arXiv subjects

Simonetta Filippi

Publications and source records attributed to Simonetta Filippi.

18 recordsLinked to original sources

arXiv2025

Impact of Electric Spatially Discordant Alternans on Cardiac Magnetic Field

Spatially discordant alternans (SDA) play a crucial role in cardiac arrhythmogenesis by creating steep repolarization gradients facilitating conduction block and reentry. While traditionally studied using electrical indicators, this work provides a novel perspective by characterizing SDA through their magnetic field signatures. Using a one-dimensional cardiac fiber model, we demonstrate that magnetic field measurements effectively detect SDA and temperature dependent changes in cardiac action potentials, offering a non-invasive alternative to conventional electrophysiological metrics. Our results reveal that the spatial organization of SDA is mirrored in the magnetic field distribution, with SDA nodes clearly identifiable via spatial mapping. Notably, magnetic restitution curves exhibit a distinct pattern from APD-based indicators, closely following the dynamics of the action potential upstroke. These findings establish the cardiac magnetic field as a powerful diagnostic tool for detecting SDA, opening new avenues for biomagnetic monitoring of arrhythmic risk.

physics.med-ph↗

arXiv2024

A statistical mechanics investigation of Unfolded Protein Response across organisms

Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a critical threshold. It maintains cell homeostasis by enhancing protein folding, initiating quality control, and activating degradation pathways when damage is irreversible. This response functions as a dynamic signaling network, with proteins as nodes and their interactions as edges. We analyze these protein-protein networks across different organisms to understand their intricate intra-cellular interactions and behaviors. In this work, analyzing twelve organisms, we assess how fundamental measures in network theory can individuate seed-proteins and specific pathways across organisms. We employ network robustness to evaluate and compare the strength of the investigated PPI networks, and the structural controllability of complex networks to find and compare the sets of driver nodes necessary to control the overall networks. We find that network measures are related to phylogenetics, and advanced network methods can identify main pathways of significance in the complete Unfolded Protein Response mechanism.

physics.bio-ph↗

arXiv2024

Magnetic Signature of Thermo-Electric Cardiac Dynamics

Developing new methods for predicting electromagnetic instabilities in cardiac activity is of primary importance. However, we still need a comprehensive view of the heart's magnetic activity at the tissue scale. To fill this gap, we present a model of soft active matter, including thermo-electric coupling, suitably modified to reproduce cardiac magnetic field. Our theoretical framework shows that periodic stimulations of cardiac cells create an external magnetic field evidencing restitution features of nonlinear cardiac dynamics and magnetic restitution curves better discriminate instabilities and bifurcations in cardiac activity. This new framework lays the foundation for innovative, non-invasive diagnostic tools for cardiac arrhythmias.

physics.med-ph↗

arXiv2023

Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as test case for Lattice Boltzmann -- All Atom Molecular Dynamics Coupling

Physiological solvent flows surround biological structures triggering therein collective motions. Notable examples are virus/host-cell interactions and solvent-mediated allosteric regulation. The present work describes a multiscale approach joining the Lattice Boltzmann fluid dynamics (for solvent flows) with the all-atom atomistic molecular dynamics (for proteins) to model functional interactions between flows and molecules. We present, as an applicative scenario, the study of the SARS-CoV-2 virus spike glycoprotein protein interacting with the surrounding solvent, modeled as a mesoscopic fluid. The equilibrium properties of the wild-type spike and of the Alpha variant in implicit solvent are described by suitable observables. The mesoscopic solvent description is critically compared to the all-atom solvent model, to quantify the advantages and limitations of the mesoscopic fluid description.

physics.comp-ph↗

arXiv2023

Structural Controllability to Unveil Hidden Regulation Mechanisms in Unfolded Protein Response: the Role of Network Models

The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biological point of view, much of the literature lacks a quantitative analysis of such a central signaling pathway. In this work, we aim to fill this gap by applying structural controllability analysis of complex networks to several Unfolded Protein Response networks to identify crucial nodes in the signaling flow. In particular, we first build different network models of the Unfolded Protein Response mechanism, relying on data contained in various protein-protein interaction databases. Then, we identify the driver nodes, essential for overall network control, i.e., the key proteins on which external stimulation may be optimally delivered to control network behavior. Our structural controllability analysis results show that the driver nodes commonly identified across databases match with known endoplasmic reticulum stress sensors. This potentially confirms that the theoretically identified drivers correspond to the biological key proteins associated with fundamental cellular activities and diseases. In conclusion, we prove that structural controllability is a reliable quantitative tool to investigate biological signaling pathways, and it can be potentially applied to networks more complex and less explored than Unfolded Protein Response.

