Massively parallel simulations of hemodynamics in the primary large arteries of the human vasculature

We present a computational model of three-dimensional and unsteady hemodynamics within the primary large arteries in the human on 1,572,864 cores of the IBM Blue Gene/Q. Models of large regions of the circulatory system are needed to study the impact of local factors on global hemodynamics and to inform next generation drug delivery mechanisms. The HARVEY code successfully addresses key challenges that can hinder effective solution of image-based hemodynamics on contemporary supercomputers, such as limited memory capacity and bandwidth, flexible load balancing, and scalability. This work is the first demonstration of large fluid dynamics simulations of the aortofemoral region of the circulatory system at resolutions as small as 10 μm.

High-resolution fluid-structure interaction simulations of flow through a bi-leaflet mechanical heart valve in an anatomic aorta

We have performed high-resolution fluid-structure interaction simulations of physiologic pulsatile flow through a bi-leaflet mechanical heart valve (BMHV) in an anatomically realistic aorta. The results are compared with numerical simulations of the flow through an identical BMHV implanted in a straight aorta. The comparisons show that although some of the salient features of the flow remain the same, the aorta geometry can have a major effect on both the flow patterns and the motion of the valve leaflets. For the studied configuration, for instance, the BMHV leaflets in the anatomic aorta open much faster and undergo a greater rebound during closing than the same valve in the straight axisymmetric aorta. Even though the characteristic triple-jet structure does emerge downstream of the leaflets for both cases, for the anatomic case the leaflet jets spread laterally and diffuse much faster than in the straight aorta due to the aortic curvature and complex shape of the anatomic sinus. Consequently the leaflet shear layers in the anatomic case remain laminar and organized for a larger portion of the accelerating phase as compared to the shear layers in the straight aorta, which begin to undergo laminar instabilities well before peak systole is reached. For both cases, however, the flow undergoes a very similar explosive transition to the small-scale, turbulent-like state just prior to reaching peak systole. The local maximum shear stress is used as a metric to characterize the mechanical environment experienced by blood cells. Pockets of high local maximum shear are found to be significantly more widespread in the anatomic aorta than in the straight aorta throughout the cardiac cycle. Pockets of high local maximum shear were located near the leaflets and in the aortic arc region. This work clearly demonstrates the importance of the aortic geometry on the flow phenomena in a BMHV and demonstrates the potential of our computational method to carry out image-based patient-specific simulations for clinically relevant studies of heart valve hemodynamics.

Radio frequency ablation registration, segmentation, and fusion tool

The radio frequency ablation segmentation tool (RFAST) is a software application developed using the National Institutes of Health's medical image processing analysis and visualization (MIPAV) API for the specific purpose of assisting physicians in the planning of radio frequency ablation (RFA) procedures. The RFAST application sequentially leads the physician through the steps necessary to register, fuse, segment, visualize, and plan the RFA treatment. Three-dimensional volume visualization of the CT dataset with segmented three dimensional (3-D) surface models enables the physician to interactively position the ablation probe to simulate burns and to semimanually simulate sphere packing in an attempt to optimize probe placement. This paper describes software systems contained in RFAST to address the needs of clinicians in planning, evaluating, and simulating RFA treatments of malignant hepatic tissue.

Distribution of wall shear rate throughout the arterial tree: a case study

The generally accepted assumption that the arterial system remodels itself to maintain constant wall shear stress throughout is based on Murray's law, utilising the principle of minimum work for steady flow. However, blood flow in the human arterial system is pulsatile. In this work we outline a method allowing for estimation of wall shear rate in arteries using the flow waveforms as the input signal and estimate wall shear rates in the common carotid, brachial, and femoral arteries to determine the uniformity of distribution of wall shear rates throughout the arterial system. Time-dependent wall shear rates occurring in fully developed pulsatile flow were obtained using Womersley's theory. Flow waveforms and radii of the arteries measured in a young healthy male subject without any known cardiac disease using magnetic resonance taken from the literature were used as the input to the model. Peak/mean wall shear rates were found to be (1640/403.2 s(-1)) in common carotid, (908.8/84.95 s(-1)) in brachial, and (1251/134.2 s(-1)) in femoral arteries. Our findings suggest a non-uniform distribution of wall shear rates throughout the arterial system. The advantage of using this method is that such input data are being routinely recorded during diagnostic ultrasonography.

