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Alessandro Coclite

Publications and source records attributed to Alessandro Coclite.

18 recordsLinked to original sources

Efficient and well-conditioned ghost-point discretization of boundary operators on unfitted domains

Unfitted boundary methods are widely used to numerically solve partial differential equations (PDEs) on irregular domains, avoiding the computational burden of generating boundary-conforming grids. In the finite-difference framework, structured Cartesian grids offer advantages such as ease of implementation and efficient parallelization, while geometry is represented implicitly, for instance, through level-set functions. In this setting, ghost point methods are commonly employed to enforce boundary conditions by introducing additional relations between interior and ghost nodes. However, constructing these relations becomes challenging for high-order accurate discretizations, which often rely on wide stencils that can reduce computational efficiency and degrade performance in large-scale parallel simulations. In this work, we investigate alternative ghost-point discretizations based on compact stencils. We introduce a formulation based on a boundary operator that locally approximates the boundary condition near each ghost node, replacing it with linear relations involving both interior and ghost points. The operator is constructed via least-squares reconstruction, allowing flexible stencil configurations while preserving the desired order of accuracy. Several strategies for selecting and adapting compact stencils are proposed, guided by conditioning criteria and iterative refinement procedures to improve global stability. Numerical experiments on various geometries and convection-diffusion regimes demonstrate the effectiveness of the proposed approach, showing that it maintains high accuracy even in the presence of boundary layers and improves stencil compactness and conditioning of the resulting linear systems.

math.NA

Neural Preconditioning via Krylov Subspace Geometry

We propose a geometry-aware strategy for training neural preconditioners tailored to parametrized linear systems arising from the discretization of mixed-dimensional partial differential equations (PDEs). These systems are typically ill-conditioned because of the presence of embedded lower-dimensional structures and are solved using Krylov subspace methods. Our approach yields an approximation of the inverse operator employing a learning algorithm consisting of a two-stage training framework: an initial static pre-training phase, based on residual minimization, followed by a dynamic fine-tuning phase that incorporates solver convergence dynamics into training via a novel loss functional. This dynamic loss is defined by the principal angles between the residuals and the Krylov subspaces. It is evaluated using a differentiable implementation of the Flexible GMRES algorithm, which enables backpropagation through both the Arnoldi process and Givens rotations. The resulting neural preconditioner is explicitly optimized to improve early-stage convergence and reduce iteration counts in a family of 3D-1D mixed-dimensional problems with geometric variability of the 1D domain. Numerical experiments show that our solver-aligned approach significantly improves convergence rate, robustness, and generalization.

math.NA

Mathematical modeling and sensitivity analysis of hypoxia-activated drugs

Hypoxia-activated prodrugs offer a promising strategy for targeting oxygen-deficient regions in solid tumors, which are often resistant to conventional therapies. However, modeling their behavior is challenging because of the complex interplay between oxygen availability, drug activation, and cell survival. In this work, we develop a multiscale and mixed-dimensional model that couples spatially resolved drug and oxygen transport with pharmacokinetics and pharmacodynamics to simulate the cellular response. The model integrates blood flow, oxygen diffusion and consumption, drug delivery, and metabolism. To reduce computational cost, we mitigate the global nonlinearity through a one-way coupling of the multiscale and mixed/dimensional models with a reduced 0D model for the drug metabolism. The global sensitivity analysis is then used to identify key parameters influencing drug activation and therapeutic outcome. This approach enables efficient simulation and supports the design of optimized hypoxia-targeted therapies.

math.NA

A Numerical Framework For Nonlinear Peridynamics On Two-dimensional Manifolds Based On Implicit P-(Ec)k Schemes

