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Pablo Fernandez

Publications and source records attributed to Pablo Fernandez.

17 recordsLinked to original sources

Interpolated Adaptive Linear Reduced Order Modeling for Deformation Dynamics

Linear reduced-order modeling (ROM) is widely used for efficient simulation of deformation dynamics, but its accuracy is often limited by the fixed linearization of the reduced mapping. We propose a new adaptive strategy for linear ROM that allows the reduced mapping to vary dynamically in response to the evolving deformation state, significantly improving accuracy over traditional linear approaches. To further handle large deformations, we introduce a historical displacement basis combined with Grassmann interpolation, enabling the system to recover robustly even in challenging scenarios. We evaluate our method through quantitative online-error analysis and qualitative comparisons with principal component analysis (PCA)-based linear ROM simulations, demonstrating substantial accuracy gains while preserving comparable computational costs.

cs.GR

Pricing4APIs: A Rigorous Model for RESTful API Pricings

APIs are increasingly becoming new business assets for organizations and consequently, API functionality and its pricing should be precisely defined for customers. Pricing is typically composed by different plans that specify a range of limitations, e.g., a Free plan allows 100 monthly requests while a Gold plan has 10000 requests per month. In this context, the OpenAPI Specification (OAS) has emerged to model the functional part of an API, becoming a de facto industry standard and boosting a rich ecosystem of vendor-neutral tools to assist API providers and consumers. In contrast, there is no proposal for modeling API pricings (i.e. their plans and limitations) and this lack hinders the creation of tools that can leverage this information. To deal with this gap, this paper presents a pricing modeling framework that includes: (a) Pricing4APIs model, a comprehensive and rigorous model of API pricings, along SLA4OAI, a serialization that extends OAS; (b) an operation to validate the description of API pricings, with a toolset (sla4oai-analyzer) that has been developed to automate this operation. Additionally, we analyzed 268 real-world APIs to assess the expressiveness of our proposal and created a representative dataset of 54 pricing models to validate our framework.

cs.SE

Bluejay: A Cross-Tooling Audit Framework For Agile Software Teams

Agile software teams are expected to follow a number of specific Team Practices (TPs) during each iteration, such as estimating the effort ("points") required to complete user stories and coordinating the management of the codebase with the delivery of features. For software engineering instructors trying to teach such TPs to student teams, manually auditing teams if teams are following the TPs and improving over time is tedious, time-consuming and error-prone. It is even more difficult when those TPs involve two or more tools. For example, starting work on a feature in a project-management tool such as Pivotal Tracker should usually be followed relatively quickly by the creation of a feature branch on GitHub. Merging a feature branch on GitHub should usually be followed relatively quickly by deploying the new feature to a staging server for customer feedback. Few systems are designed specifically to audit such TPs, and existing ones, as far as we know, are limited to a single specific tool. We present Bluejay, an open-source extensible platform that uses the APIs of multiple tools to collect raw data, synthesize it into TP measurements, and present dashboards to audit the TPs. A key insight in Bluejay's design is that TPs can be expressed in terminology similar to that used for modeling and auditing Service Level Agreement (SLA) compliance. Bluejay therefore builds on mature tools used in that ecosystem and adapts them for describing, auditing, and reporting on TPs. Bluejay currently consumes data from five different widely-used development tools, and can be customized by connecting it to any service with a REST API. Video showcase available at governify.io/showcase/bluejay

cs.SE

Feasibility analysis of ensemble sensitivity computation in turbulent flows

In chaotic systems, such as turbulent flows, the solutions to tangent and adjoint equations exhibit an unbounded growth in their norms. This behavior renders the instantaneous tangent and adjoint solutions unusable for sensitivity analysis. The Lea-Allen-Haine ensemble sensitivity (ES) estimates provide a way of computing meaningful sensitivities in chaotic systems by utilizing tangent/adjoint solutions over short trajectories. In this paper, we analyze the feasibility of ES computations under optimistic mathematical assumptions on the flow dynamics. Furthermore, we estimate upper bounds on the rate of convergence of the ES method in numerical simulations of turbulent flow. Even at the optimistic upper bound, the ES method is computationally intractable in each of the numerical examples considered.

