arXiv subjects

Francesco Viola

Publications and source records attributed to Francesco Viola.

18 recordsLinked to original sources

arXiv2026

Amphibian water to land transition reveals physical limits of olfaction

The evolutionary transition from water to land required animals to sense and respond to drastically different environments. Chemicals diffuse four orders of magnitude more slowly in water than in air, requiring significant remodeling of the olfactory system. Amphibians provide a powerful model to analyze these adaptations because they transition from an aquatic to terrestrial state during a single lifetime following metamorphosis. Here we exploit laboratory-induced metamorphosis of adult Ambystoma mexicanum to ask how fundamental chemical properties impact aquatic versus terrestrial olfaction. By combining asymptotic theory with numerical simulations using reconstructed olfactory chamber morphologies, we find that odor adsorption takes tens of seconds in water compared to milliseconds in air. Adsorption of an ephemeral odor whiff is maximized at an inhalation speed of $\sim$\SI{20}{\centi\meter\per\second} in air vs near zero in water, matching our measurements of negligible aquatic inhalation. Nevertheless, aquatic axolotls quickly respond to introduced odorant molecules. While morphological differences in the olfactory chamber of aquatic versus terrestrial axolotls are nearly irrelevant, aquatic olfactory cilia may pump water to significantly speed up the rate of odor adsorption. Together with adaptive behavioral responses that reduce proximity to the target, the wait time can reduce to less than one second. Thus, while aquatic olfaction is slower than terrestrial olfaction, aquatic animals exhibit anatomical and behavioral adaptations that support chemical detection as a proximal sense.

physics.bio-ph↗

arXiv2026

An interaction potential method for passive and active dynamics of hyperelastic materials

Simulating active biological tissues, such as the myocardium, requires constitutive models that are both physically faithful and computationally efficient. The most common approach relies on finite element methods that accurately discretize the underlying continuum hyperelastic problem which, in turn, require global nonlinear solve at each time step. On the other hand, fast, interaction-potential methods replace the continuum with a network of independent links approximating the mechanical response. We propose an interaction potential formulation for simulating active biological tissues that bridges this gap. The method recasts continuum hyperelastic constitutive laws in terms of tetrahedral edge strain. Unlike classical mass-spring models, the proposed formulation does not approximate the tissue as independent spring elements but preserves the energetic coupling between adjacent edges. Passive tissue mechanics is described by hyperelastic constitutive laws, while active contraction is incorporated through the active-strain multiplicative decomposition. Within the edge-based formulation, the active strain is incorporated through a time-dependent activated reference configuration. We further introduce a strategy for enforcing the material incompressibility constraint while avoiding volumetric locking. The resulting method can be interpreted as an edge-strain representation of a constant-strain tetrahedral continuum element, providing a bridge between continuum mechanics and discrete interaction potential solvers. Numerical tests demonstrate the capability of the method to effectively simulate different hyperelastic constitutive laws and to properly preserve the energy balance equation. Finally, the proposed method is applied to the active deformation of a realistic ventricle, reproducing longitudinal shortening and wall-thickening values consistent with the literature.

physics.comp-ph↗

arXiv2026

Flexibility as a Universal Nature-Inspired Mechanism for Thrust Enhancement

Nature has equipped jet-propelled swimmers with flexible nozzles that outperform rigid ones, yet the origin of this advantage has remained unexplained. By tracking where and when energy is exchanged between fluid and structure, three-dimensional numerical simulations resolve the underlying mechanism: a standing-wave response of the nozzle, in which the structure dilates and then recoils synchronously, charging and releasing energy to enhance thrust. Outside of this regime, the structure exhibits a traveling wave response, with expansion and contraction coexisting along the nozzle, reducing the thrust gain. We propose a physics-based model that captures the boundary between standing and traveling responses in a closed form, showing that the optimum occurs when the natural period of the structure matches the pulse duration. Beyond this optimum the strain imposed by the nozzle curvature required for steering selects the geometry observed across marine species. The propulsion and maneuverability are reconciled within a single framework that yields design principles for soft robotic propulsors.

physics.flu-dyn↗

arXiv2026

From Raw Segmentations to Simulation-Ready Cardiac Meshes: An Automated Framework for Anatomical Reconstruction and Virtual Cohort Generation