In this manuscript, an original numerical procedure for the nonlinear peridynamics on arbitrarily--shaped two-dimensional (2D) closed manifolds is proposed. When dealing with non parameterized 2D manifolds at the discrete scale, the problem of computing geodesic distances between two non-adjacent points arise. Here, a routing procedure is implemented for computing geodesic distances by re-interpreting the triangular computational mesh as a non-oriented graph; thus returning a suitable and general method. Moreover, the time integration of the peridynamics equation is demanded to a P-(EC)$^k$ formulation of the implicit $β$-Newmark scheme. The convergence of the overall proposed procedure is questioned and rigorously proved. Its abilities and limitations are analyzed by simulating the evolution of a two-dimensional sphere. The performed numerical investigations are mainly motivated by the issues related to the insurgence of singularities in the evolution problem. The obtained results return an interesting picture of the role played by the nonlocal character of the integrodifferential equation in the intricate processes leading to the spontaneous formation of singularities in real materials.

math.NA

Dispersive effects in two- and three-dimensional peridynamics

In this paper we study the dispersive properties related to a model of peridynamic evolution, governed by a non local initial value problem, in the cases of two and three spatial dimensions. The features of the wave propagation characterized by the nontrivial interactions between nonlocality and the regimes of low and high frequencies are studied and suitable numerical investigations are exposed.

math.AP

Bond-based peridynamics, a survey prospecting nonlocal theories of fluid-dynamics

Peridynamic (PD) theories have gained widespread diffusion among various research areas, due to the ability of modeling discontinuities formation and evolution in materials. Bond-Based Peridynamics (BB-PD), notwithstanding some modeling limitations, is widely employed in numerical simulations, due to its easy implementation combined with physical intuitiveness and stability. In the present paper, several aspects of bond-based peridynamic models have been reviewed and investigated. A detailed description of peridynamics theory, applications and numerical models has been presented. Employed BB-PD integral kernels have been displayed, together with their differences and commonalities; then, some consequences of their mathematical structure have been discussed. The kinematic role of nonlocality, the relation between kernel structure and material impenetrability, and the role of PD kernel nonlinearity in cracks formation prediction have been critically analyzed and commented. Finally the idea of extending BB-PD to fluids is proposed and presented in the framework of fading memory material, drawing some perspectives for a deeper and more comprehensive understanding of the peridynamics in fluids.

math.NA

Characterization of micro-Capsules Deformation in Branching Channels

In this paper, the dynamic of inertial capsules into microfluidic bifurcations is studied. The fluid evolution is based on the solution of the BGK -- lattice Boltzmann scheme including a forcing term accounting for immersed geometries. The dynamic-Immersed Boundary forcing strategy is adopted for imposing no-slip boundary conditions on moving deformable or rigid structures, while, on fixed immersed geometries the Bouzidi-Firdaouss-Lallemand second-order bounce back technique is implemented. The proposed computational framework is employed to detail dynamics and deformation of rigid and deformable capsules traveling into a branching duct. This journey is characterized in terms of i) the capsule/bifurcation interaction depending on the sharpness of the branching channels junction; ii) daughter branches aperture angle; iii) occlusion ratio, the ratio between capsule size and main channel diameter; iv) flowing capsules stiffness; v) number of flowing particles.

physics.flu-dyn

A Lattice Boltzmann dynamic-Immersed Boundary scheme for the transport of deformable inertial capsules in low-Re flows

In this work, a dynamic-Immersed--Boundary method combined with a BGK-Lattice--Boltzmann technique is developed and critically discussed. The fluid evolution is obtained on a three-dimensional lattice with 19 reticular velocities (D3Q19 computational molecule) while the immersed body surface is modeled as a collection of Lagrangian points responding to an elastic potential and a bending resistance. A moving least squares reconstruction is used to accurately interpolate flow quantities and the forcing field needed to enforce the boundary condition on immersed bodies. The proposed model is widely validated against well known benchmark data for rigid and deformable objects. Rigid transport is validated by computing the settling of a sphere under gravity for five different conditions. Then, the tumbling of inertial particles with different shape is considered, recovering the Jefferey orbit for a prolate spheroid. Moreover, the revolution period for an oblate spheroid and for a disk-like particle is obtained as a function of the Reynolds number. The existence of a critical Reynolds number is demonstrated for both cases above which revolution is inhibited. The transport of deformable objects is also considered. The steady deformation of a membrane under shear for three different mechanical stiffness is assessed. Then, the tumbling of a weakly-deformable spheroid under shear is systematically analyzed as a function strain stiffness, bending resistance and membrane mass.

