Probing active nematics with in situ microfabricated elastic inclusions.

In this work, we report a direct measurement of the forces exerted by a tubulin/kinesin active nematic gel as well as its complete rheological characterization, including the quantification of its shear viscosity, η, and its activity parameter, α. For this, we develop a method that allows us to rapidly photo-polymerize compliant elastic inclusions in the continuously remodeling active system. Moreover, we quantitatively settle long-standing theoretical predictions, such as a postulated relationship encoding the intrinsic time scale of the active nematic in terms of η and α. In parallel, we infer a value for the nematic elasticity constant, K, by combining our measurements with the theorized scaling of the active length scale. On top of the microrheology capabilities, we demonstrate strategies for defect encapsulation, quantification of defect mechanics, and defect interactions, enabled by the versatility of the microfabrication strategy that allows to combine elastic motifs of different shapes and stiffnesses that are fabricated in situ.

Multimodal fluorescence microscope with fast adaptive polarimetry.

Polarized light microscopy is a widely used technique to observe specimens that are optically anisotropic, or birefringent. It has a broad applicability in the study of minerals, soft materials such as polymers, complex fluids or liquid crystals, and organic tissues in biology and medicine. Most of these observations are qualitative in nature, as it is not obvious to quantify the spatial distribution of optical anisotropy of specimens. Moreover, existing commercial implementations for quantitative polarimetry are costly and slow in nature, precluding real time observation of dynamical processes. Here, we present a custom-made implementation of an optical microscope for quantitative polarimetry at the cost of a standard scientific polarizing microscope. The instrument allows to extract the local optical axis and birefringence of transparent materials with a frequency of several Hz. The instrument is built using off-the-shelf optomechanical components, which optimizes cost, availability, and modularity. An example of the latter is the fact that we combine the polarimetry measurements with simultaneous fluorescence microscopy, which results in a powerful multimodal instrument with broad potential applications.

Active boundary layers in confined active nematics.

The role of boundary layers in conventional liquid crystals is commonly related to the mesogen anchoring on confining walls. In the classical view, anchoring enslaves the orientational field of the passive material under equilibrium conditions. In this work, we show that an active nematic can develop active boundary layers that topologically polarize the confining walls. We find that negatively-charged defects accumulate in the boundary layer, regardless of the wall curvature, and they influence the overall dynamics of the system to the point of fully controlling the behavior of the active nematic in situations of strong confinement. Further, we show that wall defects exhibit behaviors that are essentially different from those of their bulk counterparts, such as high motility or the ability to recombine with another defect of like-sign topological charge. These exotic behaviors result from a change of symmetry induced by the wall in the director field around the defect. Finally, we suggest that the collective dynamics of wall defects might be described in terms of a model equation for one-dimensional spatio-temporal chaos.

Stability analysis of flow of active extensile fibers in confined domains.

In this article, we study shear flow of active extensile filaments confined in a narrow channel. They behave as nematic liquid crystals that we assumed are governed by the Ericksen-Leslie equations of balance of linear and angular momentum. The addition of an activity source term in the Leslie stress captures the role of the biofuel prompting the dynamics. The dimensionless form of the governing system includes the Ericksen, activity, and Reynolds numbers together with the aspect ratio of the channel as the main driving parameters affecting the stability of the system. The active system that guides our analysis is composed of microtubules concentrated in bundles, hundreds of microns long, placed in a narrow channel domain, of aspect ratios in the range between 10-2 and 10-3 dimensionless units, which are able to align due to the combination of adenosine triphosphate-supplied energy and confinement effects. Specifically, this work aims at studying the role of confinement on the behavior of active matter. It is experimentally observed that, at an appropriately low activity and channel width, the active flow is laminar, with the linear velocity profile and the angle of alignment analogous to those in passive shear, developing defects and becoming chaotic, at a large activity and a channel aspect ratio. The present work addresses the laminar regime, where defect formation does not play a role. We perform a normal mode stability analysis of the base shear flow. A comprehensive description of the stability properties is obtained in terms of the driving parameters of the system. Our main finding, in addition to the geometry and magnitude of the flow profiles, and also consistent with the experimental observations, is that the transition to instability of the uniformly aligned shear flow occurs at a threshold value of the activity parameter, with the transition also being affected by the channel aspect ratio. The role of the parameters on the vorticity and angular profiles of the perturbing flow is also analyzed and found to agree with the experimentally observed transition to turbulent regimes. A spectral method based on Chebyshev polynomials is used to solve the generalized eigenvalue problems arising in the stability analysis.

