Matthias Christen

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Stencil calculations comprise an important class of kernels in many scientific computing applications ranging from simple PDE solvers to constituent kernels in multigrid methods as well as image processing applications. In such types of solvers, stencil kernels are often the dominant part of the computation, and an efficient parallel implementation of the(More)
— We report on our experience with integrating and using graphics processing units (GPUs) as fast parallel floating-point co-processors to accelerate two fundamental computational scientific kernels on the GPU: sparse direct factorization and non-linear interior-point optimization. Since a full re-implementation of these complex kernels is typically not(More)
The bacterial second messenger cyclic diguanosine monophosphate (c-di-GMP) regulates cellular motility and the synthesis of organelles and molecules that promote adhesion to a variety of biological and nonbiological surfaces. These properties likely require tight spatial and temporal regulation of c-di-GMP concentration. We have developed genetically(More)
We report on our experience with integrating and using graphics processing units (GPUs) as fast parallel floating-point co-processors to accelerate two fundamental computational scientific kernels on the GPU: sparse direct factorization and nonlinear interior-point optimization. Since a full re-implementation of these complex kernels is typically not(More)
We present a PDE-constrained optimization algorithm which is designed for parallel scalability on distributed-memory architectures with thousands of cores. The method is based on a line-search interior-point algorithm for large-scale continuous optimization, it is matrix-free in that it does not require the factorization of derivative matrices. Instead, it(More)
In this paper, we present PATUS, a code generation and auto-tuning framework for stencil computations targeted at multi-and manycore processors, such as mul-ticore CPUs and graphics processing units. PATUS, which stands for " Parallel Autotuned Stencils, " generates a compute kernel from a specification of the stencil operation and a strategy which(More)
Patus is a code generation and auto-tuning framework for stencil computations targeting modern multi and many-core processors. The goals of the framework are productivity and portability for achieving high performance on the target platform. Its stencil specification language allows the programmer to express the computation in a concise way independently of(More)
Novel micro-architectures including the Cell Broadband Engine Architecture and graphics processing units are attractive platforms for compute-intensive simulations. This paper focuses on stencil computations arising in the context of a biomedical simulation and presents performance benchmarks on both the Cell BE and GPUs and contrasts them with a benchmark(More)
Synthetic devices for traceless remote control of gene expression may provide new treatment opportunities in future gene- and cell-based therapies. Here we report the design of a synthetic mind-controlled gene switch that enables human brain activities and mental states to wirelessly programme the transgene expression in human cells. An(More)
BACKGROUND The main goals of the standard treatment for advanced symptomatic knee osteoarthritis, total knee arthroplasty (TKA), are pain reduction and restoration of knee motion.The aim of this study was to analyse the outcome of the patient-based Knee Injury and Osteoarthritis Outcome Score (KOOS), and the surgeon-based Knee Society Score (KSS) and its(More)