Estimating pulmonary arterial remodeling via an animal-specific computational model of pulmonary artery stenosis.

Pulmonary artery stenosis (PAS) often presents in children with congenital heart disease, altering blood flow and pressure during critical periods of growth and development. Variability in stenosis onset, duration, and severity result in variable growth and remodeling of the pulmonary vasculature. Computational fluid dynamics (CFD) models enable investigation into the hemodynamic impact and altered mechanics associated with PAS. In this study, a one-dimensional (1D) fluid dynamics model was used to simulate hemodynamics throughout the pulmonary arteries of individual animals. The geometry of the large pulmonary arteries was prescribed by animal-specific imaging, whereas the distal vasculature was simulated by a three-element Windkessel model at each terminal vessel outlet. Remodeling of the pulmonary vasculature, which cannot be measured in vivo, was estimated via model-fitted parameters. The large artery stiffness was significantly higher on the left side of the vasculature in the left pulmonary artery (LPA) stenosis group, but neither side differed from the sham group. The sham group exhibited a balanced distribution of total distal vascular resistance, whereas the left side was generally larger in the LPA stenosis group, with no significant differences between groups. In contrast, the peripheral compliance on the right side of the LPA stenosis group was significantly greater than the corresponding side of the sham group. Further analysis indicated the underperfused distal vasculature likely moderately decreased in radius with little change in stiffness given the increase in thickness observed with histology. Ultimately, our model enables greater understanding of pulmonary arterial adaptation due to LPA stenosis and has potential for use as a tool to noninvasively estimate remodeling of the pulmonary vasculature.

VpROM: a novel variational autoencoder-boosted reduced order model for the treatment of parametric dependencies in nonlinear systems.

Reduced Order Models (ROMs) are of considerable importance in many areas of engineering in which computational time presents difficulties. Established approaches employ projection-based reduction, such as Proper Orthogonal Decomposition. The limitation of the linear nature of such operators is typically tackled via a library of local reduction subspaces, which requires the assembly of numerous local ROMs to address parametric dependencies. Our work attempts to define a more generalisable mapping between parametric inputs and reduced bases for the purpose of generative modeling. We propose the use of Variational Autoencoders (VAEs) in place of the typically utilised clustering or interpolation operations, for inferring the fundamental vectors, termed as modes, which approximate the manifold of the model response for any and each parametric input state. The derived ROM still relies on projection bases, built on the basis of full-order model simulations, thus retaining the imprinted physical connotation. However, it additionally exploits a matrix of coefficients that relates each local sample response and dynamics to the global phenomena across the parametric input domain. The VAE scheme is utilised for approximating these coefficients for any input state. This coupling leads to a high-precision low-order representation, which is particularly suited for problems where model dependencies or excitation traits cause the dynamic behavior to span multiple response regimes. Moreover, the probabilistic treatment of the VAE representation allows for uncertainty quantification on the reduction bases, which may then be propagated to the ROM response. The performance of the proposed approach is validated on an open-source simulation benchmark featuring hysteresis and multi-parametric dependencies, and on a large-scale wind turbine tower characterised by nonlinear material behavior and model uncertainty.

Efficient approximation of cardiac mechanics through reduced-order modeling with deep learning-based operator approximation.

Reducing the computational time required by high-fidelity, full-order models (FOMs) for the solution of problems in cardiac mechanics is crucial to allow the translation of patient-specific simulations into clinical practice. Indeed, while FOMs, such as those based on the finite element method, provide valuable information on the cardiac mechanical function, accurate numerical results can be obtained at the price of very fine spatio-temporal discretizations. As a matter of fact, simulating even just a few heartbeats can require up to hours of wall time on high-performance computing architectures. In addition, cardiac models usually depend on a set of input parameters that are calibrated in order to explore multiple virtual scenarios. To compute reliable solutions at a greatly reduced computational cost, we rely on a reduced basis method empowered with a new deep learning-based operator approximation, which we refer to as Deep-HyROMnet technique. Our strategy combines a projection-based POD-Galerkin method with deep neural networks for the approximation of (reduced) nonlinear operators, overcoming the typical computational bottleneck associated with standard hyper-reduction techniques employed in reduced-order models (ROMs) for nonlinear parametrized systems. This method can provide extremely accurate approximations to parametrized cardiac mechanics problems, such as in the case of the complete cardiac cycle in a patient-specific left ventricle geometry. In this respect, a 3D model for tissue mechanics is coupled with a 0D model for external blood circulation; active force generation is provided through an adjustable parameter-dependent surrogate model as input to the tissue 3D model. The proposed strategy is shown to outperform classical projection-based ROMs, in terms of orders of magnitude of computational speed-up, and to return accurate pressure-volume loops in both physiological and pathological cases. Finally, an application to a forward uncertainty quantification analysis, unaffordable if relying on a FOM, is considered, involving output quantities of interest such as, for example, the ejection fraction or the maximal rate of change in pressure in the left ventricle.

