arXiv subjects

Davide Marenduzzo

Publications and source records attributed to Davide Marenduzzo.

At least 73 records · Page 4Linked to original sources

arXiv2019

Morphology and flow patterns in highly asymmetric active emulsions

We investigate numerically, by a hybrid lattice Boltzmann method, the morphology and the dynamics of an emulsion made of a polar active gel, contractile or extensile, and an isotropic passive fluid. We focus on the case of a highly off-symmetric ratio between the active and passive components. In absence of any activity we observe an hexatic-ordered droplets phase, with some defects in the layout. We study how the morphology of the system is affected by activity both in the contractile and extensile case. In the extensile case a small amount of activity favors the elimination of defects in the array of droplets, while at higher activities, first aster-like rotating droplets appear, and then a disordered pattern occurs. In the contractile case, at sufficiently high values of activity, elongated structures are formed. Energy and enstrophy behavior mark the transitions between the different regimes.

cond-mat.soft↗

arXiv2018

Physical Principles of Retroviral Integration in the Human Genome

Certain retroviruses, including HIV, insert their DNA in a non-random fraction of the host genome via poorly understood selection mechanisms. Here, we develop a biophysical model for retroviral integrations as stochastic and quasi-equilibrium topological reconnections between polymers. We discover that physical effects, such as DNA accessibility and elasticity, play important and universal roles in this process. Our simulations predict that integration is favoured within nucleosomal and flexible DNA, in line with experiments, and that these biases arise due to competing energy barriers associated with DNA deformations. By considering a long chromosomal region in human T-cells during interphase, we discover that at these larger scales integration sites are predominantly determined by chromatin accessibility. Finally, we propose and solve a reaction-diffusion problem that recapitulates the distribution of HIV hot-spots within T-cells. With few generic assumptions, our model can rationalise experimental observations and identifies previously unappreciated physical contributions to retroviral integration site selection.

q-bio.SC↗

arXiv2018

Magnetic Polymer Models for Epigenomic Organisation and Phase Separation

The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks and three-dimensional genome folding. Yet, the physical principles underlying the dynamical coupling between three-dimensional genomic organisation and one-dimensional epigenetic patterns remain elusive. To shed light on this issue, here we study by mean field theory and Brownian dynamics simulations a magnetic polymer model for chromosomes, where each monomer carries a dynamic epigenetic mark. At the single chromosome level, we show that a first order transition describes the unlimited spreading of epigenetic marks, a phenomenon that is often observed in vivo. At the level of the whole nucleus, experiments suggest chromosomes form micro-phase separated compartments with distinct epigenetic marks. We here discover that for a melt of magnetic polymers such a morphology is thermodynamically unstable, but can be stabilised by a non- equilibrium and ATP-mediated epigenetic switch between different monomer states.

cond-mat.soft↗

arXiv2018

Dry active turbulence in microtubule-motor mixtures

We study the dynamics and phase behaviour of a dry suspension of microtubules and molecular motors. We obtain a set of continuum equations by rigorously coarse graining a microscopic model where motor-induced interactions lead to parallel or antiparallel ordering. Through numerical simulations, we show that this model generically creates either stable stripes, or a never-settling pattern where stripes periodically form, rotate and then split up. We derive a minimal model which displays the same instability as the full model, and clarifies the underlying physical mechanism. The necessary ingredients are an extensile flux arising from microtubule sliding and an interfacial torque favouring ordering along density gradients. We argue that our minimal model unifies various previous observations of chaotic behaviour in dry active matter into a general universality class.

cond-mat.soft↗

arXiv2018

Lamellar ordering, droplet formation and phase inversion in exotic active emulsions

We study numerically the behaviour of a mixture of a passive isotropic fluid and an active polar gel, in the presence of a surfactant favouring emulsification. Focussing on parameters for which the underlying free energy favours the lamellar phase in the passive limit, we show that the interplay between nonequilibrium and thermodynamic forces creates a range of multifarious exotic emulsions. When the active component is contractile (e.g., an actomyosin solution), moderate activity enhances the efficiency of lamellar ordering, whereas strong activity favours the creation of passive droplets within an active matrix. For extensile activity (occurring, e.g., in microtubule-motor suspensions), instead, we observe an emulsion of spontaneously rotating droplets of different size. By tuning the overall composition, we can create high internal phase emulsions, which undergo sudden phase inversion when activity is switched off. Therefore, we find that activity provides a single control parameter to design composite materials with a strikingly rich range of morphologies.

