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D. Marenduzzo

Publications and source records attributed to D. Marenduzzo.

At least 19 recordsLinked to original sources

Geometry and relaxation dynamics of nematic loops

Disclination lines in three-dimensional nematic liquid crystals generically form closed loops whose topology is classified by homotopy theory. While this classification successfully captures global topological features, it does not encode the geometry of the defect profile along the loop, which can strongly influence defect dynamics. Here, we propose a geometric description of nematic disclination loops using the Clifford algebra Cl(3,0). This approach naturally captures the geometry of the local defect profile, as well as changes along the loop, which is mathematically a SU(2) holonomy. Simulations of the dynamics of defect loops with specified geometries embedded in nematic liquid crystals demonstrate that loops nucleate the growth of "topological blobs" of defects, which later dissipate leaving uniform nematic textures. Self-twist of the defect profile leads to nucleation of additional linking disclination lines, with a simple arithmetic relation between total self-twist and linking number. In contrast, loops with an even number of discrete profile transitions generate patterns with threading between loops, but no linking. These results establish a direct connection between the geometric holonomy of a disclination loop and its subsequent evolution, and may be extendable to more complex order parameter manifolds, such as cholesterics or smectics.

cond-mat.soft

On the geometric algebras of the Ising model

We revisit the classical transfer matrix solution of the one- and two-dimensional Ising model from the perspective of Clifford and conformal geometric algebras. Building on Kaufman's spinor formulation, we show that all elements entering the solution, including the transfer matrix, its eigenvectors, and the quasiparticle excitations, admit a natural and unified interpretation as elements of an appropriate conformal Clifford algebra. In particular, the transfer matrix can be viewed as a dilation generated by a conformal bivector, while its eigenvectors correspond to null combinations of Clifford generators, closely paralleling the emergence of Majorana fermionic degrees of freedom. In the two-dimensional case, the standard eigenvalue equation for the row-to-row transfer matrix is reinterpreted as a dispersion relation for quasiparticle excitations, exposing the connection between the Ising model and a theory of free Majorana fermions. While all the explicit exact results recovered are well known, this geometric reformulation provides a unified algebraic framework which is compact and physically interpretable. Specifically, this clarifies the role of scale transformations, fermionic modes, and duality in the Ising model. We believe this approach offers a useful pedagogical complement to more conventional fermionic, Grassmann, or field theoretic treatments.

cond-mat.stat-mech

Braiding and exchange statistics of liquid crystalline Majorana quasiparticles

Liquid crystalline defects in 3D can be viewed as geometric spinors, whose emergent properties are reminiscent of those of topological excitations in quantum condensed matter, such as Majorana quasiparticles. However, it is unclear how deep this analogy is, and whether this is a purely mathematical mapping, or it extends to key physical features, such as the exchange statistics or braiding behaviour. To address this question, here we consider a simple pattern made up of four nematic Majorana-like defect profiles, and ask how the defect profiles change as we braid them repeatedly around each other. Surprisingly, we find that in a large range of parameter space the defect profiles behave as classical analogues of non-Abelian anyons, which can be described in our case by defect bivectors moving on a Bloch-like hemisphere. Elastic interactions and dynamical effects enhance the complexity of the gates which can be performed by braiding these quasiparticles, making these liquid crystalline spinors promising candidates as components of topological computers.

cond-mat.soft

Spontaneous phase separation and pattern formation in a lyotropic nematic mixture

Lyotropic liquid crystals can display rich phase behaviour and self-organisation, yet the physical principles underlying their self-assembly into large scale patterns remains understudied. Here, we combine theory, simulations and experiments on Sunset Yellow-water chromonic mixtures to show that such materials spontaneously phase separate, even without assuming any underlying microscopic attraction between the molecular species. In our minimal model, demixing depends solely on the Onsager-like coupling between local nematogen density and orientational order. If such a coupling is sufficiently strong, nematic defects trigger the nucleation of isotropic droplets, which then coalesce due to elastic or interfacial tensions. We further show that strong anchoring of the director field at the interface arrests this coarsening process, resulting in a stable microphase separated lamellar pattern. This self-assembled smectic phase has striking and unusual features, including spontaneous undulations, heterogeneous layer spacing, long-lived glassy defect patterns and lamellar onions. Our results identify orientational-density coupling and elastocapillarity as fundamental mechanisms to guide self-assembly in lyotropic and chromonic liquid crystals.

