Shawn C Shadden

Shawn C Shadden
University of California, Berkeley | UCB · Department of Mechanical Engineering

PhD

About

130
Publications
25,016
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5,314
Citations
Additional affiliations
July 2013 - June 2015
University of California, Berkeley
Position
  • Professor (Assistant)
August 2009 - July 2013
Illinois Institute of Technology
Position
  • Professor (Assistant)

Publications

Publications (130)
Preprint
We study a matrix that arises in a singular formulation of the Woodbury matrix identity when the Woodbury identity no longer holds. We present generalized inverse and pseudo-determinant identities for such matrix that have direct applications to the Gaussian process regression, in particular, its likelihood representation and its precision matrix....
Preprint
We develop a computational procedure to estimate the covariance hyperparameters for semiparametric Gaussian process regression models with additive noise. Namely, the presented method can be used to efficiently estimate the variance of the correlated error, and the variance of the noise based on maximizing a marginal likelihood function. Our method...
Article
We extend our previous distributed lumped parameter (DLP) modeling approach to take into account blood vessel wall deformability. This is achieved by adding a compliance term for each vascular segment based on 1D NS equations. The results of the proposed method are compared against 1D Navier–Stokes and 3D fluid–structure interaction modeling in ide...
Article
Full-text available
Recent progress in machine learning (ML), together with advanced computational power, have provided new research opportunities in cardiovascular modeling. While classifying patient outcomes and medical image segmentation with ML have already shown significant promising results, ML for the prediction of biomechanics such as blood flow or tissue dyna...
Preprint
Full-text available
Patient-specific cardiac modeling combines geometries of the heart derived from medical images and biophysical simulations to predict various aspects of cardiac function. However, generating simulation-suitable models of the heart from patient image data often requires complicated procedures and significant human effort. We present a fast and autom...
Article
Full-text available
We introduce a poroelastic model for intraluminal thrombus (ILT) that captures both the flow within ILT and its deformation. The model for ILT is coupled with blood flow and arterial wall deformation and used to study the biomechanics in image-based abdominal aortic aneurysm (AAA) models. Three different patient-specific geometries were considered...
Article
Full-text available
Recent studies have correlated kinetic energy (KE) and viscous dissipation rate (VDR) in the left ventricle (LV) with heart health. These studies have relied on 4D-flow imaging or computational fluid dynamics modeling, which are able to measure, or compute, all 3 components (3C) of the blood flow velocity in 3 dimensional (3D) space. This richness...
Chapter
Image-based computer simulation of cardiac function can be used to probe the mechanisms of (patho)physiology, and guide diagnosis and personalized treatment of cardiac diseases. This paradigm requires constructing simulation-ready meshes of cardiac structures from medical image data–a process that has traditionally required significant time and hum...
Preprint
Full-text available
Image-based computer simulation of cardiac function can be used to probe the mechanisms of (patho)physiology, and guide diagnosis and personalized treatment of cardiac diseases. This paradigm requires constructing simulation-ready meshes of cardiac structures from medical image data--a process that has traditionally required significant time and hu...
Article
Full-text available
Anatomical and physiological changes alter airflow characteristics and aerosol distribution in the developing lung. Correlation between age and aerosol dosimetry is needed, specifically because youth are more susceptible to medication side effects. In this study, we estimate aerosol dosages (particle diameters of 1, 3, and 5 $$\upmu$$ μ m) in a 3 m...
Article
Full-text available
A pathologically formed blood clot or thrombus is central to major cardiovascular diseases like heart attack and stroke. Detailed quantitative evaluation of flow and flow-mediated transport processes in the thrombus neighborhood within large artery hemodynamics is crucial for understanding disease progression and assessing treatment efficacy. This,...
Article
Full-text available
Background: An estimated 10% of male adults have split or dribbled stream leading to poor hygiene, embarrassment, and inconvenience. There is no current metric that measures male stream deviation. Objective: To develop a novel method to measure spray in normal and abnormal anatomical conformations. Design, setting, and participants: We developed...