Computational models of the human heart are widely used to study electromechanical and fluid-dynamical cardiac function and to support applications such as in silico clinical trials. However, most studies remain limited to single or patient-specific anatomies, restricting the inclusion of population-level variability required for uncertainty quantification. A key challenge is translating medical-image segmentations, which may contain artifacts, mesh defects or disjoint domains, into topologically coherent geometries suitable for multiphysics simulations. In this work, we present a semi-automatic pipeline that converts CT-based segmentations into simulation-ready cardiac meshes within a few minutes while preserving anatomical and topological consistency. Building on modern deep learning segmentation methods, the framework incorporates a template-based registration stage to regularize artifacts and enforce mesh-quality constraints. A Chamfer-distance morphing strategy deforms a high-quality template toward each segmented heart, matching individual chambers while preserving topology. The resulting meshes are watertight, isotopological, and endowed with consistent point-to-point correspondence. The pipeline is validated on 58 healthy cardiac CT scans, including all cardiac chambers and proximal vessel segments. The resulting meshes can be represented in a unified shape space, enabling the construction of a statistical shape model of the heart and major vessels. Principal Component Analysis shows that a low-dimensional latent space efficiently captures population variability, while Gaussian Mixture Modeling enables synthetic anatomy generation. Overall, the proposed framework (released open-source) provides a pathway from raw segmentations to simulation-ready cardiac geometries, enabling anatomically consistent virtual cohorts for large-scale in silico studies.

cs.CV↗

arXiv2026

A fast and consistent sharp-interface immersed boundary method for moving bodies of arbitrary thickness

Immersed boundary methods (IBMs) are widely used to simulate flows around complex geometries and moving bodies, but they often involve a trade-off between precision and computational efficiency. Eulerian formulations require special treatments for moving walls and may generate spurious force oscillations, whereas Lagrangian formulations can suffer from slip errors at the immersed surfaces. We propose a novel sharp-interface IBM for incompressible flows involving moving, deformable, and arbitrary-thickness bodies. The method combines a fast tagging algorithm, a two-sided Eulerian forcing strategy, and a consistent mass correction that reduces the splitting error of fractional-step schemes, while preserving the structure of the discrete Laplacian operator. This formulation retains the efficiency of direct Poisson solvers, thus avoiding the overhead of cut-cell, multigrid, and projection-based approaches. The method naturally handles moving boundaries, and yields small transpiration errors with second-order accuracy in the enforcement of the no-slip condition. Numerical tests using rigid, deformable, turbulent, and biologically inspired flows demonstrate the accuracy, robustness, and efficiency of the method, without compromising computational cost.

physics.flu-dyn↗

arXiv2025

Graph-Convolutional-Beta-VAE for Synthetic Abdominal Aorta Aneurysm Generation

Synthetic data generation plays a crucial role in medical research by mitigating privacy concerns and enabling large-scale patient data analysis. This study presents a beta-Variational Autoencoder Graph Convolutional Neural Network framework for generating synthetic Abdominal Aorta Aneurysms (AAA). Using a small real-world dataset, our approach extracts key anatomical features and captures complex statistical relationships within a compact disentangled latent space. To address data limitations, low-impact data augmentation based on Procrustes analysis was employed, preserving anatomical integrity. The generation strategies, both deterministic and stochastic, manage to enhance data diversity while ensuring realism. Compared to PCA-based approaches, our model performs more robustly on unseen data by capturing complex, nonlinear anatomical variations. This enables more comprehensive clinical and statistical analyses than the original dataset alone. The resulting synthetic AAA dataset preserves patient privacy while providing a scalable foundation for medical research, device testing, and computational modeling.

cs.LG↗

arXiv2025

Lagrangian analysis of turbulent blood flow in the human left heart

We present a Lagrangian analysis of turbulent blood flow in the human left heart using high-fidelity simulations based on a patient-specific anatomical model. Leveraging a fully coupled fluid-structure-electrophysiology interaction (FSEI) framework, we track the motion of Lagrangian (passive) tracers to investigate the multiscale statistical properties of velocity fluctuations over more than four decades. Our analysis reveals strong Lagrangian intermittency throughout the left heart, reflecting the complex and unsteady nature of cardiovascular flow. The present work underscores the sensitivity of Lagrangian statistics to physiological parameters and highlights their potential for improving the understanding of pathological flow conditions in cardiovascular systems. Such Lagrangian tool provides a statistical foundation for modeling shear-induced damage in red blood cells (hemolysis), with implications for the evaluation of prosthetic valves and blood-contacting medical devices.

physics.flu-dyn↗

arXiv2025

Hemodynamic effects of intra- and supra- deployment locations for a bioprosthetic aortic valve