physics.comp-ph

On the ability of discontinuous Galerkin methods to simulate under-resolved turbulent flows

We investigate the ability of discontinuous Galerkin (DG) methods to simulate under-resolved turbulent flows in large-eddy simulation. The role of the Riemann solver and the subgrid-scale model in the prediction of a variety of flow regimes, including transition to turbulence, wall-free turbulence and wall-bounded turbulence, are examined. Numerical and theoretical results show the Riemann solver in the DG scheme plays the role of an implicit subgrid-scale model and introduces numerical dissipation in under-resolved turbulent regions of the flow. This implicit model behaves like a dynamic model and vanishes for flows that do not contain subgrid scales, such as laminar flows, which is a critical feature to accurately predict transition to turbulence. In addition, for the moderate-Reynolds-number turbulence problems considered, the implicit model provides a more accurate representation of the actual subgrid scales in the flow than state-of-the-art explicit eddy viscosity models, including dynamic Smagorinsky, WALE and Vreman. The results in this paper indicate new best practices for subgrid-scale modeling are needed with high-order DG methods.

physics.flu-dyn

Entropy-stable hybridized discontinuous Galerkin methods for the compressible Euler and Navier-Stokes equations

In the spirit of making high-order discontinuous Galerkin (DG) methods more competitive, researchers have developed the hybridized DG methods, a class of discontinuous Galerkin methods that generalizes the Hybridizable DG (HDG), the Embedded DG (EDG) and the Interior Embedded DG (IEDG) methods. These methods are amenable to hybridization (static condensation) and thus to more computationally efficient implementations. Like other high-order DG methods, however, they may suffer from numerical stability issues in under-resolved fluid flow simulations. In this spirit, we introduce the hybridized DG methods for the compressible Euler and Navier-Stokes equations in entropy variables. Under a suitable choice of the stabilization matrix, the scheme can be shown to be entropy stable and satisfy the Second Law of Thermodynamics in an integral sense. The performance and robustness of the proposed family of schemes are illustrated through a series of steady and unsteady flow problems in subsonic, transonic, and supersonic regimes. The hybridized DG methods in entropy variables show the optimal accuracy order given by the polynomial approximation space, and are significantly superior to their counterparts in conservation variables in terms of stability and robustness, particularly for under-resolved and shock flows.

physics.comp-ph

Hybridized discontinuous Galerkin methods for wave propagation

We present the recent development of hybridizable and embedded discontinuous Galerkin (DG) methods for wave propagation problems in fluids, solids, and electromagnetism. In each of these areas, we describe the methods, discuss their main features, display numerical results to illustrate their performance, and conclude with bibliography notes. The main ingredients in devising these DG methods are (i) a local Galerkin projection of the underlying partial differential equations at the element level onto spaces of polynomials of degree k to parametrize the numerical solution in terms of the numerical trace; (ii) a judicious choice of the numerical flux to provide stability and consistency; and (iii) a global jump condition that enforces the continuity of the numerical flux to obtain a global system in terms of the numerical trace. These DG methods are termed hybridized DG methods, because they are amenable to hybridization (static condensation) and hence to more efficient implementations. They share many common advantages of DG methods and possess some unique features that make them well-suited to wave propagation problems.

math.NA

A physics-based shock capturing method for large-eddy simulation

We present a shock capturing method for large-eddy simulation of turbulent flows. The proposed method relies on physical mechanisms to resolve and smooth sharp unresolved flow features that may otherwise lead to numerical instability, such as shock waves and under-resolved thermal and shear layers. To that end, we devise various sensors to detect when and where the shear viscosity, bulk viscosity and thermal conductivity of the fluid do not suffice to stabilize the numerical solution. In such cases, the fluid viscosities are selectively increased to ensure the cell Peclet number is of order one so that these flow features can be well represented with the grid resolution. Although the shock capturing method is devised in the context of discontinuous Galerkin methods, it can be used with other discretization schemes. The performance of the method is illustrated through numerical simulation of external and internal flows in transonic, supersonic, and hypersonic regimes. For the problems considered, the shock capturing method performs robustly, provides sharp shock profiles, and has a small impact on the resolved turbulent structures. These three features are critical to enable robust and accurate large-eddy simulations of shock flows.

