Software

Current Research Software

Primary author:

• heart_valves: Model generation with elasticity-based design and fluid-structure interaction (FSI) for aortic and mitral valves. Includes code that calls IBAMR for FSI and visualization. Used in publications: [Sim-Guided Design of Surgical Repair], [Clinical Translation of Surgical Repair], [Rare Disease Physiology of Truncus Arteriosus], [Mitral Elasticity-Based Design], [Aortic Elasticity-Based Design], [Sim-Guided Design of Surgical Repair II], [4D MRI Comparison], [Bicuspid Flows], [Zebrafish].

Contributor:

• IBAMR: Immersed boundary adaptive mesh refinement, fluid-structure interaction code suitable for simulating heart valve mechanics. Derived and implemented a new delta function kernel with three continuous derivatives. Used in preprint: [Gaussian-Like Kernels]

• svZeroDSolver: Lumped-parameter solver in C++ for blood flow and pressure in hemodynamic networks. Prototyped a two-hill chamber activation model and a parameter-tuning workflow, which served as drafts for features later added to the solver.

• svFSI: Multi-physics finite element solver for patient-specific blood flow simulation, including fluid-structure interaction and cardiac electrophysiology. Helped establish the open-source svFSI repository from internal legacy code.

• SimVascular: Comprehensive tools for modeling and simulation of patient-specific vascular flows. Used for image segmentation and model construction; maintained a fork adding an option to disable reslice interpolation, so MRI planes display without blurring on oblique views or widely spaced slices.

Earlier Work

Primary author:

• mc_stretch: Fast, affine-invariant, GPU parallel MCMC. Developed in thesis: [MS Thesis]

• SimplifySum: Automatic simplification of symbolic sums in Mathematica, over 1000x faster than built-in Mathematica algorithms on certain problems. Developed for and used in publication: [Auto-Simplification]

Contributor:

• ARPREC: Arbitrary precision arithmetic in C++ with overloaded operators. Handled library maintenance, documentation and user issues while at Lawrence Berkeley National Laboratory, 2009–2011; now mirrored by David H. Bailey.

• QD: Double-double and quad double precision arithmetic in C++ with overloaded operators. Handled library maintenance, documentation and user issues while at Lawrence Berkeley National Laboratory, 2009–2011; now mirrored by David H. Bailey.

• MatrixFFT: Apple’s proprietary high-performance FFT library. Developed a C/Fortran mixed-language interface as a cooperative researcher in the Advanced Computation Group in 2010.