Learning reduced-order models for cardiovascular simulations with graph neural networks.

Reduced-order models based on physics are a popular choice in cardiovascular modeling due to their efficiency, but they may experience loss in accuracy when working with anatomies that contain numerous junctions or pathological conditions. We develop one-dimensional reduced-order models that simulate blood flow dynamics using a graph neural network trained on three-dimensional hemodynamic simulation data. Given the initial condition of the system, the network iteratively predicts the pressure and flow rate at the vessel centerline nodes. Our numerical results demonstrate the accuracy and generalizability of our method in physiological geometries comprising a variety of anatomies and boundary conditions. Our findings demonstrate that our approach can achieve errors below 3% for pressure and flow rate, provided there is adequate training data. As a result, our method exhibits superior performance compared to physics-based one-dimensional models while maintaining high efficiency at inference time.

Computational models of ventricular mechanics and adaptation in response to right-ventricular pressure overload.

Pulmonary arterial hypertension (PAH) is associated with substantial remodeling of the right ventricle (RV), which may at first be compensatory but at a later stage becomes detrimental to RV function and patient survival. Unlike the left ventricle (LV), the RV remains understudied, and with its thin-walled crescent shape, it is often modeled simply as an appendage of the LV. Furthermore, PAH diagnosis is challenging because it often leaves the LV and systemic circulation largely unaffected. Several treatment strategies such as atrial septostomy, right ventricular assist devices (RVADs) or RV resynchronization therapy have been shown to improve RV function and the quality of life in patients with PAH. However, evidence of their long-term efficacy is limited and lung transplantation is still the most effective and curative treatment option. As such, the clinical need for improved diagnosis and treatment of PAH drives a strong need for increased understanding of drivers and mechanisms of RV growth and remodeling (G&R), and more generally for targeted research into RV mechanics pathology. Computational models stand out as a valuable supplement to experimental research, offering detailed analysis of the drivers and consequences of G&R, as well as a virtual test bench for exploring and refining hypotheses of growth mechanisms. In this review we summarize the current efforts towards understanding RV G&R processes using computational approaches such as reduced-order models, three dimensional (3D) finite element (FE) models, and G&R models. In addition to an overview of the relevant literature of RV computational models, we discuss how the models have contributed to increased scientific understanding and to potential clinical treatment of PAH patients.

Automated generation of 0D and 1D reduced-order models of patient-specific blood flow.

Three-dimensional (3D) cardiovascular fluid dynamics simulations typically require hours to days of computing time on a high-performance computing cluster. One-dimensional (1D) and lumped-parameter zero-dimensional (0D) models show great promise for accurately predicting blood bulk flow and pressure waveforms with only a fraction of the cost. They can also accelerate uncertainty quantification, optimization, and design parameterization studies. Despite several prior studies generating 1D and 0D models and comparing them to 3D solutions, these were typically limited to either 1D or 0D and a singular category of vascular anatomies. This work proposes a fully automated and openly available framework to generate and simulate 1D and 0D models from 3D patient-specific geometries, automatically detecting vessel junctions and stenosis segments. Our only input is the 3D geometry; we do not use any prior knowledge from 3D simulations. All computational tools presented in this work are implemented in the open-source software platform SimVascular. We demonstrate the reduced-order approximation quality against rigid-wall 3D solutions in a comprehensive comparison with N = 72 publicly available models from various anatomies, vessel types, and disease conditions. Relative average approximation errors of flows and pressures typically ranged from 1% to 10% for both 1D and 0D models, measured at the outlets of terminal vessel branches. In general, 0D model errors were only slightly higher than 1D model errors despite requiring only a third of the 1D runtime. Automatically generated ROMs can significantly speed up model development and shift the computational load from high-performance machines to personal computers.