Active microfluidic transport in two-dimensional handlebodies.

Unlike traditional nematic liquid crystals, which adopt ordered equilibrium configurations compatible with the topological constraints imposed by the boundaries, active nematics are intrinsically disordered because of their self-sustained internal flows. Controlling the flow patterns of active nematics remains a limiting step towards their use as functional materials. Here we show that confining a tubulin-kinesin active nematic to a network of connected annular microfluidic channels enables controlled directional flows and autonomous transport. In single annular channels, for narrow widths, the typically chaotic streams transform into well-defined circulating flows, whose direction or handedness can be controlled by introducing asymmetric corrugations on the channel walls. The dynamics is altered when two or three annular channels are interconnected. These more complex topologies lead to scenarios of synchronization, anti-correlation, and frustration of the active flows, and to the stabilisation of high topological singularities in both the flow field and the orientational field of the material. Controlling textures and flows in these microfluidic platforms opens unexplored perspectives towards their application in biotechnology and materials science.

Propulsion and energetics of a minimal magnetic microswimmer.

In this manuscript we describe the realization of a minimal hybrid microswimmer, composed of a ferromagnetic nanorod and a paramagnetic microsphere. The unbounded pair is propelled in water upon application of a swinging magnetic field that induces a periodic relative movement of the two composing elements, where the nanorod rotates and slides on the surface of the paramagnetic sphere. When taken together, the processes of rotation and sliding describe a finite area in the parameter space, which increases with the frequency of the applied field. We develop a theoretical approach and combine it with numerical simulations, which allow us to understand the dynamics of the propeller and explain the experimental observations. Furthermore, we demonstrate a reversal of the microswimmer velocity by varying the length of the nanorod, as predicted by the model. Finally, we determine theoretically and in experiments the Lighthill's energetic efficiency of this minimal magnetic microswimmer.

Epidemics with mutating infectivity on small-world networks.

Epidemics and evolution of many pathogens occur on similar timescales so that their dynamics are often entangled. Here, in a first step to study this problem theoretically, we analyze mutating pathogens spreading on simple SIR networks with grid-like connectivity. We have in mind the spatial aspect of epidemics, which often advance on transport links between hosts or groups of hosts such as cities or countries. We focus on the case of mutations that enhance an agent's infection rate. We uncover that the small-world property, i.e., the presence of long-range connections, makes the network very vulnerable, supporting frequent supercritical mutations and bringing the network from disease extinction to full blown epidemic. For very large numbers of long-range links, however, the effect reverses and we find a reduced chance for large outbreaks. We study two cases, one with discrete number of mutational steps and one with a continuous genetic variable, and we analyze various scaling regimes. For the continuous case we derive a Fokker-Planck-like equation for the probability density and solve it for small numbers of shortcuts using the WKB approximation. Our analysis supports the claims that a potentiating mutation in the transmissibility might occur during an epidemic wave and not necessarily before its initiation.

The 2020 motile active matter roadmap.

Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of 'active matter' in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines. The 2020 motile active matter roadmap of Journal of Physics: Condensed Matter addresses the current state of the art of the field and provides guidance for both students as well as established scientists in their efforts to advance this fascinating area.

Interaction of Graphene Nanoparticles and Lipid Membranes Displaying Different Liquid Orderings: A Molecular Dynamics Study.

Understanding the effects of graphene-based nanomaterials on lipid membranes is fundamental to determine their environmental impact and the efficiency of their biomedical use. By means of molecular dynamics simulations of simple model lipid bilayers, we analyze in detail the different interaction modes. We have studied bilayers consisting of lipid species (including cholesterol) which display different internal liquid orderings. Nanometric graphene layers can be transiently adsorbed onto the lipid membrane and/or inserted in its hydrophobic region. Once inserted, graphene nanometric flakes display a diffusive dynamics in the membrane plane, they adopt diverse orientations depending on their size and oxidation degree, and they show a particular aversion to be placed close to cholesterol molecules in the membrane. Addition of graphene to phase-segregated ternary membranes is also investigated in the context of the lipid raft model for the lipid organization of biological membranes. Our simulation results show that graphene layers can be inserted indistinctly in the ordered and disordered regions. Once inserted, nanometric flakes migrate to disordered and cholesterol-poor lipid phases.