physics.bio-ph↗

arXiv2017

Actomyosin contraction induces droplet motility

While cell crawling on a solid surface is relatively well understood, and relies on substrate adhesion, some cells can also swim in the bulk, through mechanisms that are still largely unclear. Here, we propose a minimal model for in-bulk self-motility of a droplet containing an isotropic and compressible contractile gel, representing a cell extract containing a disordered actomyosin network. In our model, contraction mediates a feedback loop between myosin-induced flow and advection-induced myosin accumulation, which leads to clustering and a locally enhanced flow. Interactions of the emerging clusters with the droplet membrane break flow symmetry and set the whole droplet into motion. Depending mainly on the balance between contraction and diffusion, this motion can be either straight or circular. Our simulations and analytical results provide a framework allowing to study in-bulk myosin-driven cell motility in living cells and to design synthetic motile active matter droplets.

cond-mat.soft↗

arXiv2017

Density Dependent Cohesion Leads to Controlled Phase Separation in Brownian Suspensions

Mechanical interactions between biological cells may be mediated by secreted products, making them dependent on the local particle density. Here, we explore the generic physics of density-dependent attractive interactions. We show using Brownian dynamics simulations that density-dependent interactions can produce interesting phase separation behaviour including control of aggregate size during a spinodal decomposition-like separation process. We show that these results are generic using continuum modelling of the appropriate Cahn-Hilliard equation. Our study suggests that density-dependent interactions can provide a generic mechanism for control of aggregate size during phase separation.

cond-mat.soft↗

arXiv2017

Shaping Epigenetic Memory via Genomic Bookmarking

Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and maintain robust yet plastic epigenetic domains via genomic bookmarking (GBM). We model chromatin as a recolourable polymer whose segments bear non-permanent histone marks (or colours) which can be modified by "writer" proteins. The three-dimensional chromatin organisation is mediated by protein bridges, or "readers", such as Polycomb Repressive Complexes and Transcription Factors. The coupling between readers and writers drives spreading of biochemical marks and sustains the memory of local chromatin states across replication and mitosis. In contrast, GBM-targeted perturbations destabilise the epigenetic patterns. Strikingly, we demonstrate that GBM alone can explain the full distribution of Polycomb marks in a whole Drosophila chromosome. We finally suggest that our model provides a starting point for an understanding of the biophysics of cellular differentiation and reprogramming.

q-bio.SC↗

arXiv2017

Kinetic theory of pattern formation in mixtures of microtubules and molecular motors

In this study we formulate a theoretical approach, based on a Boltzmann-like kinetic equation, to describe pattern formation in two-dimensional mixtures of microtubular filaments and molecular motors. Following the previous work by Aranson and Tsimring [Phys. Rev. E {\bf 74}, 031915 (2006)] we model the motor-induced reorientation of microtubules as collision rules, and devise a semi-analytical method to calculate the corresponding interaction integrals. This procedure yields an infinite hierarchy of kinetic equations that we terminate by employing a well-established closure strategy, developed in the pattern-formation community and based on a power-counting argument. We thus arrive at a closed set of coupled equations for slowly varying local density and orientation of the microtubules, and study its behaviour by performing a linear stability analysis and direct numerical simulations. By comparing our method with the work of Aranson and Tsimring, we assess the validity of the assumptions required to derive their and our theories. We demonstrate that our approximation-free evaluation of the interaction integrals and our choice of a systematic closure strategy result in a rather different dynamical behaviour than was previously reported. Based on our theory, we discuss the ensuing phase diagram and the patterns observed.

