arXiv subjects

Vincent Hakim

Publications and source records attributed to Vincent Hakim.

12 recordsLinked to original sources

arXiv2025

Place-cell heterogeneity underlies power-laws in hippocampal activity

Power-law scaling in coarse-grained data suggests critical dynamics, but the true source of this scaling often remains unclear. Here, we analyze neural activity recorded during spatial navigation, reproducing power-law scaling under a phenomenological renormalization group (PRG) procedure that clusters units by activity similarity. Such scaling was previously linked to criticality. Here, we show that the iterative nature of the procedure itself leads to the emergence of power laws when applied to heterogeneous, non-interacting units obeying spatially structured activity without requiring critical interactions. Furthermore, the scaling exponents produced by heteregeneous non-interacting units match the observed exponents in recorded neural data. A simplified version of the PRG further reveals how heterogeneity smooths transitions across scales, mimicking critical behavior. The resulting exponents depend systematically on system and population size, predictions confirmed by subsampling the data.

q-bio.NC↗

arXiv2025

From the perceptron to the cerebellum

The perceptron has served as a prototypical neuronal learning machine in the physics community interested in neural networks and artificial intelligence, which included G\'erard Toulouse as one of its prominent figures. It has also been used as a model of Purkinje cells of the cerebellum, a brain structure involved in motor learning, in the early influential theories of David Marr and James Albus. We review these theories, more recent developments in the field, and highlight questions of current interest.

q-bio.NC↗

arXiv2023

Metamorphoses of the flow past an obstacle of a resonantly-driven bistable polariton fluid

Motivated by recent experiments, we theoretically analyze the flow past an obstacle of a one-dimensional "quantum fluid of light" which is resonantly driven, and exhibits bistability. The flow is found to abruptly change several times when the fluid velocity or the obstacle potential strength are increased. In contrast to the cases of usual fluids and superfluids, the transitions take place between stationary states. They involve the fluid bistability in an essential way. Remarkably, at the transitions points, the fluid in the obstacle wake lies in the unstable intermediate density state.

cond-mat.quant-gas↗

arXiv2013

Beyond position weight matrices: nucleotide correlations in transcription factor binding sites and their description

The identification of transcription factor binding sites (TFBSs) on genomic DNA is of crucial importance for understanding and predicting regulatory elements in gene networks. TFBS motifs are commonly described by Position Weight Matrices (PWMs), in which each DNA base pair independently contributes to the transcription factor (TF) binding, despite mounting evidence of interdependence between base pairs positions. The recent availability of genome-wide data on TF-bound DNA regions offers the possibility to revisit this question in detail for TF binding {\em in vivo}. Here, we use available fly and mouse ChIPseq data, and show that the independent model generally does not reproduce the observed statistics of TFBS, generalizing previous observations. We further show that TFBS description and predictability can be systematically improved by taking into account pairwise correlations in the TFBS via the principle of maximum entropy. The resulting pairwise interaction model is formally equivalent to the disordered Potts models of statistical mechanics and it generalizes previous approaches to interdependent positions. Its structure allows for co-variation of two or more base pairs, as well as secondary motifs. Although models consisting of mixtures of PWMs also have this last feature, we show that pairwise interaction models outperform them. The significant pairwise interactions are found to be sparse and found dominantly between consecutive base pairs. Finally, the use of a pairwise interaction model for the identification of TFBSs is shown to give significantly different predictions than a model based on independent positions.

q-bio.GN↗

arXiv2008

Laws of crack motion and phase-field models of fracture

Recently proposed phase-field models offer self-consistent descriptions of brittle fracture. Here, we analyze these theories in the quasistatic regime of crack propagation. We show how to derive the laws of crack motion either by using solvability conditions in a perturbative treatment for slight departure from the Griffith threshold, or by generalizing the Eshelby tensor to phase-field models. The analysis provides a simple physical interpretation of the second component of the classic Eshelby integral in the limit of vanishing crack propagation velocity: it gives the elastic torque on the crack tip that is needed to balance the Herring torque arising from the anisotropic interface energy. This force balance condition reduces in this limit to the principle of local symmetry in isotropic media and to the principle of maximum energy release rate for smooth curvilinear cracks in anisotropic media. It can also be interpreted physically in this limit based on energetic considerations in the traditional framework of continuum fracture mechanics, in support of its general validity for real systems beyond the scope of phase-field models. Analytical predictions of crack paths in anisotropic media are validated by numerical simulations. Simulations also show that these predictions hold even if the phase-field dynamics is modified to make the failure process irreversible. In addition, the role of dissipative forces on the process zone scale as well as the extension of the results to motion of planar cracks under pure antiplane shear are discussed.

cond-mat.mtrl-sci↗

arXiv2005

A core genetic module : the Mixed Feedback Loop

The so-called Mixed Feedback Loop (MFL) is a small two-gene network where protein A regulates the transcription of protein B and the two proteins form a heterodimer. It has been found to be statistically over-represented in statistical analyses of gene and protein interaction databases and to lie at the core of several computer-generated genetic networks. Here, we propose and mathematically study a model of the MFL and show that, by itself, it can serve both as a bistable switch and as a clock (an oscillator) depending on kinetic parameters. The MFL phase diagram as well as a detailed description of the nonlinear oscillation regime are presented and some biological examples are discussed. The results emphasize the role of protein interactions in the function of genetic modules and the usefulness of modelling RNA dynamics explicitly.