cond-mat.soft

Clifford algebras and liquid crystalline fermions

We show that Clifford algebras provide a natural language to describe the physics of liquid crystal defects in 3D. This framework shows that most of these defects have fermionic nature, as the director field profile on a 2D cross section can algebraically be represented by a spinor. Defects in uniaxial, biaxial nematics and cholesterics are represented by elements belonging to different Clifford algebras, suggesting that there are fundamental distinctions between topological defects in each of these phases. Our theory allows nematic defects to be interpreted as Majorana-like spinors, as defects and antidefects are topologically equivalent, whilst some cholesteric defects, such as screw dislocations, are better viewed as Weyl-like spinors of well-defined chirality. Defects can be described by a ``defect bivector'', an algebraic element which quantifies the rototranslation associated with them. In cholesterics, fermionic defects of different types can combine to yield composite quasiparticles with either fermionic or bosonic nature. Under cylindrical confinement, these quasiparticles provide the way to understand the structure of screw dislocations. In the bulk, they may condensate to form topological phases, such as blue phases or skyrmion lattices. Our results provide a surprising link between liquid crystals, particle physics, and topological quantum matter.

cond-mat.soft

Oscillation in the SIRS model

We study the SIRS epidemic model, both analytically and on a square lattice. The analytic model has two stable solutions, post outbreak/epidemic (no infected, $I=0$) and the endemic state (constant number of infected: $I>0$). When the model is implemented with noise, or on a lattice, a third state is possible, featuring regular oscillations. This is understood as a cycle of boom and bust, where an epidemic sweeps through, and dies out leaving a small number of isolated infecteds. As immunity wanes, herd immunity is lost throughout the population and the epidemic repeats. The key result is that the oscillation is an intrinsic feature of the system itself, not driven by external factors such as seasonality or behavioural changes. The model shows that non-seasonal oscillations, such as those observed for the omicron COVID variant, need no additional explanation such as the appearance of more infectious variants at regular intervals or coupling to behaviour. We infer that the loss of immunity to the SARS-CoV-2 virus occurs on a timescale of about ten weeks.

physics.bio-ph

Modelling the 3D spatiotemporal organisation of chromatin replication

We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently discordant experimental evidence in favour of either scenario. Which of the two morphologies appears in our model depends on the balance between non-specific and origin-targeting interactions between chromatin and firing factors -- polymerases and other components of the replisome. Non-specific interactions are also necessary to yield clustering of factors and replication forks, creating structures akin to the replication foci observed in mammalian cells in vivo. We suggest that cluster formation provides an underappreciated but robust pathway to avoid stalled or faulty forks, which would otherwise diminish the efficiency of the replication process. Additionally, our simulations allow us to predict different modes of cluster growth during S-phase, which could be tested experimentally, and they show that the three dimensional chromatin context is important to understand replication patterns in fission yeast.

physics.bio-ph

The crucial role of adhesion in the transmigration of active droplets through interstitial orifices

Active fluid droplets are a class of soft materials exhibiting autonomous motion sustained by an energy supply. Such systems have been shown to capture motility regimes typical of biological cells and are ideal candidates as building-block for the fabrication of soft biomimetic materials of interest in pharmacology, tissue engineering and lab on chip devices. While their behavior is well established in unconstrained environments, much less is known about their dynamics under strong confinement. Here, we numerically study the physics of a droplet of active polar fluid migrating within a microchannel hosting a constriction with adhesive properties, and report evidence of a striking variety of dynamic regimes and morphological features, whose properties crucially depend upon droplet speed and elasticity, degree of confinement within the constriction and adhesiveness to the pore. Our results suggest that non-uniform adhesion forces are instrumental in enabling the crossing through narrow orifices, in contrast to larger gaps where a careful balance between speed and elasticity is sufficient to guarantee the transition. These observations may be useful for improving the design of artificial micro-swimmers, of interest in material science and pharmaceutics, and potentially for cell sorting in microfluidic devices.

