arXiv subjects

Massimiliano Semeraro

Publications and source records attributed to Massimiliano Semeraro.

16 recordsLinked to original sources

arXiv2026

Phase Separation in a system of Brownian inertial rotors

We uncover an emergent phase separation in a system of inertial dumbbells put into persistent rotation by a constant applied torque, breaking chiral symmetry, while interacting with each other through repulsive hard-core interactions. We numerically determine the phase diagram of the model, showing that there exists a binodal and a spinodal region where the system separates into a dense liquid and an ordered phase, which we identify as hexatic. An analysis of the system pressure unveils that the mechanism underlying the phase separation is heavily controlled by inertia. Locally injected kinetic energy is steadily stored into the system in a way that depends on density and that, at large inertia, results in a hot dilute and cool dense state, leading to a generically unstable homogeneous phase. The interplay between dumbbells' arrangement into clusters and chiral forces produces a spontaneous rigid rotation of the clusters around their centers of mass.

cond-mat.soft↗

arXiv2026

Ordering and Defect Dynamics in Passive and Active Nematopolars

The coexistence of polar and nematic interactions, observed in a broad range of biological and synthetic active systems, gives rise to a rich phenomenology that continues to challenge our theoretical understanding of non-equilibrium collective behaviour. In this paper, we numerically investigate phase ordering and defect dynamics in a newly introduced minimal single-field model for dry nematopolar systems, where competing polar and nematic contributions enter the free energy, and activity is implemented through self-advection. At optimal balance, the system develops depolarization strings connecting half-integer defects and separating domains with opposite polarization, together with closed depolarization loops. We first characterize the elementary relaxation mechanisms of defect pairs and loops, showing that the interplay between polar and nematic alignment gives rise to non-monotonic string-mediated interactions, finite equilibrium separations and distinct loop-collapse pathways. Large-scale simulations from disordered states instead show dynamic scaling with a characteristic length growing as $\sim(t/\ln t)^{1/2}$, consistent with coarsening in systems with non-conserved order parameters and point-like defects. Upon introducing self-advection, sufficiently strong activity leads to the coexistence of positive integer and negative half-integer defects, which we term motility-induced charge symmetry breaking, and to saturation of the characteristic length scales, ultimately resulting in arrested coarsening. Overall, our results provide a simple unified framework for understanding the ordering and defect dynamics in biological and synthetic nematopolar systems.

cond-mat.soft↗

arXiv2025

Morphology, Polarization Patterns, Compression, and Entropy Production in Phase-Separating Active Dumbbell Systems

Polar patterns and topological defects are ubiquitous in active matter. In this paper, we study a paradigmatic polar active dumbbell system through numerical simulations, to clarify how polar patterns and defects emerge and shape evolution. We focus on the interplay between these patterns and morphology, domain growth, irreversibility, and compressibility, tuned by dumbbell rigidity and interaction strength. Our results show that, when separated through MIPS, dumbbells with softer interactions can slide one relative to each other and compress more easily, producing blurred hexatic patterns, polarization patterns extended across entire hexatically varied domains, and stronger compression effects. Analysis of isolated domains reveals the consistent presence of inward-pointing topological defects that drive cluster compression and generate non-trivial density profiles, whose magnitude and extension are ruled by the rigidity of the pairwise potential. Investigation of entropy production reveals instead that clusters hosting an aster (spiral) defect are characterized by a flat (increasing) entropy profile mirroring the underlying polarization structure, thus suggesting an alternative avenue to distinguish topological defects on thermodynamical grounds. Overall, our study highlights how interaction strength and defect-compression interplay affect cluster evolution in particle-based active models, and also provides connections with recent studies of continuum polar active field models.

cond-mat.soft↗

arXiv2025

Cluster size determines internal structure of transcription factories in human cells

Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs). Observations indicate that these proteins tend to form macromolecular clusters, known as transcription factories, whose morphology and composition is still debated. While some microscopy experiments have revealed the presence of specialised factories, composed of similar TFs transcribing families of related genes, sequencing experiments suggest instead that mixed clusters may be prevalent, as a panoply of different TFs binds promiscuously the same chromatin region. The mechanisms underlying the formation of specialised or mixed factories remain elusive. With the aim of finding such mechanisms, here we develop a chromatin polymer model mimicking the chromatin binding-unbinding dynamics of different types of complexes of TFs. Surprisingly, both specialised (i.e., demixed) and mixed clusters spontaneously emerge, and which of the two types forms depends mainly on cluster size. The mechanism promoting mixing is the presence of non-specific interactions between chromatin and proteins, which become increasingly important as clusters become larger. This result, that we observe both in simple polymer models and more realistic ones for human chromosomes, reconciles the apparently contrasting experimental results obtained. Additionally, we show how the introduction of different types of TFs strongly affects the emergence of transcriptional networks, providing a pathway to investigate transcriptional changes following gene editing or naturally occurring mutations.

