arXiv subjects

E. Orlandini

Publications and source records attributed to E. Orlandini.

At least 19 recordsLinked to original sources

arXiv2026

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↗

arXiv2025

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↗

arXiv2023

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↗

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

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

Nonequilibrium Kinetics of One-Dimensional Bose Gases

We study cold dilute gases made of bosonic atoms, showing that in the mean-field one-dimensional regime they support stable out-of-equilibrium states. Starting from the 3D Boltzmann-Vlasov equation with contact interaction, we derive an effective 1D Landau-Vlasov equation under the condition of a strong transverse harmonic confinement. We investigate the existence of out-of-equilibrium states, obtaining stability criteria similar to those of classical plasmas.

cond-mat.quant-gas↗

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↗

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↗

arXiv2014

Interacting Elastic Lattice Polymers: a Study of the Free-Energy of Globular Rings

We introduce and implement a Monte Carlo scheme to study the equilibrium statistics of polymers in the globular phase. It is based on a model of "interacting elastic lattice polymers" and allows a sufficiently good sampling of long and compact configurations, an essential prerequisite to study the scaling behaviour of free energies. By simulating interacting self-avoiding rings at several temperatures in the collapsed phase, we estimate both the bulk and the surface free energy. Moreover from the corresponding estimate of the entropic exponent $α-2$ we provide evidence that, unlike for swollen and $Θ$-point rings, the hyperscaling relation is not satisfied for globular rings.

cond-mat.stat-mech↗

arXiv2013

Flexoelectric switching in cholesteric blue phases

We present computer simulations of the response of a flexoelectric blue phase network, either in bulk or under confinement, to an applied field. We find a transition in the bulk between the blue phase I disclination network and a parallel array of disclinations along the direction of the applied field. Upon switching off the field, the system is unable to reconstruct the original blue phase but gets stuck in a metastable phase. Blue phase II is comparatively much less affected by the field. In confined samples, the anchoring at the walls and the geometry of the device lead to the stabilisation of further structures, including field-aligned disclination loops, splayed nematic patterns, and yet more metastable states. Our results are relevant to the understanding of the switching dynamics for a class of new, "superstable", blue phases which are composed of bimesogenic liquid crystals, as these materials combine anomalously large flexoelectric coefficients, and low or near-zero dielectric anisotropy.

cond-mat.soft↗

arXiv2013

Knotting of linear DNA in nano-slits and nano-channels: a numerical study

The amount and type of self-entanglement of DNA filaments is significantly affected by spatial confinement, which is ubiquitous in biological systems. Motivated by recent advancements in single DNA molecule experiments based on nanofluidic devices, and by the introduction of algorithms capable of detecting knots in open chains, we investigate numerically the entanglement of linear, open DNA chains confined inside nano-slits. The results regard the abundance, type and length of occurring knots and are compared with recent findings for DNA inside nano-channels. In both cases, the width of the confining region, D, spans the 30nm- 1μm range and the confined DNA chains are 1 to 4μm long. It is found that the knotting probability is maximum for slit widths in the 70-100nm range. However, over the considered DNA contour lengths, the maximum incidence of knots remains below 20%, while for channel confinement it tops 50%. Further differences of the entanglement are seen for the average contour length of the knotted region which drops significantly below D ~100nm for channel-confinement, while it stays approximately constant for slit-like confinement. These properties ought to reverberate in different kinetic properties of linear DNA depending on confinement and could be detectable experimentally or exploitable in nano-technological applications.

cond-mat.soft↗

arXiv2012

Facilitated diffusion on confined DNA

In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA. The confining geometry and DNA elasticity are key parameters: we find that facilitated diffusion is most efficient inside an isotropic volume, and on a flexible polymer. By considering the typical copy numbers of proteins in vivo, we show that the speedup due to sliding becomes insensitive to fine tuning of parameters, rendering facilitated diffusion a robust mechanism to speed up intracellular diffusion-limited reactions. The parameter range we focus on is relevant for in vitro systems and for facilitated diffusion on yeast chromatin.