physics.comp-ph

Non-modal analysis of spectral element methods: Towards accurate and robust large-eddy simulations

We introduce a \textit{non-modal} analysis technique that characterizes the diffusion properties of spectral element methods for linear convection-diffusion systems. While strictly speaking only valid for linear problems, the analysis is devised so that it can give critical insights on two questions: (i) Why do spectral element methods suffer from stability issues in under-resolved computations of nonlinear problems? And, (ii) why do they successfully predict under-resolved turbulent flows even without a subgrid-scale model? The answer to these two questions can in turn provide crucial guidelines to construct more robust and accurate schemes for complex under-resolved flows, commonly found in industrial applications. For illustration purposes, this analysis technique is applied to the hybridized discontinuous Galerkin methods as representatives of spectral element methods. The effect of the polynomial order, the upwinding parameter and the P\'eclet number on the so-called \textit{short-term diffusion} of the scheme are investigated. From a purely non-modal analysis point of view, polynomial orders between $2$ and $4$ with standard upwinding are well suited for under-resolved turbulence simulations. For lower polynomial orders, diffusion is introduced in scales that are much larger than the grid resolution. For higher polynomial orders, as well as for strong under/over-upwinding, robustness issues can be expected. The non-modal analysis results are then tested against under-resolved turbulence simulations of the Burgers, Euler and Navier-Stokes equations. While devised in the linear setting, our non-modal analysis succeeds to predict the behavior of the scheme in the nonlinear problems considered.

physics.comp-ph

Sensitivity analysis on chaotic dynamical systems by Finite Difference Non-Intrusive Least Squares Shadowing (FD-NILSS)

We present the Finite Difference Non-Intrusive Least Squares Shadowing (FD-NILSS) algorithm for computing sensitivities of long-time averaged quantities in chaotic dynamical systems. FD-NILSS does not require tangent solvers, and can be implemented with little modification to existing numerical simulation software. We also give a formula for solving the least-squares problem in FD-NILSS, which can be applied in NILSS as well. Finally, we apply FD-NILSS for sensitivity analysis of a chaotic flow over a 3-D cylinder at Reynolds number 525, where FD-NILSS computes accurate sensitivities and the computational cost is in the same order as the numerical simulation.

physics.comp-ph

Toward a chaotic adjoint for LES

Adjoint-based sensitivity analysis methods are powerful tools for engineers who use flow simulations for design. However, the conventional adjoint method breaks down for scale-resolving simulations like large-eddy simulation (LES) or direct numerical simulation (DNS), which exhibit the chaotic dynamics inherent in turbulent flows. Sensitivity analysis based on least-squares shadowing (LSS) avoids the issues encountered by conventional methods, but has a high computational cost. The following report outlines a new, more computationally efficient formulation of LSS, non-intrusive LSS, and estimates its cost for several canonical flows using Lyapunov analysis.

physics.flu-dyn

Lyapunov spectrum of separated flows and its dependence on numerical discretization

We investigate the Lyapunov spectrum of separated flows and their dependence on the numerical discretization. The chaotic flow around the NACA 0012 airfoil at low Reynolds number and large angle of attack is considered to that end, and t-, h- and p-refinement studies are performed to examine each effect separately. Numerical results show that the time discretization has a small impact on the dynamics of the system, whereas the spatial discretization can dramatically change them. In particular, the asymptotic Lyapunov spectrum for time refinement is achieved for CFL numbers as large as $\mathcal{O}(10^1-10^2)$, whereas the system continues to become more and more chaotic even for meshes that are much finer than the best practice for this type of flows.

physics.flu-dyn

Implicit large-eddy simulation of compressible flows using the Interior Embedded Discontinuous Galerkin method

