arXiv subjects

D. Marenduzzo

Publications and source records attributed to D. Marenduzzo.

At least 37 records · Page 2Linked to original sources

arXiv2018

Mixtures of blue phase liquid crystal with simple liquids: elastic emulsions and cubic fluid cylinders

We investigate numerically the behaviour of a phase-separating mixture of a blue phase I liquid crystal with an isotropic fluid. The resulting morphology is primarily controlled by an inverse capillary number, $χ$, setting the balance between interfacial and elastic forces. When $χ$ and the concentration of the isotropic component are both low, the blue phase disclination lattice templates a cubic array of fluid cylinders. For larger $χ$, the isotropic phase arranges primarily into liquid emulsion droplets which coarsen very slowly, rewiring the blue phase disclination lines into an amorphous elastic network. Our blue phase/simple fluid composites can be externally manipulated: an electric field can trigger a morphological transition between cubic fluid cylinder phases with different topologies.

cond-mat.soft↗

arXiv2018

Active interface growth and pattern formation in membrane-protein systems

Inspired by recent experimental observation of patterning at the membrane of a living cell, we propose a generic model for the dynamics of a fluctuating interface driven by particle-like inclusions which stimulate its growth. We find that the coupling between interfacial and inclusions dynam- ics yields microphase separation and the self-organisation of travelling waves. These patterns are strikingly similar to those detected in the aforementioned experiments on actin-protein systems. Our results further show that the active growth kinetics does not fall into the Kardar-Parisi-Zhang universality class for growing interfaces, displaying instead a novel superposition of equilibrium-like scaling and sustained oscillations.

cond-mat.soft↗

arXiv2018

A stochastic model of supercoiling-dependent transcription

We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix, and that these enzymes bind more favourably to regions where the genome is unwound. Within this model, we show that when the transcriptionally induced flux of supercoiling increases, there is a sharp crossover from a regime where torsional stresses relax quickly and gene transcription is random, to one where gene expression is highly correlated and tightly regulated by supercoiling. In the latter regime, the model displays transcriptional bursts, waves of supercoiling, and up-regulation of divergent or bidirectional genes. It also predicts that topological enzymes which relax twist and writhe should provide a pathway to down-regulate transcription. This article has been published in Physical Review Letters, May 2016.

physics.bio-ph↗

arXiv2017

Flow of deformable droplets: discontinuous shear thinning and velocity oscillations

We study the rheology of a suspension of soft deformable droplets subjected to a pressure-driven flow. Through computer simulations, we measure the apparent viscosity as a function of droplet concentration and pressure gradient, and provide evidence of a discontinuous shear thinning behaviour, which occurs at a concentration-dependent value of the forcing. We further show that this response is associated with a nonequilibrium transition between a `hard' (or less deformable) phase, which is nearly jammed and flows very slowly, and a `soft' (or more deformable) phase, which flows much more easily. The soft phase is characterised by flow-induced time dependent shape deformations and internal currents, which are virtually absent in the hard phase. Close to the transition, we find sustained oscillations in both the droplet and fluid velocities. Polydisperse systems show similar phenomenology but with a smoother transition, and less regular oscillations.

cond-mat.soft↗

arXiv2017

Dynamical Scaling and Phase Coexistence in Topologically-Constrained DNA Melting

There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules. This finding points to an intriguing role of topology in the physics of DNA denaturation, which is however poorly understood. Here, we shed light on this issue by combining large-scale Brownian Dynamics simulations with an analytically solvable phenomenological Landau mean field theory. We find that the competition between melting and supercoiling leads to phase coexistence of denatured and intact phases at the single molecule level. This coexistence occurs in a wide temperature range, thereby accounting for the broadening of the transition. Finally, our simulations show an intriguing topology-dependent scaling law governing the growth of denaturation bubbles in supercoiled plasmids, which can be understood within the proposed mean field theory.

