological filaments across different length scales. From the molecular scale, where cytoskeletal filaments provides a robust but dynamic cellular scaffolding, over the scale of cellular appendages like cilia and flagella, to the scale of filamentous microorganisms like cyanobacteria, among the most successful genera on Earth, and even to the scale of elongated animals like worms and snakes, whose motility modes inspire robotic analogues. We highlight the general mechanisms that couple form and function. We discuss physical principles and models, such as classical elasticity and the non-reciprocity of active matter, that can be used to trace unifying themes linking these systems across about nine orders of magnitude in length.

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arXiv2024

Topological transition in filamentous cyanobacteria: from motion to structure

Many active systems are capable of forming intriguing patterns at scales significantly larger than the size of their individual constituents. Cyanobacteria are one of the most ancient and important phyla of organisms that has allowed the evolution of more complex life forms. Despite its importance, the role of motility on the pattern formation of their colonies is not understood. Here, we investigate the large-scale collective effects and rich dynamics of gliding filamentous cyanobacteria colonies, while still retaining information about the individual constituents' dynamics and their interactions. We investigate both the colony's transient and steady-state dynamics and find good agreement with experiments. We furthermore show that the Peclet number and aligning interaction strength govern the system's topological transition from an isotropic distribution to a state of large-scale reticulate patterns. Although the system is topologically non-trivial, the parallel and perpendicular pair correlation functions provide structural information about the colony, and thus can be used to extract information about the early stages of biofilm formation. Finally, we find that the effects of the filaments' length cannot be reduced to a system of interacting points. Our model proves to reproduce both cyanobacteria colonies and systems of biofilaments where curvature is transported by motility.

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arXiv2023

Active Spaghetti: Collective Organization in Cyanobacteria

Filamentous cyanobacteria can show fascinating examples of nonequilibrium self-organization, which however are not well-understood from a physical perspective. We investigate the motility and collective organization of colonies of these simple multicellular lifeforms. As their area density increases, linear chains of cells gliding on a substrate show a transition from an isotropic distribution to bundles of filaments arranged in a reticulate pattern. Based on our experimental observations of individual behavior and pairwise interactions, we introduce a nonreciprocal model accounting for the filaments' large aspect ratio, fluctuations in curvature, motility, and nematic interactions. This minimal model of active filaments recapitulates the observations, and rationalizes the appearance of a characteristic lengthscale in the system, based on the Peclet number of the cyanobacteria filaments.

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arXiv2022

Emergent probability fluxes in confined microbial navigation

When the motion of a motile cell is observed closely, it appears erratic, and yet the combination of nonequilibrium forces and surfaces can produce striking examples of organization in microbial systems. While most of our current understanding is based on bulk systems or idealized geometries, it remains elusive how and at which length scale self-organization emerges in complex geometries. Here, using experiments, analytical and numerical calculations we study the motion of motile cells under controlled microfluidic conditions, and demonstrate that probability flux loops organize active motion even at the level of a single cell exploring an isolated compartment of nontrivial geometry. By accounting for the interplay of activity and interfacial forces, we find that the boundary's curvature determines the nonequilibrium probability fluxes of the motion. We theoretically predict a universal relation between fluxes and global geometric properties that is directly confirmed by experiments. Our findings open the possibility to decipher the most probable trajectories of motile cells and may enable the design of geometries guiding their time-averaged motion.

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arXiv2022

Motility and self-organization of gliding Chlamydomonas populations

Cellular appendages such as cilia and flagella represent universal tools enabling cells and microbes, among other essential functionalities, to propel themselves in diverse environments. In its planktonic, i.e. freely swimming, state the unicellular bi-flagellated microbe Chlamydomonas reinhardtii employs a periodic breaststroke-like flagellar beating to displace the surrounding fluid. Another flagella-mediated motility mode is observed for surface-associated Chlamydomonas cells, which glide along the surface by means of force transduction through an intraflagellar transport machinery. Experiments and statistical motility analysis demonstrate that this gliding motility enhances clustering and supports self-organization of Chlamydomonas populations. We employ Minkowski functionals to characterize the spatiotemporal organization of the surface-associated cell monolayer. We find that simulations based on a purely mechanistic approach cannot capture the observed non-random cell configurations. Quantitative agreement with experimental data however is achieved when considering a minimal cognitive model of the flagellar mechanosensing.

