arXiv subjects

Davide Marenduzzo

Publications and source records attributed to Davide Marenduzzo.

At least 19 recordsLinked to original sources

arXiv2026

Topological Signatures of Hardness and Structural Order in Network-Forming Materials

Understanding how the topology of network forming materials influences their physical properties remains a longstanding challenge. Here, we investigate the topology of experimentally compatible atomistic models of amorphous silica together with the crystalline polymorphs cristobalite and quartz. By comparing multiple atomistic models of amorphous silica that equally reproduce neutron-scattering data, we show that different microscopic descriptions can imply different topological interpretations of glass stability. To characterize the network beyond conventional geometric descriptors, we introduce the linking valence, which quantifies the average number of topological links per network loop. This topological descriptor separates silica into two distinct classes: the mechanically harder quartz exhibit values more than an order of magnitude larger than those of amorphous silica and cristobalite, despite their common tetrahedral building blocks. Spectral analysis of the loop-linking networks provides a complementary distinction, separating amorphous from crystalline phases and revealing differences in the long-range organization of topological constraints. These results establish topological linking as a new framework for connecting the structure and physical properties of network-forming materials.

cond-mat.mtrl-sci↗

arXiv2026

Topological delocalisation of confined 3D active nematics

Defect lines in 3D active nematic systems are intriguing topological singularities whose out-of-equilibrium dynamics remain elusive in confined settings. Here, we numerically study 3D active nematics confined within closed cylinders to elucidate the roles of geometry and activity. We reveal a competition between passive elasticity, which causes localisation of defects near edges, and activity, which endows defects with motility and gives rise to disorderly, delocalised dynamics. Varying boundary curvature, activity strength, and cylinder radius reveals a state space of static and dynamic localisation states, including handle-like configurations and chaotic motion bounded within the cylinder endcap. As activity is tuned to induce delocalisation, we identify phase transition signatures, including pronounced fluctuations and an emergent power law scaling of defect number and average defect length. We find that these scaling properties are strongly altered by confinement: unlike in bulk systems where activity governs length distributions, confinement tunes an activity-independent characteristic length, with an exponent reminiscent of self-avoiding confined polymers. These results establish confinement of inhomogeneous curvature as a versatile mechanism for controlling active topological dynamics.

cond-mat.soft↗

arXiv2026

Flow of deformable droplets: self-pinned glasses and string-like flow

We investigate, through numerical simulations, the rheology of a dry suspension of deformable droplets under pressure-driven flow. The system exhibits two force-driven dynamical transitions. At low forcing, the suspension behaves as a yield-stress material: below a critical force, droplets remain arrested in an amorphous solid-like state. Our simulations suggest that yielding is controlled by droplet contacts and predict that the critical force strongly depends on deformability. Above yielding, the suspension does not flow steadily but rather enters an intermittent, stick-slip regime characterised by long-lived caging and non-Gaussian velocity fluctuations. This state can be interpreted as a "self-pinned'' glass, in which slowly evolving droplet overlaps generate an effective rugged energy landscape that dynamically traps droplets and produces intermittent rearrangements reminiscent of near-critical dynamics in depinning models. At larger forcing, droplets deform sufficiently to continuously exchange neighbours, progressively annealing the overlap structure and driving a dynamic transition to a string-like, flowing state. Our results identify the restructuring of overlap networks as a generic mechanism which controls flow in driven suspensions of deformable particles.

cond-mat.soft↗

arXiv2026

Nucleoid clustering drives stepwise expansion and segregation of replicating bacterial chromosomes

Bacterial chromosome replication occurs in the absence of a canonical spindle apparatus; yet it reliably produces organised and segregated genomes. While both passive and active mechanisms have been investigated, DNA replication itself is a non-equilibrium process that continuously generates new genetic material and reorganizes the nucleoid. Here, we investigate how replication-driven dynamics, combined with nucleoid-associated protein (NAP) interactions, shape spatiotemporal chromosome organisation using a three-dimensional polymer model that explicitly simulates DNA synthesis. We show that NAP-mediated interactions induce dynamic clustering of DNA, generating density fluctuations in the nucleoid. When coupled to replication, these clusters undergo cycles of stress buildup and release that produce stepwise expansion dynamics consistent with experimental observations. Chromosome segregation occurs naturally in this regime, but only within a finite range of interaction strengths: weak interactions fail to structure the nucleoid, whereas strong interactions hinder replication progression. Within this optimal balance, replication also promotes the spontaneous formation of replication factories. Our results demonstrate that bacterial chromosome organisation can be understood as a non-equilibrium system in which the interplay between replication forces and protein-mediated interactions generates nucleoid mechanics, dynamics, and segregation.