cond-mat.soft↗

arXiv2017

Anchoring-driven spontaneous rotations in active gel droplets

We study the dynamics of an active gel droplet with imposed orientational anchoring (normal or planar) at its surface. We find that if the activity is large enough droplets subject to strong anchoring spontaneously start to rotate, with the sense of rotation randomly selected by fluctuations. Contractile droplets rotate only for planar anchoring and extensile ones only for normal anchoring. This is because such a combination leads to a pair of stable elastic deformations which creates an active torque to power the rotation. Interestingly, under these conditions there is a conflict between the anchoring promoted thermodynamically and that favoured by activity. By tuning activity and anchoring strength, we find a wealth of qualitatively different droplet morphologies and spatiotemporal patterns, encompassing steady rotations, oscillations, and more irregular trajectories. The spontaneous rotations we observe are fundamentally different from previously reported instances of rotating defects in active fluids as they require the presence of strong enough anchoring and entail significant droplet shape deformations.

cond-mat.soft↗

arXiv2017

Epigenetic Transitions and Knotted Solitons in Stretched Chromatin

The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific, epigenetic pattern is still poorly understood. In this work we propose, and investigate in silico, a possible experimental strategy to illuminate the interplay between 3D chromatin structure and epigenetic dynamics. We consider a set-up where a reconstituted chromatin fibre is stretched at its two ends (e.g., by laser tweezers), while epigenetic enzymes (writers) and chromatin-binding proteins (readers) are flooded into the system. We show that, by tuning the stretching force and the binding affinity of the readers for chromatin, the fibre undergoes a sharp transition between a stretched, epigenetically disordered, state and a crumpled, epigenetically coherent, one. We further investigate the case in which a knot is tied along the chromatin fibre, and find that the knotted segment enhances local epigenetic order, giving rise to "epigenetic solitons" which travel and diffuse along chromatin. Our results point to an intriguing coupling between 3D chromatin topology and epigenetic dynamics, which may be investigated via single molecule experiments.

cond-mat.soft↗

arXiv2017

A hydrodynamic bifurcation in electroosmotically-driven periodic flows

In this paper we report a novel inertial instability that occurs in electro-osmotically driven channel flows. We assume that the charge motion under the influence of an externally applied electric field is confined to a small vicinity of the channel walls that, effectively, drives a bulk flow through a prescribed slip velocity at the boundaries. Here, we study spatially-periodic wall velocity modulations in a two-dimensional straight channel numerically. At low slip velocities, the bulk flow consists of a set of vortices along each wall that are left-right symmetric, while at sufficiently high slip velocities, this flow loses its stability though a supercritical bifurcation. Surprisingly, the new flow state that bifurcates from a left-right symmetric base flow has a rather strong mean component along the channel, which is similar to pressure-driven velocity profiles. The instability sets in at rather small Reynolds numbers of about 20-30, and we discuss its potential applications in microfluidic devices.

physics.flu-dyn↗

arXiv2017

Ring Polymers: Threadings, Knot Electrophoresis and Topological Glasses

Elucidating the physics of a concentrated suspension of ring polymers, or of an ensemble of ring polymers in a complex environment, is an important outstanding question in polymer physics. Many of the characteristic features of these systems arise due to topological interactions between polymers, or between the polymers and the environment, and it is often challenging to describe this quantitatively. Here we review recent research which suggests that a key role is played by inter-ring threadings (or penetrations), which become more abundant as the ring size increases. As we discuss, the physical consequences of such threadings are far-reaching: for instance, they lead to a topologically-driven glassy behaviour of ring polymer melts under pinning perturbations, while they can also account for the shape of experimentally observed patterns in two-dimensional gel electrophoresis of DNA knots.

cond-mat.soft↗

arXiv2017

Switching dynamics in cholesteric liquid crystal emulsions

In this work we numerically study the switching dynamics of a 2D cholesteric emulsion droplet immersed in an isotropic fluid under an electric field, which is either uniform or rotating with constant speed. The overall dynamics depend strongly on the magnitude and on the direction (with respect to the cholesteric axis) of the applied field, on the anchoring of the director at the droplet surface and on the elasticity. If the surface anchoring is homeotropic and a uniform field is parallel to the cholesteric axis, the director undergoes deep elastic deformations and the droplet typically gets stuck into metastable states which are rich in topological defects. When the surface anchoring is tangential, the effects due to the electric field are overall less dramatic, as a small number of topological defects form at equilibrium. The application of the field perpendicular to the cholesteric axis usually has negligible effects on the defect dynamics. The presence of a rotating electric field of varying frequency fosters the rotation of the defects and of the droplet as well, typically at lower speed than that of the field, due to the inertia of the liquid crystal. If the surface anchoring is homeotropic a periodic motion is found. Our results represent a first step to understand the dynamical response of a cholesteric droplet under an electric field and its possible application in designing novel liquid crystal-based devices.