physics.flu-dyn

Vascular journey and adhesion mechanics of micro-sized carriers in narrow capillaries

In this work a Lattice Boltzmann Immersed Boundary method is used for predicting the dynamics of rigid and deformable adhesive micro carriers (1 um) navigating a capillary by the size of 10 um with 20% hematocrit. Red cells and particles are modeled as a collection of mass spring elements responding to a bending potential, an elastic potential and total enclosed area conservation constraint. Furthermore, particle surfaces are uniformly decorated with adhesive molecules (ligands) interacting with receptors disposed on the walls. Particle adhesion is modeled as a short range ligad receptor interaction and in term of formation and destruction probability functions that discriminate whether a chemical bond can be formed or destroyed. If a bond is established an attractive elastic force is activated. Particle transport and adhesion are characterized in terms of their ability to reach the capillary peripheries (margination rate) and firmly adhere the vasculature. This analysis is carried out systematically by varying particles' and cells' releasing positions and stiffness (Ca = 0 and 10-2). Moreover, three rigid and soft representative particles are transported on a finer mesh (Dx = 15 nm) and the chemical strength of their adhesive coating is varied (s = 0.5, 1.0, and 2.0) to precisely analyze the resulting adhesion mechanics. Stiffness is found to weakly influence the margination rate while significantly affect the ability of such constructs to efficiently interact with the endothelium by forming stable chemical bonds.

cond-mat.soft

Unraveling the vascular fate of deformable circulating tumor cells via a hierarchical computational model

Distant spreading of primary lesions is modulated by the vascular dynamics of circulating tumor cells (CTCs) and their ability to establish metastatic niches. While the mechanisms regulating CTC homing in specific tissues are yet to be elucidated, it is well documented that CTCs possess different size, biological properties and deformability. A computational model is presented to predict the vascular transport and adhesion of CTCs in whole blood. A Lattice-Boltzmann method, which is employed to solve the Navier-Stokes equation for the plasma flow, is coupled with an Immersed Boundary Method. The vascular dynamics of a CTC is assessed in large and small microcapillaries. The CTC shear modulus k ctc is varied returning CTCs that are stiffer, softer and equally deformable as compared to RBCs. In large microcapillaries, soft CTCs behave similarly to RBCs and move away from the vessel walls; whereas rigid CTCs are pushed laterally by the fast moving RBCs and interact with the vessel walls. Three adhesion behaviors are observed, firm adhesion, rolling and crawling over the vessel walls, depending on the CTC stiffness. On the contrary, in small microcapillaries, rigid CTCs are pushed downstream by a compact train of RBCs and cannot establish any firm interaction with the vessel walls; whereas soft CTCs are squeezed between the vessel wall and the RBC train and rapidly establish firm adhesion. These findings document the relevance of cell deformability in CTC vascular adhesion and provide insights on the mechanisms regulating metastasis formation in different vascular districts.

cond-mat.soft

Injection of Deformable Capsules in a Reservoir, a Systematic Analysis

A computational study of capsule ejection from a narrow channel into a reservoir is undertaken for a combination of varying deformable capsule sizes and channel dimensions. A mass spring membrane model is coupled to an Immersed Boundary Lattice Boltzmann model solver. The aim of the present work is the description of the capsules motion, deformation and the response of the fluid due to the complex particle dynamics. The interactions between the capsules affect the local velocity field significantly and are responsible for the dynamics observed. Capsule membrane deformability is also seen to affect inter capsule interaction, and we observe that the train of three particles locally homogenizes the velocity field and the leading capsule travels faster than the other two trailing capsules. On the contrary, variations in size of the reservoir do not seem to be relevant, while the ratio of capsule diameter with respect to channel diameter plays a major role as well as the ratio of capsule diameter to inter capsule spacing. This flow set up has not been covered in the literature, and consequently we focus on describing capsule motion, membrane deformation and fluid dynamics, as a preliminary investigation in this field.

cond-mat.soft

Deciphering the relative contribution of vascular inflammation and blood rheology in metastatic spreading