cond-mat.soft↗

arXiv2017

Entropic elasticity and dynamics of the bacterial chromosome: a simulation study

We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the compressional elasticity of the bacterial nucleoid (DNA plus associated proteins), where DNA is confined into a cylindrical container and subjected to the action of a "piston" - a spherical bead to which an external force is applied. We quantify the effect of steric interactions (excluded volume) on the force-extension curves as the polymer is compressed. We find that non-DNA-binding proteins, even at low densities, exert an osmotic force which can be a lot larger than the entropic force exerted by the compressed DNA. The trends we observe are qualitatively robust with respect to changes in protein size, and are similar for neutral and charged proteins (and DNA). We also quantify the dynamics of DNA expansion following removal of the "piston": while the expansion is well fitted by power laws, the apparent exponent depends on protein concentration, and protein-DNA interaction in a significant way. We further highlight an interesting kinetic process which we observe during the expansion of DNA interacting with DNA-binding proteins when the interaction strength is intermediate: the proteins bind while the DNA is packaged by the compression force, but they "pop-off" one-by-one as the force is removed, leading to a slow unzipping kinetics. Finally, we quantify the importance of supercoiling, which is an important feature of bacterial DNA in vivo.

cond-mat.soft↗

arXiv2016

Non-equilibrium chromosome looping via molecular slip-links

We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with the CTCF protein, stabilize loops which organize the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable non-equilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favour of convergent CTCF-mediated chromosome loops observed experimentally. Importantly, our model does not require any underlying, and energetically costly, motor activity of cohesin. We also find that the diffusive motion of multiple slip-links along chromatin may be rectified by an intriguing ratchet effect that arises if slip-links bind to the chromatin at a preferred "loading site". This emergent collective behaviour is driven by a 1D osmotic pressure which is set up near the loading point, and favours the extrusion of loops which are much larger than the ones formed by single slip-links.

physics.bio-ph↗

arXiv2016

Shear dynamics of an inverted nematic emulsion

Here we study theoretically the dynamics of a 2D and a 3D isotropic droplet in a nematic liquid crystal under a shear flow. We find a large repertoire of possible nonequilibrium steady states as a function of the shear rate and of the anchoring of the nematic director field at the droplet surface. We first discuss homeotropic anchoring. For weak anchoring, we recover the typical behaviour of a sheared isotropic droplet in a binary fluid, which rotates, stretches and can be broken by the applied flow. For intermediate anchoring, new possibilities arise due to elastic effects in the nematic fluid. We find that in this regime the 2D droplet can tilt and move in the flow, or tumble incessantly at the centre of the channel. For sufficiently strong anchoring, finally, one or both of the topological defects which form close to the surface of the isotropic droplet in equilibrium detach from it and get dragged deep into the nematic state by the flow. In 3D, instead, the Saturn ring associated with normal anchoring disclination line can be deformed and shifted downstream by the flow, but remains always localized in proximity of the droplet, at least for the parameter range we explored. Tangential anchoring in 2D leads to a different dynamic response, as the boojum defects characteristic of this situation can unbind from the droplet under a weaker shear with respect to the normal anchoring case. Our results should stimulate further experiments with inverted liquid crystal emulsions under shear, as most of the predictions can be testable in principle by monitoring the evolution of liquid crystalline orientation patterns or by tracking the position and shape of the droplet over time.

cond-mat.soft↗

arXiv2016

A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA

The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide level which retains the characteristic helical structure, while being able to simulate large molecules -- up to a million base pairs -- for time-scales which are relevant to physiological processes. This is made possible by an efficient and highly-parallelised implementation of the model which we discuss here. We compare the behaviour of our model with single molecule experiments where dsDNA is manipulated by external forces or torques. We also present some results on the kinetics of denaturation of linear DNA.