Aortic valve replacement is a key surgical procedure for treating aortic valve pathologies, such as stenosis and regurgitation. The precise placement of the prosthetic valve relative to the native aortic annulus plays a critical role in the post-operative hemodynamics. This study investigates how the positioning of a biological prosthetic valve -- either intra-annular (within the native annulus) or supra-annular (slightly downstream, in the widened portion of the aortic root) -- affects cardiac fluid dynamics. Using high-fidelity numerical simulations on a patient-specific left heart model derived from CT imaging, we simulate physiological flow conditions to isolate the impact of valve placement. Unlike previous clinical studies that compare different patients and valve models, our approach evaluates the same valve in both positions within a single virtual patient, ensuring a controlled comparison. Key hemodynamic parameters are assessed, including transvalvular pressure drop, effective orifice area, wall shear stress, and hemolysis. Results reveal that supra-annular implantation offers significant advantages: lower pressure gradients, larger orifice area, and reduced shear-induced stress. Furthermore, hemolysis analysis using advanced red blood cell stress models indicates a decreased risk of blood damage in the supra-annular configuration. These findings offer valuable insights to guide valve selection and implantation strategies, ultimately supporting improved patient outcomes.

physics.med-ph↗

arXiv2025

An Insight into Parameter Identifiability Issues in the Carreau-Yasuda Model: a More Consistent Rheological Formulation for Shear-thinning non-Newtonian Inelastic Fluids

The Carreau-Yasuda rheological model is widely employed in both research and industrial applications to describe the shear-thinning behaviour of non-Newtonian inelastic fluids. However, the model parameter traditionally employed to characterize the shear thinning response exhibits only a weak correlation with the actual shear thinning rate observed in experimental data. This limitation leads to intrinsic identifiability issues, which may result in misleading physical interpretations of the model parameters and unreliable flow predictions. Aiming to contribute to overcoming these issues, this paper introduces a novel heuristic rheological formulation for shear-thinning non-Newtonian inelastic fluids, as an alternative to the Carreau-Yasuda model. Analytical results and exemplary numerical case studies demonstrate that the proposed formulation is based on physically meaningful model parameters, whose identifiability is not compromised by the key limitations of the Carreau-Yasuda model. The new approach allows for effective parameter estimation through a straightforward direct identification strategy, eliminating the need for inverse identification procedures based on nonlinear regression techniques. Moreover, the proposed formulation naturally enables the identication of two Carreau numbers based on the two characteristic shear rates of the fluid.

physics.flu-dyn↗

arXiv2025

A Quasi-Analytical Solution for "Carreau-Yasuda-like" Shear-thinning Fluids Flowing in Slightly Tapered Pipes

This paper presents a quasi-analytical framework for "Carreau-Yasuda-like" fluids with a viscosity characterized by two constant plateau at low and high shear rates connected by a shear-thinning branch, and flowing in slightly tapered pipes. This setup is common in research and industrial applications since the last century, by assuming both a Newtonian or a non-Newtonian inelastic behaviour. Nevertheless, an analytical solution for "Carreau-Yasuda-like" fluids is still lacking. The expressions have been derived by using the order-of-magnitude analysis and neglecting the inertial terms in the momentum balance equations. The analytical solutions are employed to an extrusion bioprinting process as an application example, and verified through numerical procedures.

physics.flu-dyn↗

arXiv2025

Effect of swimming mode on shielding of odor traces in turbulence

Marine organisms manipulate their surrounding flow through their swimming dynamics, which affects the transport of their own odor cues. We demonstrate by direct numerical simulations how a group of swimmers, moving at intermediate Reynolds numbers, immersed in a turbulent flow, alter the shape of the odor plume they release in the water. Odor mixing is enhanced by increased velocity fluctuations and a swimmer-induced flow circulation that widens the odor plume at close range while speeding up dilution of the chemical trace. Beyond a short-range increase in the likelihood of being detected, swimming considerably reduces detections with effects that can persist at distances on the order of ten times the size of the group or more. We find that pullerlike swimmers are more effective at olfactory shielding than pusherlike swimmers. We trace this difference back to the dynamics at the swimmer location, which tends to trap odor at the source for pushers and to dilute it for pullers. Olfactory shielding is robust to changes in the conditions, and is more pronounced for weak turbulent Reynolds numbers and large swimmer Reynolds numbers. Our results suggest that olfactory shielding may play a role in the emergence of different swimming modalities by marine organisms.