Vascular adhesion of circulating tumor cells (CTCs) is a key step in cancer spreading. If inflammation is recognized to favor the formation of vascular metastatic niches, little is known about the contribution of blood rheology to CTC deposition. Herein, a microfluidic chip, covered by a confluent monolayer of endothelial cells, is used for analyzing the adhesion and rolling of colorectal (HCT 15) and breast (MDA MB 231) cancer cells under different biophysical conditions. These include the analysis of cell transport in a physiological solution and whole blood; over a healthy and a TNF alpha inflamed endothelium; with a flow rate of 50 and 100 nL/min. Upon stimulation of the endothelial monolayer with TNF alpha (25 ng/mL), CTC adhesion increases by 2 to 4 times whilst cell rolling velocity only slightly reduces. Notably, whole blood also enhances cancer cell deposition by 2 to 3 times, but only on the unstimulated vasculature. For all tested conditions, no statistically significant difference is observed between the two cancer cell types. Finally, a computational model for CTC transport demonstrates that a rigid cell approximation reasonably predicts rolling velocities while cell deformability is needed to model adhesion. These results would suggest that, within microvascular networks, blood rheology and inflammation contribute similarly to CTC deposition thereby facilitating the formation of metastatic niches along the entire network, including the healthy endothelium. In microfluidic based assays, neglecting blood rheology would significantly underestimate the metastatic potential of cancer cells.

physics.bio-ph

A combined Lattice Boltzmann and Immersed Boundary approach for predicting the vascular transport of differently shaped particles

Modelling the vascular transport and adhesion of man-made particles is crucial for optimizing their efficacy in the detection and treatment of diseases. Here, a Lattice Boltzmann and Immersed Boundary methods are combined together for predicting the near wall dynamics of particles with different shapes in a laminar flow. For the lattice Boltzmann modelling, a Gauss-Hermite projection is used to derive the lattice equation, wall boundary conditions are imposed through the Zou-He framework, and a moving least squares algorithm accurately reconstructs the forcing term accounting for the immersed boundary. First, the computational code is validated against two well-known test cases: the sedimentation of circular and elliptical cylinders in a quiescent fluid. A very good agreement is observed between the present results and those available in the literature. Then, the transport of circular, elliptical, rectangular, square and triangular particles is analyzed in a Couette flow, at Re=20. All particles drifted laterally across the stream lines reaching an equilibrium position, independently of the initial conditions. For this large Reynolds number, the particle shape has no significant effect on the final equilibrium position but it does affect the absolute value and periodicity of the angular velocity. Specifically, elongated particles show longer oscillation periods and, most interestingly, larger variations in angular velocity. The longest particles exhibit a zero angular velocity for almost the whole rotational period. Collectively, this data demonstrates that the proposed approach can be efficiently used for predicting complex particle dynamics in biologically relevant flows. This computational strategy could have significant impact in the field of computational nanomedicine for optimizing the specific delivery of therapeutic and imaging agents.

physics.flu-dyn

LES of the Sandia Flame D Using an FPV Combustion Model

The simulation of turbulent combustion phenomena is still an open problem in modern fluid dynamics. Considering the economical importance of hydrocarbon combustion in energy production processes, it is evident the need of an accurate tool with a relatively low computational cost for the prediction of this kind of reacting flows. In the present work, a comparative study is carried out among large eddy simulations, performed with various grid resolutions, a Reynolds averaged Navier-Stokes simulation, and experimental data concerning the well-known Sandia D flame test case. In all the simulations, a flamelet progress variable model has been employed using various hypotheses for the joint probability density function closure. The filtered approach proved to be more accurate than the averaged one, even for the coarser grid used in this work. In fact both approaches have shown poorly accurate predictions in the first part of the combustion chamber, but only by the large eddy simulation one is capable to recover the inlet discrepancies with respect to the experimental data going along the streamwise direction.

physics.flu-dyn

An SMLD joint PDF model for turbulent non-premixed combustion using the flamelet progress-variable approach