A Simple Matlab Code for Material Design Optimization Using Reduced Order Models.

The main part of the computational cost required for solving the problem of optimal material design with extreme properties using a topology optimization formulation is devoted to solving the equilibrium system of equations derived through the implementation of the finite element method (FEM). To reduce this computational cost, among other methodologies, various model order reduction (MOR) approaches can be utilized. In this work, a simple Matlab code for solving the topology optimization for the design of materials combined with three different model order reduction approaches is presented. The three MOR approaches presented in the code implementation are the proper orthogonal decomposition (POD), the on-the-fly reduced order model construction and the approximate reanalysis (AR) following the combined approximations approach. The complete code, containing all participating functions (including the changes made to the original ones), is provided.

A multiparametric advection-diffusion reduced-order model for molecular transport in scaffolds for osteoinduction.

Scaffolds are microporous biocompatible structures that serve as material support for cells to proliferate, differentiate and form functional tissue. In particular, in the field of bone regeneration, insertion of scaffolds in a proper physiological environment is known to favour bone formation by releasing calcium ions, among others, triggering differentiation of mesenchymal cells into osteoblasts. Computational simulation of molecular distributions through scaffolds is a potential tool to study the scaffolds' performance or optimal designs, to analyse their impact on cell differentiation, and also to move towards reduction in animal experimentation. Unfortunately, the required numerical models are often highly complex and computationally too costly to develop parametric studies. In this context, we propose a computational parametric reduced-order model to obtain the distribution of calcium ions in the interstitial fluid flowing through scaffolds, depending on several physical parameters. We use the well-known Proper Orthogonal Decomposition (POD) with two different variations: local POD and POD with quadratic approximations. Computations are performed using two realistic geometries based on a foamed and a 3D-printed scaffolds. The location of regions with high concentration of calcium in the numerical simulations is in fair agreement with regions of bone formation shown in experimental observations reported in the literature. Besides, reduced-order solutions accurately approximate the reference finite element solutions, with a significant decrease in the number of degrees of freedom, thus avoiding computationally expensive simulations, especially when performing a parametric analysis. The proposed reduced-order model is a competitive tool to assist the design of scaffolds in osteoinduction research.

Fault Identification in Electric Servo Actuators of Robot Manipulators Described by Nonstationary Nonlinear Dynamic Models Using Sliding Mode Observers.

The problem of fault identification in electric servo actuators of robot manipulators described by nonstationary nonlinear dynamic models under disturbances is considered. To solve the problem, sliding mode observers are used. The suggested approach is based on the reduced order model of the original system having different sensitivity to faults and disturbances. This model is realized in canonical form that enables relaxing the limitation imposed on the original system. Theoretical results are illustrated by practical example.

Digital twins based on bidirectional LSTM and GAN for modelling the COVID-19 pandemic.

The outbreak of the coronavirus disease 2019 (COVID-19) has now spread throughout the globe infecting over 150 million people and causing the death of over 3.2 million people. Thus, there is an urgent need to study the dynamics of epidemiological models to gain a better understanding of how such diseases spread. While epidemiological models can be computationally expensive, recent advances in machine learning techniques have given rise to neural networks with the ability to learn and predict complex dynamics at reduced computational costs. Here we introduce two digital twins of a SEIRS model applied to an idealised town. The SEIRS model has been modified to take account of spatial variation and, where possible, the model parameters are based on official virus spreading data from the UK. We compare predictions from one digital twin based on a data-corrected Bidirectional Long Short-Term Memory network with predictions from another digital twin based on a predictive Generative Adversarial Network. The predictions given by these two frameworks are accurate when compared to the original SEIRS model data. Additionally, these frameworks are data-agnostic and could be applied to towns, idealised or real, in the UK or in other countries. Also, more compartments could be included in the SEIRS model, in order to study more realistic epidemiological behaviour.