physics.bio-ph↗

arXiv2022

Smectic Layering: Landau theory for a complex-tensor order parameter

Composed of microscopic layers that stack along one direction while maintaining fluid-like positional disorder within layers, smectics are excellent systems for exploring topology, defects and geometric memory in complex confining geometries. However, the coexistence of crystalline-like characteristics in one direction and fluid-like disorder within layers makes lamellar liquid crystals notoriously difficult to model - especially in the presence of defects and large distortions. Nematic properties of smectics can be comprehensively described by the Q-tensor but to capture the features of the smectic layering alone, we develop a phenomenological Landau theory for a complex-tensor order parameter E, which is capable of describing the local degree of lamellar ordering, layer displacement, and orientation of the layers. This theory can account for both parallel and perpendicular elastic contributions. In addition to resolving the potential ambiguities inherent to complex scalar order parameter models, this model reduces to previous employed models of simple smectics, and opens new possibilities for numerical studies on smectics possessing many defects, within complex geometries and under extreme confinement.

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arXiv2022

Complex-tensor theory of simple smectics

Smectic materials represent a unique state between fluids and solids, characterized by orientational and partial positional order, making them notoriously difficult to model, particularly in confining geometries. We propose a complex order parameter tensor to describe the local degree of lamellar ordering, layer displacement and orientation. The theory accounts for both dislocations and disclinations, as well as arrested configurations and colloid-induced local ordering. It considerably simplifies numerics, facilitating studies on the dynamics of topologically complex lamellar systems.

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arXiv2020

Light controls motility and phase separation of photosynthetic microbes

Large ensembles of interacting, out-of-equilibrium agents are a paradigm of active matter. Their constituents' intrinsic activity may entail the spontaneous separation into localized phases of high and low densities. Motile microbes, equipped with ATP-fueled engines, are prime examples of such phase-separating active matter, which is fundamental in myriad biological processes. The fact that spontaneous spatial aggregation is not widely recognized as a general feature of microbial communities challenges the generalisation of phase separation beyond artificial active systems. Here, we report on the phase separation of populations of Chlamydomonas reinhardtii that can be controlled by light in a fully reversible manner. We trace this phenomenon back to the light- and density-dependent motility, thus bridging the gap from light perception on the single-cell level to collective spatial self-organization into regions of high and low density. Its spectral sensitivity suggests that microbial motility and phase separation are regulated by the activity of the photosynthetic machinery. Characteristic fingerprints of the stability and dynamics of this active system paint a picture that cannot be reconciled with the current physical understanding of phase separation in artificial active matter, whereby collective behavior can emerge from inherent motility modulation in response to changing stimuli. Our results therefore point towards the existence of a broader class of self-organization phenomena in living systems.

physics.bio-ph↗

arXiv2019

Self-Assembly of Liquid Crystals in Nanoporous Solids for Adaptive Photonic Metamaterials

Nanoporous media exhibit structures significantly smaller than the wavelengths of visible light and can thus act as photonic metamaterials. Their optical functionality is not determined by the properties of the base materials, but rather by tailored, multiscale structures, in terms of precise pore shape, geometry, and orientation. Embedding liquid crystals in pore space provides additional opportunities to control light-matter interactions at the single-pore, meta-atomic scale. Here, we present temperature-dependent 3D reciprocal space mapping using synchrotron-based X-ray diffraction in combination with high-resolution birefringence experiments on disk-like mesogens (HAT6) imbibed in self-ordered arrays of parallel cylindrical pores 17 to 160 nm across in monolithic anodic aluminium oxide (AAO). In agreement with Monte Carlo computer simulations we observe a remarkably rich self-assembly behaviour, unknown from the bulk state. It encompasses transitions between the isotropic liquid state and discotic stacking in linear columns as well as circular concentric ring formation perpendicular and parallel to the pore axis. These textural transitions underpin an optical birefringence functionality, tuneable in magnitude and in sign from positive to negative via pore size, pore surface-grafting and temperature. Our study demonstrates that the advent of large-scale, self-organised nanoporosity in monolithic solids along with confinement-controllable phase behaviour of liquid-crystalline matter at the single-pore scale provides a reliable and accessible tool to design materials with adjustable optical anisotropy, and thus offers versatile pathways to fine-tune polarisation-dependent light propagation speeds in materials. Such a tailorability is at the core of the emerging field of transformative optics, allowing, e.g., adjustable light absorbers and extremely thin metalenses.