physics.bio-ph↗

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

Phase Separation Kinetics in a Polar Active Field Model

A milestone of phase separation kinetics is the emergence of universal power laws $\sim t^{1/z}$ governing the domain growth evolution. We investigate a phase-separating polar active model comprising a scalar density field with an advective coupling to a polarization field. Our analysis reveals a novel $\sim t^{0.6}$ regime, which agrees well with the accelerated growth recently observed in simulations of polar active particles. We provide analytical arguments to explain how advection facilitates the creation of topological defects and compresses the domains leading to faster growth. We also show that the $\sim t^{0.6}$ regime is robust to several model generalizations.

cond-mat.soft↗

arXiv2025

Transverse Self-Propulsion Enhances the Aggregation of Active Dumbbells

We investigate a two-dimensional system of active Brownian dumbbells using molecular dynamics simulations. In this model, each dumbbell is driven by an active force oriented perpendicular to the axis connecting its two constituent beads. We characterize the resulting phase behavior and find that, across all values of activity, the system undergoes phase separation between dilute and dense phases. The dense phase exhibits hexatic order, and for large enough activity, we observe a marked increase in local polarization, with dumbbells predominantly oriented towards the interior of the clusters. Compared to the case of axially self-propelled dumbbells, we find that the binodal region is enlarged towards lower densities at all activities. This shift arises because dumbbells with transverse propulsion can more easily form stable cluster cores, serving as nucleation seeds, and show a highly suppressed escaping rate from the cluster boundary. Finally, we observe that clusters exhibit spontaneous rotation, with the modulus of the angular velocity scaling as $ω\sim r_g^{-2}$, where $r_g$ is the cluster's radius of gyration. This contrasts with axially propelled dumbbells, where the scaling follows $ω\sim r_g^{-1}$. We develop a simplified analytical model to rationalize this scaling behavior.

cond-mat.soft↗

arXiv2024

Work fluctuations for a confined Brownian particle: the role of initial conditions

We study the large fluctuations of the work injected by the random force into a Brownian particle under the action of a confining harmonic potential. In particular, we compute analytically the rate function for generic uncorrelated initial conditions, showing that, depending on the initial spread, it can exhibit no, one, or two singularities associated to the onset of linear tails. A dependence on the potential strength is observed for large initial spreads (entailing two singularities), which is lost for stationary initial conditions (giving one singularity) and concentrated initial values (no singularity). We discuss the mechanism responsible for the singularities of the rate function, identifying it as a big jump in the initial values. Analytical results are corroborated by numerical simulations.

cond-mat.stat-mech↗

arXiv2024

Entropy production of active Brownian particles going from liquid to hexatic and solid phases

Due to its inherent intertwinement with irreversibility, entropy production is a prime observable to monitor in systems of active particles. In this numerical study, entropy production in the liquid, hexatic and solid phases of a two-dimensional system of active Brownian particles is examined at both average and fluctuation level. The trends of averages as functions of density show no singularity and marked changes in their derivatives at the hexatic-solid transition. Distributions show instead peculiar tail structures interpreted by looking at microscopic configurations. Particles in regions of low local order generate tail values according to different dynamical mechanisms: they move towards empty regions or bounce back and forth into close neighbours. The tail structures are reproduced by a simple single-particle model including an intermittent harmonic potential.

cond-mat.soft↗

arXiv2024

Fluctuation Theorems for Heat exchanges between passive and active baths

In addition to providing general constraints on probability distributions, fluctuation theorems allow to infer essential information on the role played by temperature in heat exchange phenomena. In this numerical study, we measure the temperature of an out of equilibrium active bath using a fluctuation theorem that relates the fluctuations of the heat exchanged between two baths to their temperatures. Our setup consists of a single particle moving between two wells of a quartic potential accommodating two different baths. The heat exchanged between the two baths is monitored according to two definitions: as the kinetic energy carried by the particle whenever it jumps from one well to the other and as the work performed by the particle on one of the two baths when immersed in it. First, we consider two equilibrium baths at two different temperatures and verify that a fluctuation theorem featuring the baths temperatures holds for both heat definitions. Then, we introduce an additional Gaussian coloured noise in one of the baths, so as to make it effectively an active (out-of-equilibrium) bath. We find that a fluctuation theorem is still satisfied with both heat definitions. Interestingly, in this case the temperature obtained through the fluctuation theorem for the active bath corresponds to the kinetic temperature when considering the first heat definition, while it is larger with the second one. We interpret these results by looking at the particle jump phenomenology.