Direct measurement of Lighthill's energetic efficiency of a minimal magnetic microswimmer.

The realization of artificial microscopic swimmers able to propel in viscous fluids is an emergent research field of fundamental interest and vast technological applications. For certain functionalities, the efficiency of the microswimmer in converting the input power provided through an external actuation into propulsive power output can be critical. Here we use a microswimmer composed by a self-assembled ferromagnetic rod and a paramagnetic sphere and directly determine its swimming efficiency when it is actuated by a swinging magnetic field. Using fast video recording and numerical simulations we fully characterize the dynamics of the propeller and identify the two independent degrees of freedom which allow its propulsion. We then obtain experimentally the Lighthill's energetic efficiency of the swimmer by measuring the power consumed during propulsion and the energy required to translate the propeller at the same speed. Finally, we discuss how the efficiency of our microswimmer could be increased upon suitable tuning of the different experimental parameters.

Anomalous Diffusion of Motile Colloids Dispersed in Liquid Crystals.

We study the superdiffusion of driven colloidal particles dispersed in a nematic liquid crystal. While motion is ballistic in the driving direction, our experiments show that transversal fluctuations become superdiffusive depending on the topological defect pattern around the inclusions. The phenomenon can be reproduced with different driving methods and propulsion speeds, while it is strongly dependent on particle size and temperature. We propose a mechanism based on the geometry of the liquid crystal backflow around the inclusions to justify the persistence of thermal fluctuations and to explain the observed temperature and particle size dependence of the superdiffusive behavior based on material and geometrical parameters.

Inhomogeneous assembly of driven nematic colloids.

We present a quantitative analysis of the nonequilibrium assembly of colloidal particles dispersed in a nematic liquid crystal. The driven particles assemble into reconfigurable circular clusters by liquid-crystal-enabled electrokinetic phenomena generated by an AC electric field that provides propulsion along the local director. We identify the coexistence of different aggregation states, including a central, jammed core, where short-range elastic attraction dominates, surrounded by a liquid-like corona where particles retain their mobility but reach a mechanical equilibrium that we rationalize in terms of a balance between centripetal phoretic drive and pairwise repulsion. An analysis of the compressible liquid-like region reveals a linear density profile that can be tuned with the field frequency, and a bond-orientational order that reaches a maximum at intermediate packing densities, where elastic effects are minimized. Since the phoretic propulsion force acts also on assembled particles, we compute the mechanical pressure and show that a hard-disk equation of state can be used to describe the assembly of this driven system.

Active nematics.

Active matter extracts energy from its surroundings at the single particle level and transforms it into mechanical work. Examples include cytoskeleton biopolymers and bacterial suspensions. Here, we review experimental, theoretical and numerical studies of active nematics - a type of active system that is characterised by self-driven units with elongated shape. We focus primarily on microtubule-kinesin mixtures and the hydrodynamic theories that describe their properties. An important theme is active turbulence and the associated motile topological defects. We discuss ways in which active turbulence may be controlled, a pre-requisite to harvesting energy from active materials, and we consider the appearance, and possible implications, of active nematics and topological defects to cellular systems and biological processes.

Active nematic emulsions.

The formation of emulsions from multiple immiscible fluids is governed by classical concepts such as surface tension, differential chemical affinity and viscosity, and the action of surface-active agents. Much less is known about emulsification when one of the components is active and thus inherently not constrained by the laws of thermodynamic equilibrium. We demonstrate one such realization consisting in the encapsulation of an active liquid crystal (LC)-like gel, based on microtubules and kinesin molecular motors, into a thermotropic LC. These active nematic emulsions exhibit a variety of dynamic behaviors that arise from the cross-talk between topological defects separately residing in the active and passive components. Using numerical simulations, we show a feedback mechanism by which active flows continuously drive the passive defects that, in response, resolve the otherwise degenerated trajectories of the active defects. Our experiments show that the choice of surfactant, which stabilizes the active/passive interface, allows tuning the regularity of the self-sustained dynamic events. The hybrid active-passive system demonstrated here provides new perspectives for dynamic self-assembly driven by an active material but regulated by the equilibrium properties of the passive component.

Chemical Leslie effect in Langmuir monolayers: a complete experimental characterization.