Article
Subclinical leaflet thrombosis is becoming a major concern in valve-in-valve procedures, whereby a transcatheter aortic valve device is deployed inside a failed bioprosthetic surgical valve. Blood flow stagnation and prolonged residence times in the neo-sinuses have been suggested as possible explanations for leaflet thrombosis. The BASILICA techni...
Article
Full-text available
Leaflet thrombosis has been suggested as the reason for the reduced leaflet motion in cases of hypoattenuated leaflet thickening of bioprosthetic aortic valves. This work aimed to estimate the risk of leaflet thrombosis in two post-valve-in-valve (ViV) configurations, using five different numerical approaches. Realistic ViV configurations were calc...
Article
Leaflet thrombosis has been suggested as the reason for the reduced leaflet motion in cases of hypoattenuated leaflet thickening of bioprosthetic aortic valves. This work aimed to estimate the risk of leaflet thrombosis in two post-valve-in-valve (ViV) configurations, using five different numerical approaches. Realistic ViV configurations were calc...
Article
Full-text available
Computational modeling of cardiovascular biomechanics should generally start from a homeostatic state. This is particularly relevant for image-based modeling, where the reference configuration is the loaded in vivo state obtained from imaging. This state includes residual stress of the vascular constituents, as well as anisotropy from the spatially...
Preprint
We develop heuristic interpolation methods for the function $t \mapsto \operatorname{trace}\left( (\mathbf{A} + t \mathbf{B})^{-1} \right)$, where the matrices $\mathbf{A}$ and $\mathbf{B}$ are symmetric and positive definite and $t$ is a real variable. This function is featured in many applications in statistics, machine learning, and computationa...
Article
We propose a distributed lumped parameter (DLP) modeling framework to efficiently compute blood flow and pressure in vascular domains. This is achieved by developing analytical expressions describing expected energy losses along vascular segments, including from viscous dissipation, unsteadiness, flow separation, vessel curvature and vessel bifurca...
Article
Computational modeling of cardiovascular flows is becoming increasingly important in a range of biomedical applications, and understanding the fundamentals of computational modeling is important for engineering students. In addition to their purpose as research tools, integrated image-based computational fluid dynamics platforms can be used to teac...
Preprint
A pathologically formed blood clot or thrombus is central to major cardiovascular diseases like heart attack and stroke. Detailed quantitative evaluation of flow and flow-mediated transport processes in the thrombus neighborhood within large artery hemodynamics is crucial for understanding disease progression and assessing treatment efficacy. This,...
Preprint
Full-text available
The iterative ensemble Kalman filter (IEnKF) is widely used in inverse problems to estimate system parameters from limited observations. However, the IEnKF, when applied to nonlinear systems, can be plagued by poor convergence. Here we provide a comprehensive convergence analysis of the IEnKF and propose a new method to improve its convergence. A t...
Article
Full-text available
Using observation data to estimate unknown parameters in computational models is broadly important. This task is often challenging because solutions are non-unique due to the complexity of the model and limited observation data. However, the parameters or states of the model are often known to satisfy additional constraints beyond the model. Thus,...
Article
Mathematical modeling of thrombosis typically involves modeling the coagulation cascade. Models of coagulation generally involve the reaction kinetics for dozens of proteins. The resulting system of equations is difficult to parameterize and its numerical solution is challenging when coupled to blood flow or other physics important to clotting. Pri...
Article
Full-text available
Precise management of patients with cerebral diseases often requires intracranial pressure (ICP) monitoring, which is highly invasive and requires a specialized ICU setting. The ability to noninvasively estimate ICP is highly compelling as an alternative to, or screening for, invasive ICP measurement. Most existing approaches for noninvasive ICP es...