q-bio.MN↗

arXiv2004

Crack Path Prediction in Anisotropic Brittle Materials

A force balance condition to predict quasistatic crack paths in anisotropic brittle materials is derived from an analysis of diffuse interface continuum models that describe both short-scale failure inside a microscopic process zone and macroscopic linear elasticity. The derivation exploits the gradient dynamics and translation symmetry properties of this class of models to define a generalized energy-momentum tensor whose integral around an arbitrary closed path enclosing the crack tip yields all forces acting on this tip, including Eshelby's configurational forces, cohesive forces, and dissipative forces. This condition is validated quantitatively by numerical simulations.

cond-mat.mtrl-sci↗

arXiv2002

Scroll waves in isotropic excitable media : linear instabilities, bifurcations and restabilized states

Scroll waves are three-dimensional analogs of spiral waves. The linear stability spectrum of untwisted and twisted scroll waves is computed for a two-variable reaction-diffusion model of an excitable medium. Different bands of modes are seen to be unstable in different regions of parameter space. The corresponding bifurcations and bifurcated states are characterized by performing direct numerical simulations. In addition, computations of the adjoint linear stability operator eigenmodes are also performed and serve to obtain a number of matrix elements characterizing the long-wavelength deformations of scroll waves.

cond-mat↗

arXiv2001

Giant vortices in the Ginzburg-Landau description of superconductivity

Recent experiments on mesoscopic samples and theoretical considerations lead us to analyze multiply charged ($n>1$) vortex solutions of the Ginzburg-Landau equations for arbitrary values of the Landau-Ginzburg parameter $κ$. For $n\gg 1$, they have a simple structure and a free energy ${\cal F}\sim n$. In order to relate this behaviour to the classic Abrikosov result ${\cal F}\sim n^2$ when $κ\to +\infty$, we consider the limit where both $n\gg 1$ and $κ\gg1$, and obtain a scaling function of the variable $κ/n$ that describes the cross-over between these two behaviours of ${\cal F}$. It is then shown that a small-n expansion can also be performed and the first two terms of this expansion are calculated. Finally, large and small n expansions are given for recently computed phenomenological exponents characterizing the free energy growth with $κ$ of a giant vortex.

cond-mat.supr-con↗

arXiv1999

Theory of spiral wave dynamics in weakly excitable media: asymptotic reduction to a kinematic model and applications

In a weakly excitable medium, characterized by a large threshold stimulus, the free end of an isolated broken plane wave (wave tip) can either rotate (steadily or unsteadily) around a large excitable core, thereby producing a spiral pattern, or retract causing the wave to vanish at boundaries. An asymptotic analysis of spiral motion and retraction is carried out in this weakly excitable large core regime starting from the free-boundary limit of the reaction-diffusion models, valid when the excited region is delimited by a thin interface. The wave description is shown to naturally split between the tip region and a far region that are smoothly matched on an intermediate scale. This separation allows us to rigorously derive an equation of motion for the wave tip, with the large scale motion of the spiral wavefront slaved to the tip. This kinematic description provides both a physical picture and exact predictions for a wide range of wave behavior, including: (i) steady rotation (frequency and core radius), (ii) exact treatment of the meandering instability in the free-boundary limit with the prediction that the frequency of unstable motion is half the primary steady frequency (iii) drift under external actions (external field with application to axisymmetric scroll ring motion in three-dimensions, and spatial or/and time-dependent variation of excitability), and (iv) the dynamics of multi-armed spiral waves with the new prediction that steadily rotating waves with two or more arms are linearly unstable. Numerical simulations of FitzHug-Nagumo kinetics are used to test several aspects of our results. In addition, we discuss the semi-quantitative extension of this theory to finite cores and pinpoint mathematical subtleties related to the thin interface limit of singly diffusive reaction-diffusion models.

cond-mat.soft↗

arXiv1996

Persistent spins in the linear diffusion approximation of phase ordering and zeros of stationary gaussian processes

The fraction r(t) of spins which have never flipped up to time t is studied within a linear diffusion approximation to phase ordering. Numerical simulations show that, even in this simple context, r(t) decays with time like a power-law with a non-trival exponent $θ$ which depends on the space dimension. The local dynamics at a given point is a special case of a stationary gaussian process of known correlation function and the exponent $θ$ is shown to be determined by the asymptotic behavior of the probability distribution of intervals between consecutive zero-crossings of this process. An approximate way of computing this distribution is proposed, by taking the lengths of the intervals between successive zero-crossings as independent random variables. The approximation gives values of the exponent $θ$ in close agreement with the results of simulations.

cond-mat↗

arXiv1995

Exact first-passage exponents of 1D domain growth: relation to a reaction diffusion model

In the zero temperature Glauber dynamics of the ferromagnetic Ising or $q$-state Potts model, the size of domains is known to grow like $t^{1/2}$. Recent simulations have shown that the fraction $r(q,t)$ of spins which have never flipped up to time $t$ decays like a power law $r(q,t) \sim t^{-θ(q)}$ with a non-trivial dependence of the exponent $θ(q)$ on $q$ and on space dimension. By mapping the problem on an exactly soluble one-species coagulation model ($A+A\rightarrow A$), we obtain the exact expression of $θ(q)$ in dimension one.

hep-th↗