physics.bio-ph↗

arXiv2026

Topological localisation and motility of active knots

Nonequilibrium active polymers provide a minimal framework to investigate biopolymers such as DNA and chromatin under the action of molecular motors. Here we study active ring polymers with controlled topology and show that knot type qualitatively determines their nonequilibrium behaviour. We find that activity induces opposite localisation responses in different topological families: torus knots systematically delocalise and inflate, whereas twist knots tighten and remain localised. We trace this divergent behaviour to the distinct symmetry properties of their tangent fields, which control the alignment of active forces along the chain. We show that topology also governs internal and emergent dynamics. Active torus knots behave as soft chiral self-propelled particles exhibiting persistent motion with a well-defined handedness fixed by their topological chirality. In contrast, achiral knots show no net handedness. The knot thus acts as a deformable topological quasiparticle whose morphology and propulsion are selected by topology. These results suggest potential routes toward programmable soft chiral particles with controllable morphology and emergent motility modes.

cond-mat.soft↗

arXiv2026

Field-induced phase transitions in ferro-antiferromagnetic diblock copolymers

We study the equilibrium properties of a model of magnetic diblock copolymer where each monomer is decorated with an Ising-like spin. Spins interact ferromagnetically within each block and antiferromagnetically across blocks, generating frustration between magnetic ordering and spatial organization. By employing a mean-field approach and Monte Carlo simulations for self-avoiding walks on the cubic lattice, we investigate the system's response to an external magnetic field. We discover a rich phase diagram that includes: a swollen phase with both filaments magnetically disordered and spatially extended; a mixed compact phase characterized by a single globule in which the two filaments are strongly intertwined; a segregated compact phase composed of two globular, magnetically ordered, and spatially separated blocks. Further, if the magnitude of the intra-block ferromagnetic interaction differs between the two blocks, we observe a hybrid segregated (``tadpole'') phase where one extended block coexists with a collapsed one. Mean-field predictions are in quantitative agreement with Monte Carlo results for the location of the phase boundaries. These findings provide a minimal statistical-mechanical framework for field-controlled self-assembly of tunable patterns by magnetically heterogeneous polymers. They may also serve as a simple platform to investigate the coupling between internal epigenetic-like states and chromatin folding.

cond-mat.soft↗

arXiv2026

Supercoiling DNA with a free end

In this work, we combine coarse-grained Brownian dynamics simulations and mean-field theory to study supercoiling dynamics, as well as the steady-state profiles of twist and writhe, in an open DNA polymer where one of the free ends is subjected to a constant torque. Even though the other end is free, and hence can spin and release torsional stress, we observe that the entire chain transitions between a swollen and a plectonemic phase as the torque increases beyond a critical threshold. In the plectonemic phase, we observe a non-linear twist profile in the steady state, resulting from the mutual interconversion between the injected twist and geometrical writhe, which distributes inhomogeneously along the chain. We also show that the non-equilibrium dynamics of twist accumulation is diffusive, and that writhe diffusion is negligible in this geometry, as plectonemes remain localised near the end that is being rotated. We discuss the feasibility of testing our results with single-molecule experiments.

cond-mat.soft↗

arXiv2025

Passive polymers in active turbulence undergo a collapse-stretch transition

Active processes in living systems generate nonequilibrium forces that deform embedded passive macromolecules. To understand how such dynamics influence polymer conformation, we study a flexible passive chain in an active nematic fluid. Using hybrid simulations, we uncover a length-dependent transition in polymer behavior: long chains align with and stretch along defect-driven flows, while short chains bend and collapse due to localized stresses. These responses are controlled by a competition between the polymer size and the emergent length scale of the active turbulence. Our results reveal a defect-mediated mechanism for conformational control and point toward general physical principles for designing responsive soft materials that couple passive structure to active dynamics.

cond-mat.soft↗

arXiv2025

Modelling transcriptional silencing and its coupling to 3D genome organisation

Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially by modelling. This study employs 3D simulations to study the biophysics of a chromatin fibre where active transcription factors compete with repressors for binding to transcription units along the fibre, and investigates how different silencing mechanisms affect 3D chromatin structure and transcription. We examine three gene silencing feedback mechanisms: positive, negative, and neutral. These mechanisms capture different silencing pathways observed or proposed in biological systems. Our findings reveal that, whilst all mechanisms lead to a silencing transition, the signatures of this transition depend on the choice of the feedback. The latter controls the morphologies of the emergent 3D transcription factor clusters, the average gene expression and its variability, or gene noise, and the network of ensuing correlations between activities of neighbouring transcription units. These results provide insights into the biophysics of gene silencing, as well as into the interplay between transcriptional regulation and 3D genome organisation.