cond-mat.soft↗

arXiv2017

The role of correlations in the collective behaviour of microswimmer suspensions

In this Letter, we study the collective behaviour of a large number of self-propelled microswimmers immersed in a fluid. Using unprecedently large-scale lattice Boltzmann simulations, we reproduce the transition to bacterial turbulence. We show that, even well below the transition, swimmers move in a correlated fashion that cannot be described by a mean-field approach. We develop a novel kinetic theory that captures these correlations and is non-perturbative in the swimmer density. To provide an experimentally accessible measure of correlations, we calculate the diffusivity of passive tracers and reveal its non-trivial density dependence. The theory is in quantitative agreement with the lattice Boltzmann simulations and captures the asymmetry between pusher and puller swimmers below the transition to turbulence.

cond-mat.soft↗

arXiv2017

Contractile and chiral activities co-determine the helicity of swimming droplet trajectories

Active fluids are a class of non-equilibrium systems where energy is injected into the system continuously by the constituent particles themselves. Many examples, such as bacterial suspensions and actomyosin networks, are intrinsically chiral at a local scale, so that their activity involves torque dipoles alongside the force dipoles usually considered. Although many aspects of active fluids have been studied, the effects of chirality on them are much less known. Here we study by computer simulation the dynamics of an unstructured droplet of chiral active fluid in three dimensions. Our model only considers the simplest possible combination of chiral and achiral active stresses, yet this leads to an unprecedented range of complex motilities, including oscillatory swimming, helical swimming, and run-and-tumble motion. Strikingly, while the chirality of helical swimming is the same as the microscopic chirality of torque dipoles in one regime, the two are opposite in another. Some of the features of these motility modes resemble those of some single-celled protozoa, suggesting that underlying mechanisms may be shared by some biological systems and synthetic active droplets.

cond-mat.soft↗

arXiv2017

Phoretic Interactions Generically Induce Dynamic Clusters and Wave Patterns in Active Colloids

We introduce a representative minimal model for phoretically interacting active colloids. Combining kinetic theory, linear stability analyses, and a general relation between self-propulsion and phoretic interactions in auto-diffusiophoretic and auto-thermophoretic Janus colloids collapses the parameter space to two dimensions: area fraction and Péclet number. This collapse arises when the lifetime of the self-generated phoretic fields is not too short, and leads to a universal phase diagram showing that phoretic interactions {\it generically} induce pattern formation in typical Janus colloids, even at very low density. The resulting patterns include waves and dynamic aggregates closely resembling the living clusters found in experiments on dilute suspension of Janus colloids.

cond-mat.soft↗

arXiv2017

Motility of active nematic films driven by "active anchoring"

We provide a minimal model for an active nematic film in contact with both a solid substrate and a passive isotropic fluid, and explore its dynamics in one and two dimensions using a combination of hybrid Lattice Boltzmann simulations and analytical calculations. By imposing nematic anchoring at the substrate while active flows induce a preferred alignment at the interface ("active anchoring"), we demonstrate that directed fluid flow spontaneously emerges in cases where the two anchoring types are opposing. In one dimension, our model reduces to an analogue of a loaded elastic column. Here, the transition from a stationary to a motile state is akin to the buckling bifurcation, but offers the possilibity to reverse the flow direction for a given set of parameters and boundary conditions solely by changing initial conditions. The two-dimensional variant of our model allows for additional tangential instabilities, leading to self-assembled propagating surface waves for intermediate activity and for a continously deforming irregular surface at high activity. Our results might be relevant for designing active microfluidic geometries, but also for curvature-guided self-assembly or switchable diffraction gratings.

cond-mat.soft↗