cond-mat.stat-mech↗

arXiv2024

A unified-field theory of genome organization and gene regulation

Our aim is to predict how often genic and non-genic promoters fire within a cell. We first review a parsimonious pan-genomic model for genome organization and gene regulation, where transcription rate is determined by proximity in 3D space of promoters to clusters containing appropriate factors and RNA polymerases -- structures variously called transcription factories, hubs, and condensates. This model allows reconciliation of conflicting results indicating that regulatory mammalian networks are both simple (as over-expressing just 4 transcription factors switches cell state) and complex (as genome-wide association studies show phenotypes like cell type are determined by thousands of loci rarely encoding such factors). It also yields simple explanations of how mysterious motifs like quantitative trait loci, enhancers, and silencers work. We then present 3D polymer simulations, and a proximity formula based on our biological model that enables prediction of transcriptional activities of all promoters in three human cell types. This simple fitting-free formula contains just one variable (distance on the genetic map to the nearest active promoter), and we suggest it can be applied to any organism.

physics.bio-ph↗

arXiv2023

Work fluctuations for a harmonically confined Active Ornstein-Uhlenbeck Particle

We study the active work fluctuations of an active Ornstein-Uhlenbeck particle in the presence of a confining harmonic potential. We tackle the problem analytically both for stationary and generic uncorrelated initial states. Our results show that harmonic confinement can induce singularities in the active work rate function, with linear stretches at large positive and negative active work, at sufficiently large active and harmonic force constants. These singularities originate from big jumps in the displacement and in the active force, occurring at the initial or ending points of trajectories and marking the relevance of boundary terms in this problem.

cond-mat.stat-mech↗

arXiv2023

Diffusion Properties of a Brownian Ratchet with Coulomb Friction

The motion of a Brownian particle in the presence of Coulomb friction and an asymmetric spatial potential was evaluated in this study. The system exhibits a ratchet effect, i.e., an average directed motion even in the absence of an external force, induced by the coupling of non-equilibrium conditions with the spatial asymmetry. Both the average motion and the fluctuations of the Brownian particle were analysed. The stationary velocity shows a non-monotonic behaviour as a function of both the temperature and the viscosity of the bath. The diffusion properties of the particle, which show several time regimes, were also investigated. To highlight the role of non-linear friction in the dynamics, a comparison is presented with a linear model of a Brownian particle driven by a constant external force, which allows for analytical treatment. In particular, the study unveils that the passage times between different temporal regimes are strongly affected by the presence of Coulomb friction.

cond-mat.stat-mech↗

arXiv2022

3D polymer simulations of genome organization and transcription across different chromosomes and cell types

We employ the diffusing transcription factors model for numerical simulation of chromatin topology conformations and transcriptional processes of human chromatin. Simulations of a short chromatin filament reveal different possible pathways to regulate transcription: it is shown that the transcriptional activity profile can be regulated and controlled by either acting on the chain structural properties, or on external factors, such as the number of transcription factors. Additionally, comparisons between GRO-seq experimental data and large scale numerical simulation of entire chromosomes from the human umbilical vein endothelial cell and the B-lmphocyte GM12878 show that the model provides reliable and statistically significant predictions for transcription across different cell-lines.

cond-mat.soft↗

arXiv2022

Large deviations for quadratic functionals of stable Gauss-Markov chains and entropy production

In this paper we establish a large deviation principle for the entropy production rate of possible non-stationary, centered stable Gauss-Markov chains, verifying the Gallavotti-Cohen symmetry. We reach this goal by developing a large deviation theory for quasi-Toeplitz quadratic functionals of multivariate centered stable Gauss-Markov chains, which differ from a perfect Toeplitz form by the addition of quadratic boundary terms.

math.PR↗

arXiv2021

Work Fluctuations in the Active Ornstein- Uhlenbeck Particle model

We study the large deviations of the power injected by the active force for an Active Ornstein-Uhlenbeck Particle (AOUP), free or in a confining potential. For the free-particle case, we compute the rate function analytically in d-dimensions from a saddle-point expansion, and numerically in two dimensions by it a) direct sampling of the active work in numerical solutions of the AOUP equations and b) Legendre-Fenchel transform of the scaled cumulant generating function obtained via a cloning algorithm. The rate function presents asymptotically linear branches on both sides and it is independent of the system's dimensionality, apart from a multiplicative factor. For the confining potential case, we focus on two-dimensional systems and obtain the rate function numerically using both methods a) and b). We find a different scenario for harmonic and anharmonic potentials: in the former case, the phenomenology of fluctuations is analogous to that of a free particle, but the rate function might be non-analytic; in the latter case the rate functions are analytic, but fluctuations are realised by entirely different means, which rely strongly on the particle-potential interaction. Finally, we check the validity of a fluctuation relation for the active work distribution. In the free-particle case, the relation is satisfied with a slope proportional to the bath temperature. The same slope is found for the harmonic potential, regardless of activity, and for an anharmonic potential with low activity. In the anharmonic case with high activity, instead, we find a different slope which is equal to an effective temperature obtained from the fluctuation-dissipation theorem.

cond-mat.stat-mech↗