physics.bio-ph↗

arXiv2025

Topological weight and structural diversity of polydisperse chromatin loop networks

Current biophysical models for transcriptionally active chromatin view this as a polymer with sticky sites, mimicking transcription units such as promoters and enhancers which interact via the binding of multivalent complexes of chromatin-binding proteins. It has been demonstrated that this model spontaneously leads to microphase separation, resulting in the formation of a network of loops with transcription units serving as anchors. Here, we demonstrate how to compute the topological weights of loop networks with an arbitrary 1D pattern of transcription units along the fibre (or `polydisperse' loop networks), finding an analogy with networks of electric resistors in parallel or in series. We also show how the BEST (de Bruijn, van Aardenne-Ehrenfest, Smith and Tutte) theorem in combinatorics can be used to find the combinatorial multiplicity of any class of loop networks. Our results can be used to compute the structural diversity, or Shannon entropy, of loop networks: we show that this quantity depends on the 1D patterning of transcription units along the chain, possibly providing a pathway to control transcriptional noise in eukaryotic genes.

physics.bio-ph↗

arXiv2025

Equilibrium phases and phase transitions in multicritical magnetic polymers

Magnetic polymers are examples of composite soft materials in which the competition between the large configurational entropy of the soft substrate (polymer) and the magnetic interaction may give rise to rich equilibrium phase diagrams as well as non-standard critical phenomena. Here, we study a self-avoiding walk model decorated by Ising spins of value $0$ and $\pm 1$ that interact according to a Blume-Emery-Griffith-like Hamiltonian. By using mean-field approximations and Monte Carlo simulations, we report the existence of three distinct equilibrium phases: swollen disordered, compact ordered, and compact disordered. Notably, these phases are separated by phase boundaries that meet at multicritical points, whose nature and location are tunable and depend on the strength of the interactions. In our conclusion, we discuss the relevance of the phase diagrams we have obtained to the physics of magnetic polymers and their application to chromatin biophysics.

cond-mat.soft↗

arXiv2024

Bridging-Induced Phase Separation and Loop Extrusion Drive Noise in Chromatin Transcription

Transcriptional noise, or heterogeneity, is important in cellular development and in disease. The molecular mechanisms driving it are, however, elusive and ill-understood. Here, we use computer simulations to explore the role of 3D chromatin structure in driving transcriptional noise. We study a simple polymer model where proteins - modeling complexes of transcription factors and polymerases - bind multivalently to transcription units - modeling regulatory elements such as promoters and enhancers. We also include cohesin-like factors which extrude chromatin loops that are important for the physiological folding of chromosomes. We find that transcription factor binding creates spatiotemporal patterning and a highly variable correlation time in transcriptional dynamics, providing a mechanism for intrinsic noise within a single cell. Instead, loop extrusion contributes to extrinsic noise, as the stochastic nature of this process leads to different networks of cohesin loops in different cells in our simulations. Our results could be tested with single-cell experiments and provide a pathway to understanding the principles underlying transcriptional plasticity in vivo.

physics.bio-ph↗

arXiv2024

Entangled nematic disclinations using multi-particle collision dynamics

Colloids dispersed in nematic liquid crystals form topological composites in which colloid-associated defects mediate interactions while adhering to fundamental topological constraints. Better realising the promise of such materials requires numerical methods that model nematic inclusions in dynamic and complex scenarios. We employ a mesoscale approach for simulating colloids as mobile surfaces embedded in a fluctuating nematohydrodynamic medium to study the kinetics of colloidal entanglement. In addition to reproducing far-field interactions, topological properties of disclination loops are resolved to reveal their metastable states and topological transitions during relaxation towards ground state. The intrinsic hydrodynamic fluctuations distinguish formerly unexplored far-from-equilibrium disclination states, including configurations with localised positive winding profiles. The adaptability and precision of this numerical approach offers promising avenues for studying the dynamics of colloids and topological defects in designed and out-of-equilibrium situations.