cond-mat.soft↗

arXiv2012

Numerical study of linear and circular model DNA chains confined in a slit: metric and topological properties

Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $μ$m range and slits widths spanning continuously the 50--1250nm range. The metric scaling predicted by de Gennes' blob model is shown to hold for both linear and circularised DNA up to the strongest levels of confinement. More notably, the topological properties of the circularised DNA molecules have two major differences compared to three-dimensional confinement. First, the overall knotting probability is non-monotonic for increasing confinement and can be largely enhanced or suppressed compared to the bulk case by simply varying the slit width. Secondly, the knot population consists of knots that are far simpler than for three-dimensional confinement. The results suggest that nano-slits could be used in nano-fluidic setups to produce DNA rings having simple topologies (including the unknot) or to separate heterogeneous ensembles of DNA rings by knot type.

physics.bio-ph↗

arXiv2011

Bistable defect structures in blue phase devices

Blue phases (BPs) are liquid crystals made up by networks of defects, or disclination lines. While existing phase diagrams show a striking variety of competing metastable topologies for these networks, very little is known as to how to kinetically reach a target structure, or how to switch from one to the other, which is of paramount importance for devices. We theoretically identify two confined blue phase I systems in which by applying an appropriate series of electric field it is possible to select one of two bistable defect patterns. Our results may be used to realise new generation and fast switching energy-saving bistable devices in ultrathin surface treated BPI wafers.

cond-mat.soft↗

arXiv2011

Switching dynamics in cholesteric blue phases

Blue phases are networks of disclination lines, which occur in cholesteric liquid crystals near the transition to the isotropic phase. They have recently been used for the new generation of fast switching liquid crystal displays. Here we study numerically the steady states and switching hydrodynamics of blue phase I (BPI) and blue phase II (BPII) cells subjected to an electric field. When the field is on, there are three regimes: for very weak fields (and strong anchoring at the boundaries) the blue phases are almost unaffected, for intermediate fields the disclinations twist (for BPI) and unzip (for BPII), whereas for very large voltages the network dissolves in the bulk of the cell. Interestingly, we find that a BPII cell can recover its original structure when the field is switched off, whereas a BPI cell is found to be trapped more easily into metastable configurations. The kinetic pathways followed during switching on and off entails dramatic reorganisation of the disclination networks. We also discuss the effect of changing the director field anchoring at the boundary planes and of varying the direction of the applied field.

cond-mat.soft↗

arXiv2011

Topological signatures of globular polymers

Simulations in which a globular ring polymer with delocalized knots is separated in two interacting loops by a slipping link, or in two non-interacting globuli by a wall with a hole, show how the minimal crossing number of the knots controls the equilibrium statistics. With slipping link the ring length is divided between the loops according to a simple law, but with unexpectedly large fluctuations. These are suppressed only for unknotted loops, whose length distribution shows always a fast power law decay. We also discover and explain a topological effect interfering with that of surface tension in the globule translocation through a membrane nanopore.

cond-mat.soft↗

arXiv2011

Switching and defect dynamics in multistable liquid crystal devices

We investigate the switching dynamics of multistable nematic liquid crystal devices. In particular we identify a remarkably simple 2-dimensional (2D) device which exploits hybrid alignment at the surfaces to yield a bistable response. We also consider a 3-dimensional (3D) tristable nematic device with patterned anchoring, recently implemented in practice, and discuss how the director and disclination patterns change during switching.

cond-mat.soft↗

arXiv2009

Supercoil formation in DNA denaturation

We generalize the Poland-Scheraga (PS) model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional stress induced by denaturation enforces formation of supercoils whose writhe absorbs the linking number expelled by the loops. Our model predicts that, when the entropy parameter of a loop satisfies $c \le 2$, denaturation transition does not take place. On the other hand for $c>2$ a first-order denaturation transition is consistent with our model and may take place in the actual system, as in the case with no supercoils. These results are in contrast with other treatments of circular DNA melting where denaturation is assumed to be accompanied by an increase in twist rather than writhe on the bound segments.

cond-mat.soft↗