cond-mat.soft

Soft channel formation and symmetry breaking in exotic active emulsions

We use computer simulations to study the morphology and rheological properties of a bidimensional emulsion resulting from a mixture of a passive isotropic fluid and an active contractile polar gel, in the presence of a surfactant that favours the emulsification of the two phases. By varying the intensity of the contractile activity and of an externally imposed shear flow, we find three possible morphologies. For low shear rates, a simple lamellar state is obtained. For intermediate activity and shear rate, an asymmetric state emerges, which is characterized by shear and concentration banding at the polar/isotropic interface. A further increment in the active forcing leads to the self-assembly of a soft channel where an isotropic fluid flows between two layers of active material. We characterize the stability of this state by performing a dynamical test varying the intensity of the active forcing and shear rate. Finally, we address the rheological properties of the system by measuring the effective shear viscosity, finding that this increases as active forcing is increased, so that the fluid thickens with activity.

cond-mat.soft

Electrostatic inactivation of RNA viruses at air-water and liquid-liquid interfaces

Understanding the interactions between viruses and surfaces or interfaces is important, as they provide the principles underpinning the cleaning and disinfection of contaminated surfaces. Yet, the physics of such interactions is currently poorly understood. For instance, there are longstanding experimental observations suggesting that the presence of air-water interfaces can generically inactivate and kill viruses, yet the mechanism underlying this phenomenon remains unknown. Here we use theory and simulations to show that electrostatics provides one such mechanism, and that this is very general. Thus, we predict that the free energy of an RNA virus should increase by several thousands of $k_BT$ as the virion breaches an air-water interface. We also show that the fate of a virus approaching a generic liquid-liquid interface depends strongly on the detailed balance between interfacial and electrostatic forces, which can be tuned, for instance, by choosing different media to contact a virus-laden respiratory droplet. We propose that these results can be used to design effective strategies for surface disinfection. Intriguingly, tunability requires electrostatic and interfacial forces to scale similarly with viral size, which naturally occurs when charges are arranged in a double-shell distribution as in RNA viruses like influenza and all coronaviruses.

cond-mat.soft

Simulating topological domains in human chromosomes with a fitting-free model

We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by a string of beads, with each bead being "colored" according to 1D bioinformatic data (e.g., chromatin state, histone modification, GC content). Individual spheres (representing bi- and multi-valent transcription factors) can bind reversibly and selectively to beads with the appropriate color. During molecular dynamics simulations, the factors bind, and the string spontaneously folds into loops, rosettes, and topologically-associating domains (TADs). This organization occurs in the absence of any specified interactions between distant DNA segments, or between transcription factors. A comparison with Hi-C data shows that simulations predict the location of most boundaries between TADs correctly. The model is "fitting-free" in the sense that it does not use Hi-C data as an input; consequently, one of its strengths is that it can -- in principle -- be used to predict the 3D organization of any region of interest, or whole chromosome, in a given organism, or cell line, in the absence of existing Hi-C data. We discuss how this simple model might be refined to include more transcription factors and binding sites, and to correctly predict contacts between convergent CTCF binding sites.

physics.bio-ph

Non-Equilibrium Effects of Molecular Motors on Polymers

We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are represented as freely diffusing beads which, upon encountering the substrate, bind to it through a short-ranged attractive potential. When bound, motors and polymer beads experience an equal and opposite active force, directed tangential to the polymer; this leads to motion of the motors along the polymer contour. The inclusion of explicit motors differentiates our model from other recent active polymer models. We study, by means of Langevin dynamics simulations, the effect of the motor activity on both the conformational and dynamical properties of the substrate. We find that activity leads, in addition to the expected enhancement of polymer diffusion, to an effective reduction of its persistence length. We discover that this effective "softening" is a consequence of the emergence of double-folded branches, or hairpins, and that it can be tuned by changing the number of motors or the force they generate. Finally, we investigate the effect of the motors on the probability of knot formation. Counter-intuitively our simulations reveal that, even though at equilibrium a more flexible substrate would show an increased knotting probability, motor activity leads to a marked decrease in the occurrence of knotted conformations with respect to equilibrium.