Hemodynamic modeling of the circle of Willis reveals unanticipated functions during cardiovascular stress.

The circle of Willis (CW) allows blood to be redistributed throughout the brain during local ischemia; however, it is unlikely that the anatomic persistence of the CW across mammalian species is driven by natural selection of individuals with resistance to cerebrovascular disease typically occurring in elderly humans. To determine the effects of communicating arteries (CoAs) in the CW on cerebral pulse wave propagation and blood flow velocity, we simulated young, active adult humans undergoing different states of cardiovascular stress (i.e., fear and aerobic exercise) using discrete transmission line segments with stress-adjusted cardiac output, peripheral resistance, and arterial compliance. Phase delays between vertebrobasilar and carotid pulses allowed bidirectional shunting through CoAs: both posteroanterior shunting before the peak of the pulse waveform and anteroposterior shunting after internal carotid pressure exceeded posterior cerebral pressure. Relative to an absent CW without intact CoAs, the complete CW blunted anterior pulse waveforms, although limited to 3% and 6% reductions in peak pressure and pulse pressure, respectively. Systolic rate of change in pressure (i.e., ∂P/∂t) was reduced 15%-24% in the anterior vasculature and increased 23%-41% in the posterior vasculature. Bidirectional shunting through posterior CoAs was amplified during cardiovascular stress and increased peak velocity by 25%, diastolic-to-systolic velocity range by 44%, and blood velocity acceleration by 134% in the vertebrobasilar arteries. This effect may facilitate stress-related increases in blood flow to the cerebellum (improving motor coordination) and reticular-activating system (enhancing attention and focus) via a nitric oxide-dependent mechanism, thereby improving survival in fight-or-flight situations.NEW & NOTEWORTHY Hemodynamic modeling reveals potential evolutionary benefits of the intact circle of Willis (CW) during fear and aerobic exercise. The CW equalizes pulse waveforms due to bidirectional shunting of blood flow through communicating arteries, which boosts vertebrobasilar blood flow velocity and acceleration. These phenomena may enhance perfusion of the brainstem and cerebellum via nitric oxide-mediated vasodilation, improving performance of the reticular-activating system and motor coordination in survival situations.

Personalising left-ventricular biophysical models of the heart using parametric physics-informed neural networks.

We present a parametric physics-informed neural network for the simulation of personalised left-ventricular biomechanics. The neural network is constrained to the biophysical problem in two ways: (i) the network output is restricted to a subspace built from radial basis functions capturing characteristic deformations of left ventricles and (ii) the cost function used for training is the energy potential functional specifically tailored for hyperelastic, anisotropic, nearly-incompressible active materials. The radial bases are generated from the results of a nonlinear Finite Element model coupled with an anatomical shape model derived from high-resolution cardiac images. We show that, by coupling the neural network with a simplified circulation model, we can efficiently generate computationally inexpensive estimations of cardiac mechanics. Our model is 30 times faster than the reference Finite Element model used, including training time, while yielding satisfactory average errors in the predictions of ejection fraction (-3%), peak systolic pressure (7%), stroke work (4%) and myocardial strains (14%). This physics-informed neural network is well suited to efficiently augment cardiac images with functional data and to generate large sets of synthetic cases for training deep network classifiers while it provides efficient personalization to the specific patient of interest with a high level of detail.

A computational study of the hemodynamics of bioprosthetic aortic valves with reduced leaflet motion.

We employ a reduced degree-of-freedom aortic valve model to investigate the flow physics associated with early-stage reduced leaflet motion in bioprosthetic aortic valves. The model is coupled with a sharp-interface immersed boundary based incompressible flow solver to efficiently simulate the fluid-structure interaction. A total of 19 cases of flow through aortic valves with varying degrees of reduced leaflet motion (RLM) are considered. The characteristics of the aortic jet and the consequent aorta wall loading patterns are analyzed. Our results show that asymmetric RLM tilts the aortic jet and leads to large reverse and recirculating flow regions downstream from leaflets with restricted mobility. The changes in flow patterns increase wall pressure and shear stress fluctuations, and result in asymmetric oscillating shear on the aorta wall. These findings have implications for auscultation based diagnosis of this condition as well as the health of the aorta.