physics.flu-dyn↗

arXiv2023

A revised gap-averaged Floquet analysis of Faraday waves in Hele-Shaw cells

Existing theoretical analyses of Faraday waves in Hele-Shaw cells rely on the Darcy approximation and assume a parabolic flow profile in the narrow direction. However, Darcy's model is known to be inaccurate when convective or unsteady inertial effects are important. In this work, we propose a gap-averaged Floquet theory accounting for inertial effects induced by the unsteady terms in the Navier-Stokes equations, a scenario that corresponds to a pulsatile flow where the fluid motion reduces to a two-dimensional oscillating Poiseuille flow, similarly to the Womersley flow in arteries. When gap-averaging the linearized Navier-Stokes equation, this results in a modified damping coefficient, which is a function of the ratio between the Stokes boundary layer thickness and the cell's gap, and whose complex value depends on the frequency of the wave response specific to each unstable parametric region. We first revisit the standard case of horizontally infinite rectangular Hele-Shaw cells by also accounting for a dynamic contact angle model. A comparison with existing experiments shows the predictive improvement brought by the present theory and points out how the standard gap-averaged model often underestimates the Faraday threshold. The analysis is then extended to the less conventional case of thin annuli. A series of dedicated experiments for this configuration highlights how Darcy's thin-gap approximation overlooks a frequency detuning that is essential to correctly predict the locations of the Faraday tongues in the frequency-amplitude parameter plane. These findings are well rationalized and captured by the present model.

physics.flu-dyn↗

arXiv2022

Sub-harmonic parametric instability in nearly-brimful circular-cylinders: a weakly nonlinear analysis

In lab-scale Faraday experiments, meniscus waves respond harmonically to small-amplitude forcing without threshold, hence potentially cloaking the instability onset of parametric waves. Their suppression can be achieved by resorting to a contact line pinned at the container brim with static contact angle $\theta_s=90^{\circ}$ (brimful condition). However, tunable meniscus waves are desired in some applications as those of liquid-based biosensors, where they can be controlled adjusting the shape of the static meniscus by slightly under/over-filling the vessel ($\theta_s\ne90^{\circ}$) while keeping the contact line fixed at the brim. Here, we refer to this wetting condition as nearly-brimful. Although classic inviscid theories based on Floquet analysis have been reformulated for the case of a pinned contact line (Kidambi 2013), accounting for (i) viscous dissipation and (ii) static contact angle effects, including meniscus waves, makes such analyses practically intractable and a comprehensive theoretical framework is still lacking. Aiming at filling this gap, in this work we formalize a weakly nonlinear analysis via multiple timescale method capable to predict the impact of (i) and (ii) on the instability onset of viscous sub-harmonic standing waves in both brimful and nearly-brimful circular-cylinders. Notwithstanding that the form of the resulting amplitude equation is in fact analogous to that obtained by symmetry arguments (Douady 1990), the normal form coefficients are here computed numerically from first principles, thus allowing us to rationalize and systematically quantify the modifications on the Faraday tongues and on the associated bifurcation diagrams induced by the interaction of meniscus and sub-harmonic parametric waves.

physics.flu-dyn↗

arXiv2021

A fast computational model for the electrophysiology of the whole human heart

In this study we present a novel computational model for unprecedented simulations of the whole cardiac electrophysiology. According to the heterogeneous electrophysiologic properties of the heart, the whole cardiac geometry is decomposed into a set of coupled conductive media having different topology and electrical conductivities: (i) a network of slender bundles comprising a fast conduction atrial network, the AV-node and the ventricular bundles; (ii) the Purkinje network; and (iii) the atrial and ventricular myocardium. The propagation of the action potential in these conductive media is governed by the bidomain/monodomain equations, which are discretized in space using an in-house finite volume method and coupled to three different cellular models, the Courtemanche model [1] for the atrial myocytes, the Stewart model [2] for the Purkinje Network and the ten Tusscher-Panfilov model [3] for the ventricular myocytes. The developed numerical model correctly reproduces the cardiac electrophysiology of the whole human heart in healthy and pathologic conditions and it can be tailored to study and optimize resynchronization therapies or invasive surgical procedures. Importantly, the whole solver is GPU-accelerated using CUDA Fortran providing an unprecedented speedup, thus opening the way for systematic parametric studies and uncertainty quantification analyses.