cond-mat.soft↗

arXiv2024

Multiphase Field Model of Cells on a Substrate: From 3D to 2D

Multiphase field models have emerged as an important computational tool for understanding biological tissue while resolving single-cell properties. While they have successfully reproduced many experimentally observed behaviors of living tissue, the theoretical underpinnings have not been fully explored. We show that a two-dimensional version of the model, which is commonly employed to study tissue monolayers, can be derived from a three-dimensional version in the presence of a substrate. We also show how viscous forces, which arise from friction between different cells, can be included in the model. Finally, we numerically simulate a tissue monolayer, and find that intercellular friction tends to solidify the tissue.

cond-mat.soft↗

arXiv2024

3D active nematic disclinations behave as Majorana quasiparticles

Quasiparticles are low-energy excitations with important roles in condensed matter physics. An intriguing example is provided by Majorana fermions, quasiparticles which are identical to their antiparticles. Despite being implicated in neutrino oscillations and topological superconductivity, their experimental realisations remain scarce. Here we propose a purely classical realisation of Majorana fermions, in terms of 3-dimensional disclination lines in active nematics. Activity is required to overcome the elastic cost associated with these excitations, so they can appear in steady state. We combine topology and simulations to show that active nematics under confinement spontaneously create in their interior topologically charged disclination lines and loops, akin to Majorana quasiparticles with finite momentum. Within an elongated channel, we find a phenomenology similar to that of the Kitaev chain, as local Majorana-like excitations appear near surfaces, while a non-local system-spanning helical disclination line can arise along the centre. In unconfined active turbulence, Majorana-like charged loops are instead exceedingly rare, suggesting that boundaries are crucial to generate these quasiparticles, as in quantum condensed matter. We suggest that 3-dimensional active disclinations can be used to probe the physics of Majorana spinors at a much larger scale than traditionally considered, potentially facilitating the experimental observation of their dynamics.

cond-mat.soft↗

arXiv2024

Controlling flow patterns and topology in active emulsions

Active emulsions and liquid crystalline shells are intriguing and experimentally realisable types of topological matter. Here we numerically study the morphology and spatiotemporal dynamics of a double emulsion, where one or two passive small droplets are embedded in a larger active droplet. We find activity introduces a variety of rich and nontrivial nonequilibrium states in the system. First, a double emulsion with a single active droplet becomes self-motile, and there is a transition between translational and rotational motion: both of these regimes remain defect-free, hence topologically trivial. Second, a pair of particles nucleate one or more disclination loops, with conformational dynamics resembling a rotor or chaotic oscillator, accessed by tuning activity. In the first state a single, topologically charged, disclination loop powers the rotation. In the latter state, this disclination stretches and writhes in 3D, continuously undergoing recombination to yield an example of an active living polymer. These emulsions can be self-assembled in the lab, and provide a pathway to form flow and topology patterns in active matter in a controllable way, as opposed to bulk systems that typically yield active turbulence.

cond-mat.soft↗

arXiv2023

Combinatorics and topological weights of chromatin loop networks

Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop networks, both in the case where TUs are labelled and where they are unlabelled. We then combine these mathematical results with those of computer simulations aimed at finding the inter-TU energy required to form a target loop network. We show that different topologies are vastly different in terms of both their combinatorial weight and energy of formation. We explain the latter result qualitatively by computing the topological weight of a given network -- i.e., its partition function in statistical mechanics language -- in the approximation where excluded volume interactions are neglected. Our results show that networks featuring local loops are statistically more likely with respect to networks including more non-local contacts. We suggest our classification of loop networks, together with our estimate of the combinatorial and topological weight of each network, will be relevant to catalogue 3D structures of chromatin fibres around eukaryotic genes, and to estimate their relative frequency in both simulations and experiments.

physics.bio-ph↗

arXiv2023

Topological spectra and entropy of chromatin loop networks

The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors and RNA polymerases. This physical model leads to the natural emergence of clusters of proteins and binding sites, accompanied by the folding of chromatin into a set of topologies, each associated with a different network of loops. Here we combine numerics and analytics to first classify these networks and then find their relative importance or statistical weight, when the properties of the underlying polymer are those relevant to chromatin. Unlike polymer networks previously studied, our chromatin networks have finite average distances between successive binding sites, and this leads to giant differences between the weights of topologies with the same number of edges and nodes but different wiring. These weights strongly favour rosette-like structures with a local cloud of loops with respect to more complicated non-local topologies. Our results suggest that genes should overwhelmingly fold into a small fraction of all possible 3D topologies, which can be robustly characterised by the framework we propose here.

physics.bio-ph↗