We present a high-order implicit large-eddy simulation (ILES) approach for simulating transitional turbulent flows. The approach consists of an Interior Embedded Discontinuous Galerkin (IEDG) method for the discretization of the compressible Navier-Stokes equations and a parallel preconditioned Newton-GMRES solver for the resulting nonlinear system of equations. The IEDG method arises from the marriage of the Embedded Discontinuous Galerkin (EDG) method and the Hybridizable Discontinuous Galerkin (HDG) method. As such, the IEDG method inherits the advantages of both the EDG method and the HDG method to make itself well-suited for turbulence simulations. We propose a minimal residual Newton algorithm for solving the nonlinear system arising from the IEDG discretization of the Navier-Stokes equations. The preconditioned GMRES algorithm is based on a restricted additive Schwarz (RAS) preconditioner in conjunction with a block incomplete LU factorization at the subdomain level. The proposed approach is applied to the ILES of transitional turbulent flows over a NACA 65-(18)10 compressor cascade at Reynolds number 250,000 in both design and off-design conditions. The high-order ILES results show good agreement with a subgrid-scale LES model discretized with a second-order finite volume code while using significantly less degrees of freedom. This work shows that high-order accuracy is key for predicting transitional turbulent flows without a SGS model.

physics.flu-dyn

The role of the cytoskeleton in volume regulation and beading transitions in PC12 neurites

We present investigations on volume regulation and beading shape transitions in PC12 neurites conducted using a flow-chamber technique. By disrupting the cell cytoskeleton with specific drugs we investigate the role of its individual components in the volume regulation response. We find that microtubule disruption increases both swelling rate and maximum volume attained, but does not affect the ability of the neurite to recover its initial volume. In addition, investigation of axonal beading --also known as pearling instability-- provides additional clues on the mechanical state of the neurite. We conclude that the initial swelling phase is mechanically slowed down by microtubules, while the volume recovery is driven by passive diffusion of osmolites. Our experiments provide a framework to investigate the role of cytoskeletal mechanics in volume homeostasis.

physics.bio-ph

Inelastic mechanics of sticky biopolymer networks

We propose a physical model for the nonlinear inelastic mechanics of sticky biopolymer networks with potential applications to inelastic cell mechanics. It consists in a minimal extension of the glassy wormlike chain (GWLC) model, which has recently been highly successful as a quantitative mathematical description of the viscoelastic properties of biopolymer networks and cells. To extend its scope to nonequilibrium situations, where the thermodynamic state variables may evolve dynamically, the GWLC is furnished with an explicit representation of the kinetics of breaking and reforming sticky bonds. In spite of its simplicity the model exhibits many experimentally established non-trivial features such as power-law rheology, stress stiffening, fluidization, and cyclic softening effects.

cond-mat.soft

A unit-cell approach to the nonlinear rheology of biopolymer solutions

We propose a nonlinear extension of the standard tube model for semidilute solutions of freely-sliding semiflexible polymers. Non-affine filament deformations at the entanglement scale, the renormalisation of direct interactions by thermal fluctuations, and the geometry of large deformations are systematically taken into account. The stiffening response predicted for athermal solutions of stiff rods is found to be thermally suppressed. Instead, we obtain a broad linear response regime, supporting the interpretation of shear stiffening at finite frequencies in polymerised actin solutions as indicative of coupling to longitudinal modes. We observe a destabilizing effect of large strains (about 100%), suggesting shear banding as a plausible explanation for the widely observed catastrophic collapse of in-vitro biopolymer solutions, usually attributed to network damage. In combination with friction-type interactions, our analysis provides an analytically tractable framework to address the nonlinear viscoplasticity of biological tissue on a molecular basis.

cond-mat.soft

A master relation defines the nonlinear viscoelasticity of single fibroblasts

Cell mechanical functions like locomotion, contraction and division are controlled by the cytoskeleton, a dynamic biopolymer network whose mechanical properties remain poorly understood. We perform single-cell uniaxial stretching experiments on 3T3 fibroblasts. By superimposing small amplitude oscillations on a mechanically prestressed cell, we find a transition from linear viscoelastic behavior to power-law stress stiffening. Data from different cells over several stress decades can be uniquely scaled to obtain a master-relation between the viscoelastic moduli and the average force. Remarkably, this relation holds independently of deformation history, adhesion biochemistry, and intensity of active contraction. In particular, it is irrelevant whether force is actively generated by the cell or externally imposed by stretching. We propose that the master-relation reflects the mechanical behavior of the force bearing actin cytoskeleton, in agreement with stress stiffening known from semiflexible filament networks.

physics.bio-ph