A simultaneous solution procedure for fully coupled fluid flows with structural interactions

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1999.Includes bibliographical references (p. 85-88).by Sandra Rugonyi.S.M

Characterization of the dynamic response of continuous system discretized using finite element methods

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2001.Includes bibliographical references (leaves 122-125).Nonlinear dynamic physical systems exhibit a rich variety of behaviors. In many cases, the system response is unstable, and the behavior may become unpredictable. Since an unstable or unpredictable response is usually undesirable in engineering practice, the stability characterization of a system's behavior becomes essential. In this work, a numerical procedure to characterize the dynamic stability of continuous solid media, discretized using finite element methods, is proposed. The procedure is based on the calculation of the maximum Lyapunov characteristic exponent (LCE), which provides information about the asymptotic stability of the system response. The LCE is a measure of the average divergence or convergence of nearby trajectories in the system phase space, and a positive LCE indicates that the system asymptotic behavior is chaotic, or, in other words, asymptotically dynamically unstable. In addition, a local temporal stability indicator is proposed to reveal the presence of local dynamic instabilities in the response. Using the local stability indicator, dynamic instabilities can be captured shortly after they occur in a numerical calculation. The indicator can be obtained from the successive approximations of the response LCE calculated at each discretized time step. Both procedures can also be applied to fluid-structure interaction problems in which the analysis focuses on the behavior of the structural part.(cont.) The response of illustrative structural systems and fluid flow-structure interaction systems, in which the fluid is modeled using the Navier-Stokes equations, was calculated. The systems considered present both stable and unstable behaviors, and their LCEs and local stability indicators were computed using the proposed procedures. The stability of the complex behaviors exhibited by the problems considered was properly captured by both approaches, confirming the validity of the procedures proposed in this work.by Sandra Rugonyi.Ph.D

4-D Computational Modeling of Cardiac Outflow Tract Hemodynamics over Looping Developmental Stages in Chicken Embryos

Cardiogenesis is interdependent with blood flow within the embryonic system. Recently, a number of studies have begun to elucidate the effects of hemodynamic forces acting upon and within cells as the cardiovascular system begins to develop. Changes in flow are picked up by mechanosensors in endocardial cells exposed to wall shear stress (the tangential force exerted by blood flow) and by myocardial and mesenchymal cells exposed to cyclic strain (deformation). Mechanosensors stimulate a variety of mechanotransduction pathways which elicit functional cellular responses in order to coordinate the structural development of the heart and cardiovascular system. The looping stages of heart development are critical to normal cardiac morphogenesis and have previously been shown to be extremely sensitive to experimental perturbations in flow, with transient exposure to altered flow dynamics causing severe late stage cardiac defects in animal models. This paper seeks to expand on past research and to begin establishing a detailed baseline for normal hemodynamic conditions in the chick outflow tract during these critical looping stages. Specifically, we will use 4-D (3-D over time) optical coherence tomography to create in vivo geometries for computational fluid dynamics simulations of the cardiac cycle, enabling us to study in great detail 4-D velocity patterns and heterogeneous wall shear stress distributions on the outflow tract endocardium. This information will be useful in determining the normal variation of hemodynamic patterns as well as in mapping hemodynamics to developmental processes such as morphological changes and signaling events during and after the looping stages examined here

Few-shot hypercolumn-based mitochondria segmentation in cardiac and outer hair cells in focused ion beam-scanning electron microscopy (FIB-SEM) data

We present a novel AI-based approach to the few-shot automated segmentation of mitochondria in large-scale electron microscopy images. Our framework leverages convolutional features from a pre-trained deep multilayer convolutional neural network, such as VGG-16. We then train a binary gradient boosting classifier on the resulting high-dimensional feature hypercolumns. We extract VGG-16 features from the first four convolutional blocks and apply bilinear upsampling to resize the obtained maps to the input image size. This procedure yields a 2688-dimensional feature hypercolumn for each pixel in a 224 x 224 input image. We then apply L1-regularized logistic regression for supervised active feature selection to reduce dependencies among the features, to reduce overfitting, as well as to speed-up gradient boosting-based training. During inference we block process 1728 x 2022 large microscopy images. Our experiments show that in such a formulation of transfer learning our processing pipeline is able to achieve high-accuracy results on very challenging datasets containing a large number of irregularly shaped mitochondria in cardiac and outer hair cells. Our proposed few-shot training approach gives competitive performance with the state-of-the-art using far less training data

A domain decomposition approach for coupled modelling of nonlinear soil-structure interaction

Accepted versio

Measurement of absolute blood flow velocity in outflow tract of HH18 chicken embryo based on 4D reconstruction using spectral domain optical coherence tomography

The measurement of blood-plasma absolute velocity distributions with high spatial and temporal resolution in vivo is important for the investigation of embryonic heart at its early stage of development. We introduce a novel method to measure absolute blood flow velocity based on high speed spectral domain optical coherence tomography (OCT) and apply it to measure velocities across the heart outflow tract (OFT) of a chicken embryo (stage HH18). First, we use the OCT system to acquire 4D 
[(x,y,z) + t] images of the OFT in vivo. Second, we reconstruct the 4D microstructural images and obtain the orientation of the OFT at its maximum expansion, from which the centerline of the OFT is calculated based on the OFT boundary segmentation. Assuming flow is parallel to the vessel orientation, the obtained centerline indicates the flow direction. Finally, the absolute flow velocity is evaluated based on the direction given by the centerline and the axial velocity obtained from Doppler OCT. Using this method, we compare flow velocity profiles at various positions along the chicken embryo OFT

Effect of altered haemodynamics on the developing mitral valve in chick embryonic heart

Intracardiac haemodynamics is crucial for normal cardiogenesis, with recent evidence showing valvulogenesis is haemodynamically dependent and inextricably linked with shear stress. Although valve anomalies have been associated with genetic mutations, often the cause is unknown. However, altered haemodynamics have been suggested as a pathogenic contributor to bicuspid aortic valve disease. Conversely, how abnormal haemodynamics impacts mitral valve development is still poorly understood. In order to analyse altered blood flow, the outflow tract of the chick heart was constricted using a ligature to increase cardiac pressure overload. Outflow tract-banding was performed at HH21, with harvesting at crucial valve development stages (HH26, HH29 and HH35). Although normal valve morphology was found in HH26 outflow tract banded hearts, smaller and dysmorphic mitral valve primordia were seen upon altered haemodynamics in histological and stereological analysis at HH29 and HH35. A decrease in apoptosis, and aberrant expression of a shear stress responsive gene and extracellular matrix markers in the endocardial cushions were seen in the chick HH29 outflow tract banded hearts. In addition, dysregulation of extracellular matrix (ECM) proteins fibrillin-2, type III collagen and tenascin were further demonstrated in more mature primordial mitral valve leaflets at HH35, with a concomitant decrease of ECM cross-linking enzyme, transglutaminase-2. These data provide compelling evidence that normal haemodynamics are a prerequisite for normal mitral valve morphogenesis, and abnormal blood flow could be a contributing factor in mitral valve defects, with differentiation as a possible underlying mechanism