cond-mat.soft↗

arXiv2016

Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domains

Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on this, we perform large-scale Brownian dynamics simulations of a chromatin fiber interacting with an ensemble of (multivalent) DNA-binding proteins; these proteins switch between two states -- active (binding) and inactive (non-binding). This system provides a model for any DNA-binding protein that can be modified post-translationally to change its affinity for DNA (e.g., like the phosphorylation of a transcription factor). Due to this out-of-equilibrium process, proteins spontaneously assemble into clusters of self-limiting size, as individual proteins in a cluster exchange with the soluble pool with kinetics like those seen in photo-bleaching experiments. This behavior contrasts sharply with that exhibited by "equilibrium", or non-switching, proteins that exist only in the binding state; when these bind to DNA non-specifically, they form clusters that grow indefinitely in size. Our results point to post-translational modification of chromatin-bridging proteins as a generic mechanism driving the self-assembly of highly dynamic, non-equilibrium, protein clusters with the properties of nuclear bodies. Such active modification also reshapes intra-chromatin contacts to give networks resembling those seen in topologically-associating domains, as switching markedly favors local (short-range) contacts over distant ones.

physics.bio-ph↗

arXiv2016

Light-induced self-assembly of active rectification devices

Self-propelled colloidal objects, such as motile bacteria or synthetic microswimmers, have microscopically irreversible individual dynamics - a feature they share with all living systems. The incoherent behaviour of individual swimmers can then be harnessed (or "rectified") by microfluidic devices that create systematic motions impossible in equilibrium. Examples include flow of rotor particles round a circuit, steady rotation of a gear wheel in a bacterial bath, and pumping of bacteria between chambers by "funnel gates". Here we present a computational proof-of-concept study, showing that such active rectification devices might be created directly from an unstructured "primordial soup" of motile particles, solely by using spatially modulated illumination to control their local propulsion speed. Alongside both microscopic irreversibility and speed modulation, our mechanism requires spatial symmetry breaking, such as a chevron light pattern, and strong interactions between particles, such as volume exclusion causing a collisional slow-down at high density. These four factors create a many-body rectification mechanism that generically differs from one-body microfluidic antecedents. Our work suggests that standard spatial-light-modulator technology might allow the programmable, light-induced self-assembly of active rectification devices from an unstructured particle bath.

cond-mat.soft↗

arXiv2016

A 1-dimensional statistical mechanics model for nucleosome positioning on genomic DNA

The first level of folding of DNA in eukaryotes is provided by the so called '10 nm chromatin fibre', where DNA wraps around histone proteins (approx. 10 nm in size) to form nucleosomes, which go on to create a zig zagging bead on a string structure. In this work we present a 1 dimensional statistical mechanics model to study nucleosome positioning within one such 10 nm fibre. We focus on the case of genomic sheep DNA, and we start from effective potentials valid at infinite dilution and determined from high resolution in vitro salt dialysis experiments. We study positioning within a polynucleosome chain, and compare the results for genomic DNA to that obtained in the simplest case of homogeneous DNA, where the problem can be mapped to a Tonks gas. First, we consider the simple, analytically solvable, case where nucleosomes are assumed to be point like. Then, we perform numerical simulations to gauge the effect of their finite size on the nucleosomal distribution probabilities. Finally we compare nucleosome distributions and simulated nuclease digestion patterns for the two cases (homogeneous and sheep DNA), thereby providing testable predictions of the effect of sequence on experimentally observable quantities in experiments on polynucleosome chromatin fibres reconstituted in vitro.

physics.bio-ph↗

arXiv2015

Binding of bivalent transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and domains

Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a fitting-free, minimal model: bivalent red and green "transcription factors" bind to cognate sites in runs of beads ("chromatin") to form molecular bridges stabilizing loops. In the absence of additional explicit forces, molecular dynamic simulations reveal that bound "factors' spontaneously cluster -- red with red, green with green, but rarely red with green -- to give structures reminiscent of transcription factories. Binding of just two transcription factors (or proteins) to active and inactive regions of human chromosomes yields rosettes, topological domains, and contact maps much like those seen experimentally. This emergent "bridging-induced attraction" proves to be a robust, simple, and generic force able to organize interphase chromosomes at all scales.