Article
Full-text available
Remote sensing of oceanographic data often yields incomplete coverage of the measurement domain. This can limit interpretability of the data and identification of coherent features informative of ocean dynamics. Several methods exist to fill gaps of missing oceanographic data and are often based on projecting the measurements onto basis functions o...
Preprint
Full-text available
Using observation data to estimate unknown parameters in computational models is broadly important. This task is often challenging because solutions are non-unique due to the complexity of the model and limited observation data. However, the parameters or states of the model are often known to satisfy additional constraints beyond the model. Thus,...
Article
Full-text available
Purpose Image-based computational fluid dynamics (CFD) is widely used to predict intracranial aneurysm wall shear stress (WSS), particularly with the goal of improving rupture risk assessment. Nevertheless, concern has been expressed over the variability of predicted WSS and inconsistent associations with rupture. Previous challenges, and studies f...
Article
Many cardiovascular processes involve mass transport between blood and the vessel wall. Finite element methods are commonly used to numerically simulate these processes. Cardiovascular mass transport problems are typically characterized by high Péclet numbers, requiring fine near‐wall mesh resolution as well as the use of stabilization techniques t...
Preprint
Remote sensing of oceanographic data often yields incomplete coverage of the measurement domain. This can limit interpretability of the data and identification of coherent features informative of ocean dynamics. Several methods exist to fill gaps of missing oceanographic data, and are often based on projecting the measurements onto basis functions...
Preprint
Full-text available
Precise management of patients with cerebral diseases often requires intracranial pressure (ICP) monitoring, which is highly invasive and requires a specialized ICU setting. The ability to noninvasively estimate ICP is highly compelling as an alternative to, or screening for, invasive ICP measurement. Most existing approaches for noninvasive ICP es...
Article
Image-based modeling is an active and growing area of biomedical research that utilizes medical imaging to create patient-specific simulations of physiological function. Under this paradigm, anatomical structures are segmented from a volumetric image, creating a geometric model that serves as a computational domain for physics-based modeling. A com...
Article
Full-text available
A hybrid, multiscale, particle–continuum numerical method is developed for resolving the interaction of a realistic thrombus geometry with unsteady hemodynamics typically occurring within large arteries. The method is based on a discrete particle/element description of the thrombus, coupled to blood flow using a fictitious domain finite element met...
Article
We describe a patient-specific simulation based investigation on the role of Circle of Willis anatomy in cardioembolic stroke. Our simulation framework consists of medical image-driven modeling of patient anatomy including the Circle, 3D blood flow simulation through patient vasculature, embolus transport modeling using a discrete particle dynamics...
Preprint
We describe a patient-specific simulation based investigation on the role of Circle of Willis anatomy in cardioembolic stroke. Our simulation framework consists of medical image-driven modeling of patient anatomy including the Circle, 3D blood flow simulation through patient vasculature, embolus transport modeling using a discrete particle dynamics...
Article
Complex blood flow in large arteries creates rich wall shear stress (WSS) vectorial features. WSS acts as a link between blood flow dynamics and the biology of various cardiovascular diseases. WSS has been of great interest in a wide range of studies and has been the most popular measure to correlate blood flow to cardiovascular disease. Recent stu...
Article
Full-text available
The airway structure continuously evolves from birth to adulthood, influencing airflow dynamics and respiratory mechanics. We currently know very little about how airflow patterns change throughout early life and its impact on airway resistance, namely because of experimental limitations. To uncover differences in respiratory dynamics between age g...
Article
Patient-specific simulation plays an important role in cardiovascular disease research, diagnosis, surgical planning and medical device design, as well as education in cardiovascular biomechanics. SimVascular is an open-source software package encompassing an entire cardiovascular modeling and simulation pipeline from image segmentation, 3D solid m...
Conference Paper
Lagrangian coherent structures provide insight into unsteady fluid flow, but their construction has posed many challenges. These structures can be characterized as ridges of a field, but their local definition utilizes an ambiguous eigenvector direction that can point in one of two directions, and its ambiguity can lead to noise and other problems....