We propose a complete characterization of the chemical Leslie effect in a Langmuir monolayer of a chiral liquid crystal. To reach this goal, we developed new experimental techniques using an electric field and a humidifier to prepare large monodomains in which the molecules can freely rotate. We also designed six independent experiments to precisely measure the four material constants involved in the dynamics of the monolayer, namely the Leslie coefficient, the rotational viscosity, the curvature elasticity constant and the surface polarization. The relevance of the inverse Leslie effect is also discussed.

Magnetically tunable bidirectional locomotion of a self-assembled nanorod-sphere propeller.

Field-driven direct assembly of nanoscale matter has impact in disparate fields of science. In microscale systems, such concept has been recently exploited to optimize propulsion in viscous fluids. Despite the great potential offered by miniaturization, using self-assembly to achieve transport at the nanoscale remains an elusive task. Here we show that a hybrid propeller, composed by a ferromagnetic nanorod and a paramagnetic microsphere, can be steered in a fluid in a variety of modes, from pusher to puller, when the pair is dynamically actuated by a simple oscillating magnetic field. We exploit this unique design to build more complex structures capable of carrying several colloidal cargos as microscopic trains that quickly disassemble at will under magnetic command. In addition, our prototype can be extended to smaller nanorods below the diffraction limit, but still dynamically reconfigurable by the applied magnetic field.

Metabolic plasticity in synthetic lethal mutants: Viability at higher cost.

The most frequent form of pairwise synthetic lethality (SL) in metabolic networks is known as plasticity synthetic lethality. It occurs when the simultaneous inhibition of paired functional and silent metabolic reactions or genes is lethal, while the default of the functional partner is backed up by the activation of the silent one. Using computational techniques on bacterial genome-scale metabolic reconstructions, we found that the failure of the functional partner triggers a critical reorganization of fluxes to ensure viability in the mutant which not only affects the SL pair but a significant fraction of other interconnected reactions, forming what we call a SL cluster. Interestingly, SL clusters show a strong entanglement both in terms of reactions and genes. This strong overlap mitigates the acquired vulnerabilities and increased structural and functional costs that pay for the robustness provided by essential plasticity. Finally, the participation of coessential reactions and genes in different SL clusters is very heterogeneous and those at the intersection of many SL clusters could serve as supertargets for more efficient drug action in the treatment of complex diseases and to elucidate improved strategies directed to reduce undesired resistance to chemicals in pathogens.

Viscous dissipation and dynamics of defects in an active nematic interface⋆.

We consider active flow and dynamics of topological defects in an active nematic interfacial layer confined between immissible viscous fluid layers. The velocity of defects is determined by asymptotic matching of solutions in the defect core and the far field. Self-propulsion of positive defects along the direction of their "comet tails" is identified as the principal deterministic component of defect dynamics, while topological and hydrodynamic interactions among mobile defects is responsible for quasi-random jitter.

Detecting the Significant Flux Backbone of Escherichia coli metabolism.

The heterogeneity of computationally predicted reaction fluxes in metabolic networks within a single flux state can be exploited to detect their significant flux backbone. Here, we disclose the backbone of Escherichia coli, and compare it with the backbones of other bacteria. We find that, in general, the core of the backbones is mainly composed of reactions in energy metabolism corresponding to ancient pathways. In E. coli, the synthesis of nucleotides and the metabolism of lipids form smaller cores which rely critically on energy metabolism. Moreover, the consideration of different media leads to the identification of pathways sensitive to environmental changes. The metabolic backbone of an organism is thus useful to trace simultaneously both its evolution and adaptation fingerprints.

Lipid Vesicle Interaction with Hydrophobic Surfaces: A Coarse-Grained Molecular Dynamics Study.

Active surfaces are presently tailored to cause specific effects on living cells, which can be useful in many fields. Their development requires the understanding of the molecular mechanisms of interaction between lipid-enveloped entities and solid surfaces. Here, using coarse-grained molecular dynamics simulations, we have analyzed the different interaction modes of coated substrates with lipid vesicles that mimic biological envelopes. For neutral and hydrophobically functionalized substrates, three action modes on contacting vesicles have been obtained including intact, partially broken, and completely destroyed vesicles. The molecular mechanisms for each interaction pathway and the corresponding energy balances have been analyzed in detail. Interestingly, we have shown that any specific action mode can be obtained by appropriately tailoring the wetting characteristics of the surface coating. In particular, we have shown that surfaces that are simultaneously hydrophobic and oleophilic are optimal to fully disrupt the contacting vesicle lipid bilayer.