Patient-specific initial wall stress in abdominal aortic aneurysms with a backward incremental method

Patient-specific wall stress simulations on abdominal aortic aneurysms may provide a better criterion for surgical intervention than the currently used maximum transverse diameter. In these simulations, it is common practice to compute the peak wall stress by applying the full systolic pressure directly on the aneurysm geometry as it appears in medical images. Since this approach does not account for the fact that the measured geometry is already experiencing a substantial load, it may lead to an incorrect systolic aneurysm shape. We have developed an approach to compute the wall stress on the true diastolic geometry at a given pressure with a backward incremental method. The method has been evaluated with a neo-Hookean material law for several simple test problems. The results show that the method can predict an unloaded configuration if the loaded geometry and the load applied are known. The effect of incorporating the initial diastolic stress has been assessed by using three patient-specific geometries acquired with cardiac triggered MR. The comparison shows that the commonly used approach leads to an unrealistically smooth systolic geometry and therefore provides an underestimation for the peak wall stress. Our backward incremental modelling approach overcomes these issues and provides a more plausible estimate for the systolic aneurysm volume and a significantly different estimate for the peak wall stress. When the approach is applied with a more complex material law which has been proposed specifically for abdominal aortic aneurysm similar effects are observed and the same conclusion can be drawn.

Computational modeling of type I collagen fibers to determine the extracellular matrix structure of connective tissues

A method is presented for generating computer models of biological tissues. The method uses properties of extracellular matrix proteins to predict the structure and physical chemistry of the elements that make up the tissue. The method begins with Protein Data Bank coordinate positions of amino acids as input into TissueLab software. From the amino acid sequence, a type I collagen-like triple helix backbone was computationally constructed and boundary spheres were added based on known chemical and physical properties of the amino acids. Boundary spheres determined the contact surface characteristics of the collagen molecules and intermolecular interactions were then determined by considering the relationships of the contact surfaces and by resolving the energy-minimum state using feasible sequential quadratic programming. From this, the software created fibrils that corresponded exactly to known collagen parameters and were further confirmed by finite element modeling. Computationally derived fibrils were then used to create collagen fibers and three-dimensional collagen matrices. By resolving the energy-minimum state, large complex components of the extracellular space as well as other structures can be determined to provide three-dimensional structure of molecules, molecular interactions and the tissues that they form.

Level set-based integration of segmentation and computational fluid dynamics for flow correction in phase contrast angiography

RATIONALE AND OBJECTIVES

A novel method to correct flow data from magnetic resonance phase contrast (MR-PC) angiography, based on combining computational fluid dynamics and segmentation in a level set framework, was developed and tested in this study.

MATERIALS AND METHODS

The MR-PC velocity data was used in a partial differential equation-based level set method for vessel segmentation. The results were supplied as the quantitative description of the vessel wall to the flow field solver using computational fluid dynamics, based on the level set method, to obtain a physically meaningful flow. The most significant characteristic of our novel approach is that it requires light computational loads, especially insofar as it avoids generation of complex computational grid system. The integration of segmentation and computational fluid dynamics in a level set framework is shown to be both robust and economic, and yet yields a physically correct velocity field and optimal vessel geometry.

RESULTS

The application to the flow field in a straight tube with circular cross section of constant radius demonstrated the validity of out new approach, especially the treatment of the velocity boundary conditions on the solid wall. Simulation of the velocity field in both common carotid artery and bifurcation of basilar and vertebral arteries, based on clinical MR-PC data, provided with smooth and stable results.

CONCLUSION

Applying this procedure to both synthetic and clinical data, significant improvement of the blood velocity field, such as a smooth velocity distribution aligned along the vessels and removal of burst or error vectors, could be observed. This procedure also offers possibilities for improved vessel segmentation.

Characterization of flow reduction properties in an aneurysm due to a stent

We consider a lattice Boltzmann simulation of blood flow in a vessel deformed by the presence of an aneurysm. Modern clinical treatments involve introducing a stent (a tubular mesh of wires) into the cerebral artery in order to reduce the flow inside the aneurysm and favor its spontaneous reabsorption. A crucial question is to design the stent with suitable porosity so as to produce the most effective flow reduction. We propose a stent positioning factor as a characterizing tool for stent pore design in order to describe the flow reduction effect and reveal the several flow reduction mechanisms using this effect.