Article
Full-text available
Near-wall transport is of utmost importance in connecting blood flow mechanics with cardiovascular disease progression. The near-wall region is the interface for biologic and pathophysiologic processes such as thrombosis and atherosclerosis. Most computational and experimental investigations of blood flow implicitly or explicitly seek to quantify h...
Article
Background: Early diagnosis of vasospasm following subarachnoid hemorrhage can prevent cerebral ischemia and improve neurological outcomes. This study numerically evaluates the relevance of extracranial blood velocity indices to detect vasospasm. Methods: A numerical model of cerebral blood flow was used to evaluate the hemodynamics associated w...
Article
Patient-specific cardiovascular simulation has become a paradigm in cardiovascular research and is emerging as a powerful tool in basic, translational and clinical research. In this paper we discuss the recent development of a fully open-source SimVascular software package, which provides a complete pipeline from medical image data segmentation to...
Article
Full-text available
A stabilizing criterion is derived for equations governing vascular growth and remodeling. We start from the integral state equations of the continuum-based constrained mixture theory of vascular growth and remodeling and obtain a system of time-delayed differential equations describing vascular growth. By employing an exponential form of the const...
Article
The complexity of inertial particle dynamics through swirling chaotic flow structures characteristic of pulsatile large-artery hemodynamics renders significant challenges in predictive understanding of transport of such particles. This is specifically crucial for arterial embolisms, where knowledge of embolus transport to major vascular beds helps...
Article
Full-text available
Little is known about transport throughout the respiration cycle in the conducting airways. It is challenging to appropriately describe the time-dependent number of particles entering back into the model during exhalation. Modeling the entire lung is not feasible; therefore multi-domain methods must be employed. Here, we present a new framework tha...
Article
Stroke caused by an embolism accounts for about a third of all stroke cases. Understanding the source and cause of the embolism is critical for diagnosis and long-term treatment of such stroke cases. The complex nature of the transport of an embolus within large arteries is a primary hindrance to a clear understanding of embolic stroke etiology. Re...
Article
The development of discrete solid models from imaging has become a common practice in reverse engineering. This has motivated the need for tools to combine and manipulate discrete boundary representation of objects. Despite the importance of this problem in computer aided engineering, there is a lack of robust and efficient open-source implementati...
Article
Full-text available
The wall shear stress (WSS) vector field provides a signature for near-wall convective transport, and can be scaled to obtain a first-order approximation of the near-wall fluid velocity. The near-wall flow field governs mass transfer problems in convection-dominated open flows with high Schmidt number, in which case a flux at the wall will lead to...
Article
Background and Objectives: Early diagnosis of vasospasm after subarachnoid hemorrhage (SAH) can prompt aggressive treatment and improve neurological outcomes. Transcranial Doppler (TCD) is the only diagnosis modality that is noninvasive and available bedside. The purpose of this study was to numerically evaluate the relevance of various blood veloc...
Article
In the healthy heart, left ventricular (LV) filling generates different flow patterns which have been proposed to optimize blood transport by coupling diastole and systole. This work presents a novel image-based method to assess how different flow patterns influence LV blood transport in patients undergoing cardiac resynchronization therapy (CRT)....
Article
Full-text available
Wall shear stress (WSS) is one of the most studied hemodynamic parameters, used in correlating blood flow to various diseases. The pulsatile nature of blood flow, along with the complex geometries of diseased arteries, produces complicated temporal and spatial WSS patterns. Moreover, WSS is a vector, which further complicates its quantification and...
Article
Tracing the paths of collections of particles through a flow field is a key step for many flow visualization and analysis methods. When a flow field is interpolated from the nodes of an unstructured mesh, the process of advecting a particle must first find which cell in the unstructured mesh contains the particle. Since the paths of nearby particle...