physics.med-ph↗

arXiv2021

Direct numerical simulation of flapping flags in grid-induced turbulence

A fully-resolved direct-numerical-simulation (DNS) approach for investigating flexible bodies forced by a turbulent incoming flow is designed to study the flapping motion of a flexible flag at moderate Reynolds number. The incoming turbulent flow is generated by placing a passive grid at the inlet of the numerical domain and the turbulence level of the flow impacting the flag can be controlled by changing its downstream distance from the grid. The computational framework is based on the immersed boundary method for dealing with arbitrary geometries and implemented using a graphics-processing-unit (GPU) accelerated parallelisation to increase the computational efficiency. The grid-induced turbulent flow is first characterised by means of the comparison with well-known results for decaying turbulence and a scale-by-scale analysis. Then, the flag-in-the-wind problem is revisited by exploring the effect of the turbulence intensity on self-sustained flapping. Whilst the latter is still manifesting under strong fluctuations, the main features of the oscillation (including its amplitude and frequency) are altered by turbulence, whose fingerprint can also be qualitatively detected by spectral analysis. Besides their relevance for advancing the fundamental understanding of fluid-structure interaction in turbulence, these findings have potential impact for related applications, e.g., aeroelastic energy harvesting or flow control techniques.

physics.flu-dyn↗

arXiv2021

FSEI-GPU: GPU accelerated simulations of the fluid-structure-electrophysiology interaction in the left heart

The reliability of cardiovascular computational models depends on the accurate solution of the hemodynamics, the realistic characterization of the hyperelastic and electric properties of the tissues along with the correct description of their interaction. The resulting fluid-structure-electrophysiology interaction (FSEI) thus requires an immense computational power, usually available in large supercomputing centers, and requires long time to obtain results even if multi-CPU processors are used (MPI acceleration). In recent years, graphics processing units (GPUs) have emerged as a convenient platform for high performance computing, as they allow for considerable reductions of the time-to-solution. This approach is particularly appealing if the tool has to support medical decisions that require solutions within reduced times and possibly obtained by local computational resources. Accordingly, our multi-physics solver has been ported to GPU architectures using CUDA Fortran to tackle fast and accurate hemodynamics simulations of the human heart without resorting to large-scale supercomputers. This work describes the use of CUDA to accelerate the FSEI on heterogeneous clusters, where both the CPUs and GPUs are used in synergistically with minor modifications of the original source code. The resulting GPU accelerated code solves a single heartbeat within a few hours (from three to ten depending on the grid resolution) running on premises computing facility made of few GPU cards, which can be easily installed in a medical laboratory or in a hospital, thus opening towards a systematic computational fluid dynamics (CFD) aided diagnostic.

physics.flu-dyn↗

arXiv2021

Effects of stenotic aortic valve on the left heart hemodynamics: a fluid-structure-electrophysiology approach

The aortic valve is a three-leaflet passive structure that, driven by pressure differences between the left ventricle and the aorta, opens and closes during the heartbeat to ensure the correct stream direction and flow rate. In elderly individuals or because of particular pathologies, the valve leaflets can stiffen thus impairing the valve functioning and, in turn, the pumping efficiency of the heart. Using a multi-physics left heart model accounting for the electrophysiology, the active contraction of the myocardium, the hemodynamics and the related fluid-structure-interaction, we have investigated the changes in the flow features for different severities of the aortic valve stenosis. We have found that, in addition to the increase of the transvalvular pressure drop and of the systolic jet velocity, a stenotic aortic valve significantly alters the wall shear stresses and their spatial distribution over the aortic arch and valve leaflets, which may induce a remodelling process of the ventricular myocardium. The numerical results from the multi-physics model are fully consistent with the clinical experience, thus further opening the way for computational engineering aided medical diagnostic.

physics.flu-dyn↗

arXiv2018

Suppression of von Kármán vortex streets past porous rectangular cylinders

Although the stability properties of the wake past impervious bluff bodies have been widely examined in the literature, similar analyses regarding the flow around and through porous ones are still lacking. In this work, the effect of the porosity and permeability on the wake patterns of porous rectangular cylinders is numerically investigated at low to moderate Reynolds numbers in the framework of direct numerical simulation combined with local and global stability analyses. A modified Darcy-Brinkman formulation is employed here so as to describe the flow behavior inside the porous media, where also the convective terms are retained to correctly account for the inertial effects at high values of permeability. Different aspect ratios of the cylinder are considered, varying the thickness-to-height ratios, t/d, from 0.01 (flat plate) to 1.0 (square cylinder). The results show that the permeability of the bodies has a strong effect in modifying the characteristics of the wakes and of the associated flow instabilities, while the porosity weakly affects the resulting flow patterns. In particular, the fluid flows through the porous bodies and, thus, as the permeability is progressively increased, the recirculation regions, initially attached to the rear part of the bodies, at first detach from the body and, eventually, disappear even in the near wakes. Global stability analyses lead to the identification of critical values of the permeability above which any linear instability is prevented. Moreover, a different scaling of the non-dimensional permeability allows to identify a general threshold for all the configurations here studied that ensures the suppression of vortex shedding, at least in the considered parameter space.

physics.flu-dyn↗