q-bio.MN↗

arXiv2018

Modelling thermo-electro-mechanical effects in orthotropic cardiac tissue

In this paper we introduce a new mathematical model for the active contraction of cardiac muscle, featuring different thermo-electric and nonlinear conductivity properties. The passive hyperelastic response of the tissue is described by an orthotropic exponential model, whereas the ionic activity dictates active contraction incorporated through the concept of orthotropic active strain. We use a fully incompressible formulation, and the generated strain modifies directly the conductivity mechanisms in the medium through the pull-back transformation. We also investigate the influence of thermo-electric effects in the onset of multiphysics emergent spatiotemporal dynamics, using nonlinear diffusion. It turns out that these ingredients have a key role in reproducing pathological chaotic dynamics such as ventricular fibrillation during inflammatory events, for instance. The specific structure of the governing equations suggests to cast the problem in mixed-primal form and we write it in terms of Kirchhoff stress, displacements, solid pressure, electric potential, activation generation, and ionic variables. We also propose a new mixed-primal finite element method for its numerical approximation, and we use it to explore the properties of the model and to assess the importance of coupling terms, by means of a few computational experiments in 3D.

q-bio.TO↗

arXiv2018

Spatiotemporal correlation uncovers fractional scaling in cardiac tissue

Complex spatiotemporal patterns of action potential duration have been shown to occur in many mammalian hearts due to a period-doubling bifurcation that develops with increasing frequency of stimulation. Here, through high-resolution optical mapping and numerical simulations, we quantify voltage length scales in canine ventricles via spatiotemporal correlation analysis as a function of stimulation frequency and during fibrillation. We show that i) length scales can vary from 40 to 20 cm during one to one responses, ii) a critical decay length for the onset of the period-doubling bifurcation is present and decreases to less than 3 cm before the transition to fibrillation occurs, iii) fibrillation is characterized by a decay length of about 1 cm. On this evidence, we provide a novel theoretical description of cardiac decay lengths introducing an experimental-based conduction velocity dispersion relation that fits the measured wavelengths with a fractional diffusion exponent of 1.5. We show that an accurate phenomenological mathematical model of the cardiac action potential, fine-tuned upon classical restitution protocols, can provide the correct decay lengths during periodic stimulations but that a domain size scaling via the fractional diffusion exponent of 1.5 is necessary to reproduce experimental fibrillation dynamics. Our study supports the need of generalized reaction-diffusion approaches in characterizing the multiscale features of action potential propagation in cardiac tissue. We propose such an approach as the underlying common basis of synchronization in excitable biological media.

physics.bio-ph↗

arXiv2017

On the last stable orbit around rapidly rotating neutron stars

We compute the binding energy and angular momentum of a test-particle at the last stable circular orbit (LSO) on the equatorial plane around a general relativistic, rotating neutron star (NS). We present simple, analytic, but accurate formulas for these quantities that fit the numerical results and which can be used in several astrophysical applications. We demonstrate the accuracy of these formulas for three different equations of state (EOS) based on nuclear relativistic mean-field theory models and argue that they should remain still valid for any NS EOS that satisfy current astrophysical constraints. We compare and contrast our numerical results with the corresponding ones for the Kerr metric characterized by the same mass and angular momentum.

astro-ph.HE↗

arXiv2017

A note on stress-driven anisotropic diffusion and its role in active deformable media

