Designing optimal shunts for newborns with heart defects using computational modeling

By | General Interest, Happenings, News, Research

shuntFor babies born with hypoplastic left heart syndrome, several open-heart surgeries are required. During Stage I, a Norwood procedure is performed to construct an appropriate circulation to both the systemic and the pulmonary arteries. The pulmonary arteries receive flow from the systemic circulation, often by using a Blalock-Taussig (BT) shunt between the innominate artery and the right pulmonary artery. This procedure causes significantly disturbed flow in the pulmonary arteries.

A group of researchers led by U-M Drs. Ronald Grifka and Alberto Figueroa used computational hemodynamic simulations to demonstrate its capacity for examining the properties of the flow through and near the BT shunt. Initially, the researchers constructed a computational model which produces blood flow and pressure measurements matching the clinical magnetic resonance imaging (MRI) and catheterization data. Achieving this required us to determine the level of BT shunt occlusion; because the occlusion is below the MRI resolution, this information is difficult to recover without the aid of computational simulations. The researchers determined that the shunt had undergone an effective diameter reduction of 22% since the time of surgery. Using the resulting geometric model, they showed that we can computationally reproduce the clinical data. The researchers then replaced the BT shunt by with a hypothetical alternative shunt design with a flare at the distal end. Investigation of the impact of the shunt design revealed that the flare can increase pulmonary pressure by as much as 7%, and flow by as much as 9% in the main pulmonary branches, which may be beneficial to the pulmonary circulation.

Read more in Frontiers in Pediatrics.

Combining simulation and experimentation yields complex crystal nanoparticle

By | General Interest, News, Research

The most complex crystal designed and built from nanoparticles has been reported by researchers at Northwestern University and the University of Michigan. The work demonstrates that some of nature’s most complicated structures can be deliberately assembled if researchers can control the shapes of the particles and the way they connect using DNA.

The U-M researcher is Sharon C. Glotzer, the John W. Cahn Distinguished University Professor of Engineering and the Stuart W. Churchill Collegiate Professor of Chemical Engineering. The work is published in the March 3 issue of Science. ARC’s computational resources supported the work.

[SC2] DEMO: Visualizations on remote resources

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Results of adaptive simulations of a three-dimensional wing undergoing flapping motion in viscous flow. The target output of interest is the lift at the end of the simulation. Tailored meshes are created by increasing the approximation order on selected elements identified by an output-sensitivity error estimate. The resulting output converges much faster in terms of total degrees of freedom used when compared to other adaptive methods, including residual-based adaptation and uniform order refinement.

Results of adaptive simulations of a three-dimensional wing undergoing flapping motion in viscous flow. K. Fidkowski (U-M Aerospace)

One of the advantages of scientific computing research is the ability to use powerful supercomputers from the convenience of your home computer, laptop, tablet, or even phone! In the next SC2 meeting club members will be demonstrating how you can use these remote resources to run and visualize simulations. Additionally, we will be demonstrating the “scientific python” stack (Python, NumPy, Scipy) to duplicate MATLAB functionality with free, open source software.

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U-M team uses Flux HPC cluster for pre-surgery simulations

By | Flux, General Interest, News

Last summer, Alberto Figueroa’s BME lab at the University of Michigan achieved an important “first” – using computer-generated blood flow simulations to plan a complex cardiovascular procedure.

“I believe this is the first time that virtual surgical planning was done for real and not as a retrospective theoretical exercise ,” says Figueroa.

Using a patient’s medical and imaging data, Figueroa was able to create a model of her unique vasculature and blood flow, then use it to guide U-M pediatric cardiologists Aimee Armstrong, Martin Bocks, and Adam Dorfman in placing a graft in her inferior vena cava to help alleviate complications from pulmonary arteriovenous malformations (PAVMs). The simulations were done using the Flux HPC cluster.

Read more…

U-M software package HOOMD-blue chosen as benchmark for new GPU performance by NVIDIA

By | General Interest, News

HOOMD-blue, a University of Michigan-produced software package for particle simulation, was chosen as one of seven benchmark applications to demonstrate the speed of NVIDIA’s new Tesla P100 GPU.

HOOMD-blue was developed by Prof. Sharon Glotzer’s research group. It lets users define particle initial conditions and interactions in a high-level Python script. Python job scripts provide the flexibility to create custom initialization routines, control simulation parameters, and perform in situ analysis.

Webinars title “Introduction to HOOMD-blue” and “Using HOOMD-blue for Polymer Simulations and Big Systems” are available for viewing.