q-bio.BM↗

arXiv2015

Self-assembly of colloid-cholesteric composites provides a possible route to switchable optical materials

Colloidal particles dispersed in liquid crystals can form new materials with tunable elastic and electro-optic properties. In a periodic `blue phase' host, particles should template into colloidal crystals with potential uses in photonics, metamaterials, and transformational optics. Here we show by computer simulation that colloid/cholesteric mixtures can give rise to regular crystals, glasses, percolating gels, isolated clusters, twisted rings and undulating colloidal ropes. This structure can be tuned via particle concentration, and by varying the surface interactions of the cholesteric host with both the particles and confining walls. Many of these new materials are metastable: two or more structures can arise under identical thermodynamic conditions. The observed structure depends not only on the formulation protocol, but also on the history of an applied electric field. This new class of soft materials should thus be relevant to design of switchable, multistable devices for optical technologies such as smart glass and e-paper.

cond-mat.soft↗

arXiv2015

Field-controlled columnar and planar patterning of cholesteric colloids

We study how dispersions of colloidal particles in a cholesteric liquid crystal behave under a time-dependent electric field. By controlling the amplitude and shape of the applied field wave, we show that the system can be reproducibly driven out of equilibrium through different kinetic pathways and navigated through a glassy-like free energy landscape encompassing many competing metastable equilibria. Such states range from simple Saturn rings to complex structures featuring amorphous defect networks, or stacks of disclination loops. A non-equilibrium electric field can also trigger the alignment of particles into columnar arrays, through defect-mediated force impulses, or their repositioning within a plane. Our results are promising in terms of providing new avenues towards controlled patterning and self-assembly of soft colloid-liquid crystal composite materials.

cond-mat.soft↗

arXiv2015

A minimal physical model captures the shapes of crawling cells

Cell motility in higher organisms (eukaryotes) is crucial to biological functions ranging from wound healing to immune response, and also implicated in diseases such as cancer. For cells crawling on hard surfaces, significant insights into motility have been gained from experiments replicating such motion in vitro. Such experiments show that crawling uses a combination of actin treadmilling (polymerization), which pushes the front of a cell forward, and myosin-induced stress (contractility), which retracts the rear. Here we present a simplified physical model of a crawling cell, consisting of a droplet of active polar fluid with contractility throughout, but treadmilling connected to a thin layer near the supporting wall. The model shows a variety of shapes and/or motility regimes, some closely resembling cases seen experimentally. Our work strongly supports the view that cellular motility exploits autonomous physical mechanisms whose operation does not need continuous regulatory effort.

cond-mat.soft↗

arXiv2014

Filling an emulsion drop with motile bacteria

We have measured the spatial distribution of motile Escherichia coli inside spherical water droplets emulsified in oil. At low cell concentrations, the cell density peaks at the water-oil interface; at increasing concentration, the bulk of each droplet fills up uniformly while the surface peak remains. Simulations and theory show that the bulk density results from a `traffic' of cells leaving the surface layer, increasingly due to cell-cell scattering as the surface coverage rises above $\sim 10\%$. Our findings show similarities with the physics of a rarefied gas in a spherical cavity with attractive walls.

cond-mat.soft↗

arXiv2014

Threading Dynamics of Ring Polymers in a Gel

We perform large scale three-dimensional molecular dynamics simulations of unlinked and unknotted ring polymers diffusing through a background gel, here a three-dimensional cubic lattice. Taking advantage of this architecture, we propose a new method to unambiguously identify and quantify inter-ring threadings (penetrations) and to relate these to the dynamics of the ring polymers. We find that both the number and the persistence time of the threadings increase with the length of the chains, ultimately leading to a percolating network of inter-ring penetrations. We discuss the implications of these findings for the possible emergence of a topological jammed state of very long rings.

cond-mat.soft↗