We propose a new model to describe diffusion processes within active deformable media. Our general theoretical framework is based on physical and mathematical considerations, and it suggests to use diffusion tensors directly coupled to mechanical stress. A proof-of-concept experiment and the proposed generalised reaction-diffusion-mechanics model reveal that initially isotropic and homogeneous diffusion tensors turn into inhomogeneous and anisotropic quantities due to the intrinsic structure of the nonlinear coupling. We study the physical properties leading to these effects, and investigate mathematical conditions for its occurrence. Together, the experiment, the model, and the numerical results obtained using a mixed-primal finite element method, clearly support relevant consequences of stress-assisted diffusion into anisotropy patterns, drifting, and conduction velocity of the resulting excitation waves. Our findings also indicate the applicability of this novel approach in the description of mechano-electrical feedback in actively deforming bio-materials such as the heart.

q-bio.TO↗

arXiv2015

Fast Rotating Neutron Stars with Realistic Nuclear Matter Equation of State

We construct equilibrium configurations of uniformly rotating neutron stars for selected relativistic mean-field nuclear matter equations of state (EOS). We compute in particular the gravitational mass ($M$), equatorial ($R_{\rm eq}$) and polar ($R_{\rm pol}$) radii, eccentricity, angular momentum ($J$), moment of inertia ($I$) and quadrupole moment ($M_2$) of neutron stars stable against mass-shedding and secular axisymmetric instability. By constructing the constant frequency sequence $f=716$ Hz of the fastest observed pulsar, PSR J1748-2446ad, and constraining it to be within the stability region, we obtain a lower mass bound for the pulsar, $M_{\rm min}=[1.2$-$1.4] M_\odot$, for the EOS employed. Moreover we give a fitting formula relating the baryonic mass ($M_b$) and gravitational mass of non-rotating neutron stars, $M_b/M_\odot=M/M_\odot+(13/200)(M/M_\odot)^2$ [or $M/M_\odot=M_b/M_\odot-(1/20)(M_b/M_\odot)^2$], which is independent on the EOS. We also obtain a fitting formula, although not EOS independent, relating the gravitational mass and the angular momentum of neutron stars along the secular axisymmetric instability line for each EOS. We compute the maximum value of the dimensionless angular momentum, $a/M\equiv c J/(G M^2)$ (or "Kerr parameter"), $(a/M)_{\rm max}\approx 0.7$, found to be also independent on the EOS. We compare and contrast then the quadrupole moment of rotating neutron stars with the one predicted by the Kerr exterior solution for the same values of mass and angular momentum. Finally we show that, although the mass quadrupole moment of realistic neutron stars never reaches the Kerr value, the latter is closely approached from above at the maximum mass value, as physically expected from the no-hair theorem. In particular the stiffer the EOS is, the closer the Kerr solution is approached.

astro-ph.SR↗

arXiv2014

The effective geometry of the $n=1$ uniformly rotating self-gravitating polytrope

The \lq\lq effective geometry" formalism is used to study the perturbations of a perfect barotropic Newtonian self-gravitating rotating and compressible fluid coupled with gravitational backreaction. The case of a uniformly rotating polytrope with index $n=1$ is investigated, due to its analytical tractability. Special attention is devoted to the geometrical properties of the underlying background acoustic metric, focusing in particular on null geodesics as well as on the analog light cone structure.

gr-qc↗

arXiv2014

C metric: the equatorial plane and Fermi coordinates

We discuss geodesic motion in the vacuum C metric using Bondi-like spherical coordinates, with special attention to the role played by the "equatorial plane." We show that the spatial trajectory of photons on such a hypersurface is formally the same of photons on the equatorial plane of the Schwarzschild spacetime, apart from an energy shift involving the spacetime acceleration parameter. Furthermore, we show that photons starting their motion from this hypersurface with vanishing component of the momentum along $θ$, remain confined on it, differently from the case of massive particles. This effect is shown to have a counterpart also in the massless limit of the C metric, i.e. in Minkowski spacetime. Finally, we give the explict map between Bondi-like spherical coordinates and Fermi coordinates (up to the second order) for the world line of an observer at rest at a fixed spatial point of the equatorial plane of the C metric, a result which may be eventually useful to estimate both the mass and the acceleration parameter of accelerated sources.

gr-qc↗

arXiv2014

On the coherent behavior of pancreatic beta cell clusters

Beta cells in pancreas represent an example of coupled biological oscillators which via communication pathways, are able to synchronize their electrical activity, giving rise to pulsatile insulin release. In this work we numerically analyze scale free self-similarity features of membrane voltage signal power density spectrum, through a stochastic dynamical model for beta cells in the islets of Langerhans fine tuned on mouse experimental data. Adopting the algebraic approach of coherent state formalism, we show how coherent molecular domains can arise from proper functional conditions leading to a parallelism with "phase transition" phenomena of field theory.