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arXiv2019

Hybrid sideways/longitudinal swimming in the monoflagellate Shewanella oneidensis: from aerotactic band to biofilm

Shewanella oneidensis MR-1 are facultative aerobic electroactive bacteria, with an appealing potential for sustainable energy production and bioremediation. They gather around air sources, forming aerotactic bands and biofilms. Though accumulation is crucial to technological exploitation, their collective behaviour remains poorly reported. Here we establish a comprehensive framework for the study of aerotaxis, unveiling a novel hybrid locomotion pattern. Despite having only one flagellum, MR-1 combine motility features of mono- and multiflagellate bacteria, alternating longitudinal fast and sideways slow swimming. The adaptive tuning of the resulting bimodal velocity distributions fulfils different biological functions, such as aerotaxis and confinement. Overall, we reveal the mechanisms underlying the aerotactic collective behaviour of MR-1, in the process leading from accumulation to biofilm formation

physics.bio-ph↗

arXiv2019

Percolation transition of pusher-type microswimmers

We identify the presence of a continuum percolation transition in model suspensions of pusher-type microswimmers. The clusters dynamically aggregate and disaggregate resulting from a competition of attractive and repulsive hydrodynamic and steric interactions. As the microswimmers' filling fraction increases, the cluster size distribution approaches a scale-free form and there emerge large clusters spanning the entire system. We characterize this microswimmer percolation transition via the critical exponents associated to cluster size distribution $τ$, correlation length $ν$, mean cluster size $γ$, and clusters' fractal dimension $d_f$. We are able to show that two scaling relations, known from percolation theory, also hold for our microswimmers. A real-space renormalization group transformation can approximately predict the value of the exponent $ν$. This finding opens new vistas on microswimmers' congregative processes.

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arXiv2019

Electrification in granular gases leads to constrained fractal growth

The empirical observation of aggregation of dielectric particles under the influence of electrostatic forces lies at the origin of the theory of electricity. The growth of clusters formed of small grains underpins a range of phenomena from the early stages of planetesimal formation to aerosols. However, the collective effects of Coulomb forces on the nonequilibrium dynamics and aggregation process in a granular gas -- a model representative of the above physical processes -- have so far evaded theoretical scrutiny. Here, we establish a hydrodynamic description of aggregating granular gases that exchange charges upon collisions and interact via the long-ranged Coulomb forces. We analytically derive the governing equations for the evolution of granular temperature, charge variance, and number density for homogeneous and quasi-monodisperse aggregation. We find that, once the aggregates are formed, the system obeys a physical constraint of nearly constant dimensionless ratio of characteristic electrostatic to kinetic energy $\mathcal{B}(t)\le 1$. This constraint on the collective evolution of charged clusters is confirmed both by the theory and the detailed molecular dynamics simulations. The inhomogeneous aggregation of monomers and clusters in their mutual electrostatic field proceeds in a fractal manner. Our theoretical framework is extendable to more precise charge exchange mechanism, a current focus of extensive experimentation. Furthermore, it illustrates the collective role of long-ranged interactions in dissipative gases and can lead to novel designing principles in particulate systems.

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arXiv2019

Multiparticle Collision Dynamics for Tensorial Nematodynamics

Liquid crystals establish a nearly unique combination of thermodynamic, hydrodynamic, and topological behavior. This poses a challenge to their theoretical understanding and modeling. The arena where these effects come together is the mesoscopic (micron) scale. It is then important to develop models aimed at capturing this variety of dynamics. We have generalized the particle-based multiparticle collision dynamics (MPCD) method to model the dynamics of nematic liquid crystals. Following the Qian--Sheng theory of nematics, the spatial and temporal variations of the nematic director field and order parameter are described by a tensor order parameter. The key idea is to assign tensorial degrees of freedom to each MPCD particle, whose mesoscopic average is the tensor order parameter. This new nematic-MPCD method includes backflow effect, velocity-orientation coupling and thermal fluctuations. We validate the applicability of this method by testing: (i) the nematic-isotropic phase transition, (ii) the flow alignment of the director in shear and Poiseuille flows, and (iii) the annihilation dynamics of a pair of line defects. We find excellent agreement with existing literature. We also investigate the flow field around a force dipole in a nematic liquid crystal, which represents the leading-order flow field around a force-free microswimmer. The anisotropy of the medium not only affects the magnitude of velocity field around the force dipole, but can also induce hydrodynamic torques depending on the orientation of dipole axis relative to director field. A force dipole experiences a hydrodynamic torque when the dipole axis is tilted with respect to the far-field director. The direction of hydrodynamic toque is such that the pusher- (or puller-) type force dipole tends to orient along (or perpendicular to) the director field.