Article
Full-text available
Near-wall mass transport plays an important role in many cardiovascular processes, including the initiation of atherosclerosis, endothelial cell vasoregulation, and thrombogenesis. These problems are characterized by large Péclet and Schmidt numbers as well as a wide range of spatial and temporal scales, all of which impose computational difficulti...
Article
The cerebral circulation is unique in its ability to maintain blood flow to the brain under widely varying physiologic conditions. Incorporating this autoregulatory response is necessary for cerebral blood flow modeling, as well as investigations into pathological conditions. We discuss a one-dimensional (1-D) nonlinear model of blood flow in the c...
Article
Full-text available
Roughly one-third of all strokes are caused by an embolus traveling to a cerebral artery and blocking blood flow in the brain. The objective of this study is to gain a detailed understanding of the dynamics of embolic particles within arteries. Patient computed tomography image is used to construct a three-dimensional model of the carotid bifurcati...
Article
Intraluminal thrombus (ILT) in abdominal aortic aneurysm (AAA) has potential implications to aneurysm growth and rupture risk, yet the mechanisms underlying its development remain poorly understood. Some researchers have proposed that ILT development may be driven by biomechanical platelet activation within the AAA, followed by adhesion in regions...
Article
Full-text available
A computational framework to couple vascular growth and remodeling (G&R) with blood flow simulation in a 3D patient-specific geometry is presented. Hyperelastic and anisotropic properties are considered for the vessel wall material and a constrained mixture model is used to represent multiple constituents in the vessel wall, which was modeled as a...
Article
Full-text available
Abdominal aortic aneurysm (AAA) is often accompanied by intraluminal thrombus (ILT), which complicates AAA progression and risk of rupture. Patient specific computational fluid dynamics modeling of 10 small human AAA was performed to investigate relations between hemodynamics and ILT progression. The patients were imaged using magnetic resonance tw...
Article
Full-text available
Recent advances in imaging, modeling, and computing have rapidly expanded our capabilities to model hemodynamics in the large vessels (heart, arteries, and veins). This data encodes a wealth of information that is often under-utilized. Modeling (and measuring) blood flow in the large vessels typically amounts to solving for the time-varying velocit...
Article
Full-text available
Image-based in silico modeling tools provide detailed velocity and particle deposition data. However, care must be taken when prescribing boundary conditions to model lung physiology in health or disease, such as in emphysema. In this study, the respiratory resistance and compliance were obtained by solving an inverse problem; a 0D global model bas...
Article
Full-text available
Computational fluid dynamics modeling was used to investigate changes in blood transport topology between rest and exercise conditions in five patient-specific abdominal aortic aneurysm models. MRI was used to provide the vascular anatomy and necessary boundary conditions for simulating blood velocity and pressure fields inside each model. Finite-t...
Chapter
The computation of Lagrangian coherent structures (LCS) has become a standard tool for the analysis of advective transport in unsteady flow applications. LCS identification is primarily accomplished by evaluating measures based on the finite-time Cauchy Green (CG) strain tensor over the fluid domain. Sampling the CG tensor requires the advection of...
Article
Full-text available
We study coherent structures in solar photospheric flows in a plage in the vicinity of the active region AR 10930 using the horizontal velocity data derived from Hinode/SOT magnetograms. Eulerian and Lagrangian coherent structures are detected by computing the Q-criterion and the finite-time Lyapunov exponents of the velocity field, respectively. O...
Article
Full-text available
Novel processing of Doppler-echocardiography data was used to study blood transport in the left ventricle (LV) of six patients with dilated cardiomyopathy and six healthy volunteers. Bi-directional velocity field maps in the apical long axis of the LV were reconstructed from color-Doppler echocardiography. Resulting velocity field data were used to...
Conference Paper
Full-text available
Because the left ventricle (LV) is not completely emptied during systole, oxygenated blood from the left atrium interacts with residual blood from preceding cycles. It is hypothesized that LV flow is optimal for transporting blood under normal conditions; yet proving this remains a challenge. Furthermore, clinical evaluation of LV hemodynamics has...