cond-mat.soft↗

arXiv2010

Wave-train induced unpinning of weakly anchored vortices in excitable media

A free vortex in excitable media can be displaced and removed by a wave-train. However, simple physical arguments suggest that vortices anchored to large inexcitable obstacles cannot be removed similarly. We show that unpinning of vortices attached to obstacles smaller than the core radius of the free vortex is possible through pacing. The wave-train frequency necessary for unpinning increases with the obstacle size and we present a geometric explanation of this dependence. Our model-independent results suggest that decreasing excitability of the medium can facilitate pacing-induced removal of vortices in cardiac tissue.

physics.bio-ph↗

arXiv2009

Extended bodies with quadrupole moment interacting with gravitational monopoles: reciprocity relations

An exact solution of Einstein's equations representing the static gravitational field of a quasi-spherical source endowed with both mass and mass quadrupole moment is considered. It belongs to the Weyl class of solutions and reduces to the Schwarzschild solution when the quadrupole moment vanishes. The geometric properties of timelike circular orbits (including geodesics) in this spacetime are investigated. Moreover, a comparison between geodesic motion in the spacetime of a quasi-spherical source and non-geodesic motion of an extended body also endowed with both mass and mass quadrupole moment as described by Dixon's model in the gravitational field of a Schwarzschild black hole is discussed. Certain "reciprocity relations" between the source and the particle parameters are obtained, providing a further argument in favor of the acceptability of Dixon's model for extended bodies in general relativity.

gr-qc↗

arXiv2005

Dark matter from the scalar sector of 3-3-1 models without exotic electric charges

We show that three SU(2) singlet neutral scalars (two CP-even and one CP-odd) in the spectrum of models based on the gauge symmetry SU(3)_c X SU(3)_L X U(1)_X, which do not contain exotic electric charges, are realistic candidates for thermally generated self-interacting dark matter in the Universe, a type of dark matter that has been recently proposed in order to overcome some difficulties of collisionless cold dark matter models at the galactic scale. These candidates arise without introducing a new mass scale in the model and/or without the need for a discrete symmetry to stabilize them, but at the expense of tuning several combinations of parameters of the scalar potential.

hep-ph↗

arXiv2005

Using FEMLAB for Gravitational problems: numerical simulations for all

We discuss the possibility to solve Modern Numerical Relativity problems using finite element methods (FEM). Adopting a "user friendly" software for handling totally general systems of nonlinear partial differential equations, FEMLAB, we model and numerically solve in a short time a Gowdy vacuum spacetime, representing an inhomogeneous cosmology. Results agree perfectly with existing simulations in the recent literature based not of FEMs but on finite differences methods. Possible applications for non relativistic Astrophysics, General Relativity, elementary particle physics and more general theories of gravitation like EMDA and branes are discussed.

gr-qc↗

arXiv2001

Damping time and stability of density fermion perturbations in the expanding universe

The classic problem of the growth of density perturbations in an expanding Newtonian universe is revisited following the work of Bisnovatyi-Kogan and Zel'dovich. We propose a more general analytical approach: a system of free particles satisfying semi-degenerate Fermi-Dirac statistics on the background of an exact expanding solution is examined in the linear approximation. This differs from the corresponding work of Bisnovatyi-Kogan and Zel'dovich where classical particles fulfilling Maxwell-Boltzmann statistics were considered. The solutions of the Boltzmann equation are obtained by the method of characteristics. An expression for the damping time of a decaying solution is discussed and a zone in which free streaming is hampered is found, corresponding to wavelengths less than the Jeans one. In the evolution of the system, due to the decrease of the Jeans length, those perturbations may lead to gravitational collapse. At variance with current opinions, we deduce that perturbations with lambda >=lambda_(J Max)/1.48 are able to generate structures and the lower limit for substructures mass is M = M_(J max)/(1.48)^3 ~ M_(J max)/3, where M_(J max) is the maximum value of the Jeans mass.

astro-ph↗