cond-mat.soft

Extrusion without a motor: a new take on the loop extrusion model of genome organization

Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and extrusion is the only model to date which can explain this. However, the model requires a motor to generate the loops, and although cohesin is a strong candidate for the extruding factor, a suitable motor protein (or a motor activity in cohesin itself) has yet to be found. Here we explore a new hypothesis: that there is no motor, and thermal motion within the nucleus drives extrusion. Using theoretical modelling and computer simulations we ask whether such diffusive extrusion could feasibly generate loops. Our simulations uncover an interesting ratchet effect (where an osmotic pressure promotes loop growth), and suggest, by comparison to recent in vitro and in vivo measurements, that diffusive extrusion can in principle generate loops of the size observed in the data. Extra View on : C. A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi, P. R. Cook, and D. Marenduzzo "Non-equilibrium chromosome looping via molecular slip-links", Physical Review Letters 119, 138101 (2017)

physics.bio-ph

A nonequilibrium strategy for fast target search on the genome

Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on "chromophoresis", the dynamics of DNA-binding proteins up or down gradients in the density of epigenetic marks, or colours (biochemical tags on the genome). We focus on a set of proteins that deposit marks from which they are repelled---a case which is only encountered away from thermodynamic equilibrium. For suitable ranges of kinetic parameter values, chromophoretic proteins can perform unidirectional motion and are optimally redistributed along the genome. Importantly, they can also locally unravel a region of the genome which is collapsed due to self-interactions and "dive" deep into its core, for a striking enhancement of the efficiency of target search on such an inaccessible substrate. We discuss the potential relevance of chromophoresis for the location of DNA lesions.

q-bio.SC

Dynamic clustering and re-dispersion in concentrated colloid-active gel composites

We study the dynamics of quasi-two-dimensional concentrated suspensions of colloidal particles in active gels by computer simulations. Remarkably, we find that activity induces a dynamic clustering of colloids even in the absence of any preferential anchoring of the active nematic director at the particle surface. When such an anchoring is present, active stresses instead compete with elastic forces and re-disperse the aggregates observed in passive colloid-liquid crystal composites. Our quasi-two-dimensional "inverse" dispersions of passive particles in active fluids (as opposed to the more common "direct" suspensions of active particles in passive fluids) provide a promising route towards the self-assembly of new soft materials.

cond-mat.soft

Transcription-driven DNA Supercoiling: Non-Equilibrium Dynamics and Action-at-a-distance

We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for double stranded DNA. By accounting for the action of a transcribing RNA polymerase (RNAP), we characterise the geometry and non equilibrium dynamics of the twin supercoiling domains forming on each side of the RNAP. Textbook pictures depict such domains as symmetric, with plectonemes (writhed DNA) appearing close to the RNAP. On the contrary, we find that the twist generated by transcription results in asymmetric domains, with plectonemes formed far from the RNAP. We show that this translates into an "action-at-a-distance" on DNA-binding proteins: for instance, positive supercoils downstream of an elongating RNAP destabilise nucleosomes long before the transcriptional machinery reaches the histone octamer. To understand these observations we use our framework to quantitatively analyse the relaxation dynamics of supercoiled DNA. We find a striking separation of timescales between twist diffusion, which is a simple and fast process, and writhe relaxation, which is slow and entails multiple steps.

physics.bio-ph

Rheology and microrheology of deformable droplet suspensions

Dense suspensions of soft colloidal particles display a broad range of physical and rheological properties which are still far from being fully understood. To elucidate the role of deformability on colloidal flow, we employ computer simulations to measure the apparent viscosity of a system of droplets of variable surface tension subjected to a pressure-driven flow. We confirm that our suspension generically undergoes discontinuous shear thinning, and determine the dependence of the onset of the discontinuity on surface tension. We find that the effective viscosity of the suspension is mainly determined by a capillary number. We present active microrheology simulations, where a single droplet is dragged through the suspension. These also show a dynamical phase transition, analogous to the one associated with discontinuous shear thinning in our interpretation. Such a transition is signalled by a discontinuity in the droplet velocity versus applied force.

cond-mat.soft