Reduced order models of myelinated axonal compartments.

The paper presents a hierarchical series of computational models for myelinated axonal compartments. Three classes of models are considered, either with distributed parameters (2.5D EQS-ElectroQuasi Static, 1D TL-Transmission Lines) or with lumped parameters (0D). They are systematically analyzed with both analytical and numerical approaches, the main goal being to identify the best procedure for order reduction of each case. An appropriate error estimator is proposed in order to assess the accuracy of the models. This is the foundation of a procedure able to find the simplest reduced model having an imposed precision. The most computationally efficient model from the three geometries proved to be the analytical 1D one, which is able to have accuracy less than 0.1%. By order reduction with vector fitting, a finite model is generated with a relative difference of 10- 4 for order 5. The dynamical models thus extracted allow an efficient simulation of neurons and, consequently, of neuronal circuits. In such situations, the linear models of the myelinated compartments coupled with the dynamical, non-linear models of the Ranvier nodes, neuronal body (soma) and dendritic tree give global reduced models. In order to ease the simulation of large-scale neuronal systems, the sub-models at each level, including those of myelinated compartments should have the lowest possible order. The presented procedure is a first step in achieving simulations of neural systems with accuracy control.

Computational simulation of flow-induced arterial remodeling of the pancreaticoduodenal arcade associated with celiac artery stenosis.

Arterial remodeling of the pancreaticoduodenal arcade, which enables collateral flow to the liver, spleen, and stomach, is a well-recognized clinical sign of celiac artery (CA) stenosis. However, the hemodynamic changes due to remodeling are poorly understood, despite their importance in surgical procedures such as pancreaticoduodenectomy. In this study, a framework to simulate remodeling of the arterial network following pathological flow alterations was developed and applied to investigate the hemodynamic characteristics of patients with CA stenosis. A one-dimensional-zero-dimensional cardiovascular model was used for blood flow simulation. After introducing CA stenosis into the normal network, arterial remodeling was simulated by iteratively changing the diameter of each artery until time-averaged wall shear stress reached its value under normal conditions. A representative case was simulated to validate the present framework, followed by simulation cases to investigate the impact of stenosis severity on remodeling outcome. A markedly dilated arcade was observed whose diameter agreed well with the corresponding values measured in subjects with CA stenosis, confirming the ability of the framework to predict arterial remodeling. A series of simulations clarified how the geometry and hemodynamics after remodeling change with stenosis severity. In particular, the arterial remodeling and resulting blood flow redistribution were found to maintain adequate organ blood supply regardless of stenosis severity. Furthermore, it was suggested that flow conditions in patients with CA stenosis could be estimated from geometric factors, namely, stenosis severity and arcade diameter, which can be preoperatively and non-invasively measured using diagnostic medical images.

Impact of network heterogeneity on electrokinetic transport in porous media.

We present a numerical study of electrokinetic transport in porous media, focusing on the role of heterogeneity in a porous microstructure on ion concentration polarization and over-limiting current. For simplicity, the porous medium is modeled as a network of long, thin charged cylindrical pores, each governed by one-dimensional effective transport equations. For weak surface conduction, when sufficiently large potential is applied, we demonstrate that electrokinetic transport in a porous network can be dominated by electro-convection via internally induced flow loops, which is not properly captured by existing homogenized models. We systematically vary the topology and "accessivity" of the pore network and compare with simulations of traditional homogenized parallel-pore (capillary-bundle) models, in order to reveal the effects of regular and hierarchical connectivity. Our computational framework sheds light on the complex physics of electrokinetic phenomena in microstructures and may be used to design porous media for applications, such as water desalination and purification by shock electrodialysis.

Model Error, Information Barriers, State Estimation and Prediction in Complex Multiscale Systems.

