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Propagation and attenuation of mechanical signals in ultrasoft 2D solids.

ABSTRACT: The propagation of elastic waves in soft materials plays a crucial role in the spatiotemporal transmission of mechanical signals, e.g., in biological mechanotransduction or in the failure of marginal solids. At high Reynolds numbers Re ? 1, inertia dominates and wave propagation is readily observed. However, mechanical cues in soft and biological materials often occur at low Re, where waves are overdamped. Overdamped waves are not only difficult to observe experimentally, also theoretically their description remains incomplete. Here, we present direct measurements of the propagation and attenuation of mechanical signals in colloidal soft solids, induced by an optical trap. We derive an analytical theory for low Re wave propagation and damping, which is in excellent agreement with the experiments. Our results present both a previously unexplored method to characterize damped waves in soft solids and a theoretical framework showing how localized mechanical signals can provoke a remote and delayed response.

SUBMITTER: van Doorn JM

PROVIDER: S-EPMC7486091 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Propagation and attenuation of mechanical signals in ultrasoft 2D solids.

van Doorn Jan Maarten JM Higler Ruben R Wegh Ronald R Fokkink Remco R Zaccone Alessio A Sprakel Joris J van der Gucht Jasper J

Science advances 20200911 37

The propagation of elastic waves in soft materials plays a crucial role in the spatiotemporal transmission of mechanical signals, e.g., in biological mechanotransduction or in the failure of marginal solids. At high Reynolds numbers <i>Re</i> ≫ 1, inertia dominates and wave propagation is readily observed. However, mechanical cues in soft and biological materials often occur at low <i>Re</i>, where waves are overdamped. Overdamped waves are not only difficult to observe experimentally, also theo ...[more]

PMID: 32917701

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Project description:Recent developments in modern computational accelerators like Graphics Processing Units (GPUs) and coprocessors provide great opportunities for making scientific applications run faster than ever before. However, efficient parallelization of scientific code using new programming tools like CUDA requires a high level of expertise that is not available to many scientists. This, plus the fact that parallelized code is usually not portable to different architectures, creates major challenges for exploiting the full capabilities of modern computational accelerators. In this work, we sought to overcome these challenges by studying how to achieve both automated parallelization using OpenACC and enhanced portability using OpenCL. We applied our parallelization schemes using GPUs as well as Intel Many Integrated Core (MIC) coprocessor to reduce the run time of wave propagation simulations. We used a well-established 2D cardiac action potential model as a specific case-study. To the best of our knowledge, we are the first to study auto-parallelization of 2D cardiac wave propagation simulations using OpenACC. Our results identify several approaches that provide substantial speedups. The OpenACC-generated GPU code achieved more than 150x speedup above the sequential implementation and required the addition of only a few OpenACC pragmas to the code. An OpenCL implementation provided speedups on GPUs of at least 200x faster than the sequential implementation and 30x faster than a parallelized OpenMP implementation. An implementation of OpenMP on Intel MIC coprocessor provided speedups of 120x with only a few code changes to the sequential implementation. We highlight that OpenACC provides an automatic, efficient, and portable approach to achieve parallelization of 2D cardiac wave simulations on GPUs. Our approach of using OpenACC, OpenCL, and OpenMP to parallelize this particular model on modern computational accelerators should be applicable to other computational models of wave propagation in multi-dimensional media.

Dataset Information

Propagation and attenuation of mechanical signals in ultrasoft 2D solids.

Publications

Propagation and attenuation of mechanical signals in ultrasoft 2D solids.

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