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arXiv2018

Hydrodynamic interactions dominate the structure of active swimmers' pair distribution functions

Microswimmers often exhibit surprising patterns due to the nonequilibrium nature of their dynamics. Collectively, suspensions of microswimmers appear as a liquid whose properties set it apart from its passive counterpart. To understand the impact of hydrodynamic interactions on the basic statistical features of a microswimmer's liquid, we investigate its structure by means of the pair distribution function. We perform particle-based simulations of microswimmers that include steric effects, shape anisotropy, and hydrodynamic interactions. We find that hydrodynamic interactions considerably alter the orientation-dependent pair distribution function compared to purely excluded-volume models like active Brownian particles, and generally decrease the structure of the liquid. Depletion regions are dominant at lower filling fractions, while at larger filling fraction the microswimmer liquid develops a stronger first shell of neighbors in specific directions, while losing structure at larger distances. Our work is a first step towards a statistico-mechanical treatment of the structure of microswimmer suspensions.

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arXiv2018

Dynamics of sedimenting active Brownian particles

We investigate the stochastic dynamics of one sedimenting active Brownian particle in three dimensions under the influence of gravity and passive fluctuations in the translational and rotational motion. We present an analytical solution of the Fokker--Planck equation for the stochastic process which allows us to describe the dynamics of the active Brownian particle in three dimensions. We address the time evolution of the monopole, the polarization, and the steady-state solution. We also perform Brownian dynamics simulations and study the effect of the activity of the particles on their collective motion. These results qualitatively agree with our model. Finally, we compare our results with experiments [J. Palacci \emph{et al.}, Phys. Rev. Lett. \textbf{105}, 088304 (2010)] and find very good agreement.

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arXiv2018

Quantized Self-Assembly of Discotic Rings in a Liquid Crystal Confined in Nanopores

Disklike molecules with aromatic cores spontaneously stack up in linear columns with high, one-dimensional charge carrier mobilities along the columnar axes making them prominent model systems for functional, self-organized matter. We show by high-resolution optical birefringence and synchrotron-based X-ray diffraction that confining a thermotropic discotic liquid crystal in cylindrical nanopores induces a quantized formation of annular layers consisting of concentric circular bent columns, unknown in the bulk state. Starting from the walls this ring self-assembly propagates layer by layer towards the pore center in the supercooled domain of the bulk isotropic-columnar transition and thus allows one to switch on and off reversibly single, nanosized rings through small temperature variations. By establishing a Gibbs free energy phase diagram we trace the phase transition quantization to the discreteness of the layers' excess bend deformation energies in comparison to the thermal energy, even for this near room-temperature system. Monte Carlo simulations yielding spatially resolved nematic order parameters, density maps and bond-forientational order parameters corroborate the universality and robustness of the confinement-induced columnar ring formation as well as its quantized nature.

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arXiv2017

Early-stage aggregation in three-dimensional charged granular gas

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely-cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to thermal energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on the Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.

cond-mat.soft↗

arXiv2017

Maximum in density heterogeneities of active swimmers

Suspensions of unicellular microswimmers such as flagellated bacteria or motile algae exhibit spontaneous density heterogeneities at large enough concentrations. Based on the relative location of the biological actuation appendages i.e. flagella or cilia) microswimmers' propulsion mechanism can be classified into two categories: (i) pushers, like \textit{E. coli} bacteria or spermatozoa, that generate thrust in their rear, push fluid away from them and propel themselves forward; (ii) pullers, like the microalgae \textit{Chlamydomonas reinhardtii}, that have two flagella attached to their front, pull the fluid in and thereby generate thrust in their front. We introduce a novel model for biological microswimmers that creates the flow field of the corresponding microswimmers, and takes into account the shape anisotropy of the swimmer's body and stroke-averaged flagella. By employing multiparticle collision dynamics, we directly couple the swimmer's dynamics to the fluid's. We characterize the nonequilibrium phase diagram, as the filling fraction and Péclet number are varied, and find density heterogeneities in the distribution of both pullers and pushers, due to hydrodynamic instabilities. We find a maximum degree of clustering at intermediate filling fractions and at large Péclet numbers resulting from a competition of hydrodynamic and steric interactions between the swimmers. We develop an analytical theory that supports these results. This maximum might represent an optimum for the microorganisms' colonization of their environment.

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