Complex multiscale systems are ubiquitous in many areas. This research expository article discusses the development and applications of a recent information-theoretic framework as well as novel reduced-order nonlinear modeling strategies for understanding and predicting complex multiscale systems. The topics include the basic mathematical properties and qualitative features of complex multiscale systems, statistical prediction and uncertainty quantification, state estimation or data assimilation, and coping with the inevitable model errors in approximating such complex systems. Here, the information-theoretic framework is applied to rigorously quantify the model fidelity, model sensitivity and information barriers arising from different approximation strategies. It also succeeds in assessing the skill of filtering and predicting complex dynamical systems and overcomes the shortcomings in traditional path-wise measurements such as the failure in measuring extreme events. In addition, information theory is incorporated into a systematic data-driven nonlinear stochastic modeling framework that allows effective predictions of nonlinear intermittent time series. Finally, new efficient reduced-order nonlinear modeling strategies combined with information theory for model calibration provide skillful predictions of intermittent extreme events in spatially-extended complex dynamical systems. The contents here include the general mathematical theories, effective numerical procedures, instructive qualitative models, and concrete models from climate, atmosphere and ocean science.

On a sparse pressure-flow rate condensation of rigid circulation models.

Cardiovascular simulation has shown potential value in clinical decision-making, providing a framework to assess changes in hemodynamics produced by physiological and surgical alterations. State-of-the-art predictions are provided by deterministic multiscale numerical approaches coupling 3D finite element Navier Stokes simulations to lumped parameter circulation models governed by ODEs. Development of next-generation stochastic multiscale models whose parameters can be learned from available clinical data under uncertainty constitutes a research challenge made more difficult by the high computational cost typically associated with the solution of these models. We present a methodology for constructing reduced representations that condense the behavior of 3D anatomical models using outlet pressure-flow polynomial surrogates, based on multiscale model solutions spanning several heart cycles. Relevance vector machine regression is compared with maximum likelihood estimation, showing that sparse pressure/flow rate approximations offer superior performance in producing working surrogate models to be included in lumped circulation networks. Sensitivities of outlets flow rates are also quantified through a Sobol׳ decomposition of their total variance encoded in the orthogonal polynomial expansion. Finally, we show that augmented lumped parameter models including the proposed surrogates accurately reproduce the response of multiscale models they were derived from. In particular, results are presented for models of the coronary circulation with closed loop boundary conditions and the abdominal aorta with open loop boundary conditions.

Stochastic reduced order models for inverse problems under uncertainty.

This work presents a novel methodology for solving inverse problems under uncertainty using stochastic reduced order models (SROMs). Given statistical information about an observed state variable in a system, unknown parameters are estimated probabilistically through the solution of a model-constrained, stochastic optimization problem. The point of departure and crux of the proposed framework is the representation of a random quantity using a SROM - a low dimensional, discrete approximation to a continuous random element that permits e cient and non-intrusive stochastic computations. Characterizing the uncertainties with SROMs transforms the stochastic optimization problem into a deterministic one. The non-intrusive nature of SROMs facilitates e cient gradient computations for random vector unknowns and relies entirely on calls to existing deterministic solvers. Furthermore, the method is naturally extended to handle multiple sources of uncertainty in cases where state variable data, system parameters, and boundary conditions are all considered random. The new and widely-applicable SROM framework is formulated for a general stochastic optimization problem in terms of an abstract objective function and constraining model. For demonstration purposes, however, we study its performance in the specific case of inverse identification of random material parameters in elastodynamics. We demonstrate the ability to efficiently recover random shear moduli given material displacement statistics as input data. We also show that the approach remains effective for the case where the loading in the problem is random as well.

Reduced-order models for nonlinear vibrations, based on natural modes: the case of the circular cylindrical shell.

Reduced-order models are essential to study nonlinear vibrations of structures and structural components. The natural mode discretization is based on a two-step analysis. In the first step, the natural modes of the structure are obtained. Because this is a linear analysis, the structure can be discretized with a very large number of degrees of freedom. Then, in the second step, a small number of these natural modes are used to discretize the nonlinear vibration problem with a huge reduction in the number of degrees of freedom. This study finds a recipe to select the natural modes that must be retained to study nonlinear vibrations of an angle-ply laminated circular cylindrical shell that the author has previously studied by using admissible functions defined on the whole structure, so that an accuracy analysis is performed. The higher-order shear deformation theory developed by Amabili and Reddy is used to model the shell.