This paper provides an improved flamelet/progress variable (FPV) model for the simulation of turbulent combustion, employing the statistically most likely distribution (SMLD) approach for the joint probability density function (PDF) of the mixture fraction, Z, and of the progress parameter, Λ . Steady-state FPV models are built presuming the func- tional shape of the joint PDF of Z and Λ in order to evaluate Favre-averages of thermody- namic quantities. The mixture fraction is widely assumed to behave as a passive scalar with a mono-modal behaviour modelled by a \b{eta} -distribution. Moreover, under the hypothesis that Z and Λ are statistically independent, the joint PDF coincides with the product of the two marginal PDFs. In this work we discuss these two constitutive hypotheses. The proposed model evaluates the most probable joint distribution of Z and Λ , relaxing some crucial as- sumption on their statistical behaviour. This provides a more general model in the context of FPV approach and an effective tool to verify the adequateness of widely used hypotheses. The model is validated versus experimental data of well-known test cases, namely, the San- dia flames. The results are also compared with those obtained by the standard FPV approach, analysing the role of the PDF functional form on turbulent combustion simulations.

physics.flu-dyn

Pattern Formation in Liquid-Vapor Systems under Periodic Potential and Shear

In this paper the phase behavior and pattern formation in a sheared non-ideal fluid under a periodic potential is studied. An isothermal two-dimensional formulation of a lattice Boltzmann scheme for a liquid-vapor system with the van der Waals equation of state is presented and validated. Shear is applied by moving walls and the periodic potential will vary along the flow direction. A region of the parameter space, where in absence of flow a striped phase with oscillating density is stable, will be considered. At low shear rates the periodic patterns are preserved and slightly distorted by the flow. At high shear rates the striped phase looses its stability and a new phase with interface waves between the liquid and vapor regions will appear. Velocity field patterns will be also shown.

physics.flu-dyn

The role of presumed probability density function in the simulation of non premixed turbulent combustion

Flamelet Progress Variable (FPV) combustion models allow the evaluation of all thermo chemical quantities in a reacting flow by computing only the mixture fraction Z and a progress variable C. When using such a method to predict a turbulent combustion in conjunction with a turbulence model, a probability density function (PDF) is required to evaluate statistical averages (e.g., Favre average) of chemical quantities. The choice of the PDF is a compromise between computational costs and accuracy level. The aim of this paper is to investigate the influence of the PDF choice and its modeling aspects in the simulation of non premixed turbulent combustion. Three different models are considered: the standard one, based on the choice of a beta distribution for Z and a Dirac distribution for C; a model employing a beta distribution for both Z and C; a third model obtained using a beta distribution for Z and the statistical most likely distribution (SMLD) for C. The standard model, although widely used, doesn't take into account the interaction between turbulence and chemical kinetics as well as the dependence of the progress variable not only on its mean but also on its variance. The SMLD approach establishes a systematic framework to incorporate informations from an arbitrary number of moments, thus providing an improvement over conventionally employed presumed PDF closure models. The rational behind the choice of the three PDFs is described in some details and the prediction capability of the corresponding models is tested versus well known test cases, namely, the Sandia flames, and a test case for supersonic combustion provided by Cheng.

physics.flu-dyn

An extended SMLD approach for presumed probability density function in flamelet combustion model

This paper provides an extension of the standard flamelet progress variable (FPV) approach for turbulent combustion, applying the statistically most likely distribution (SMLD) framework to the joint PDF of the mixture fraction, Z, and the progress variable, C. In this way one does not need to make any assumption about the statistical correlation between Z and C and about the behaviour of the mixture fraction, as required in previous FPV models. In fact, for state-of-the-art models, with the assumption of very-fast-chemistry,Z is widely accepted to behave as a passive scalar characterized by a $β$-distribution function. Instead, the model proposed here, evaluates the most probable joint distribution of Z and C without any assumption on their behaviour and provides an effective tool to verify the adequateness of widely used hypotheses, such as their statistical independence. The model is validated versus three well-known test cases, namely, the Sandia flames. The results are compared with those obtained by the standard FPV approach, analysing the role of the PDF functional form on turbulent combustion simulations.

physics.flu-dyn