Dataset Information

In Situ Visualization for 3D Agent-Based Vocal Fold Inflammation and Repair Simulation.

ABSTRACT: A fast and insightful visualization is essential in modeling biological system behaviors and understanding underlying inter-cellular mechanisms. High fidelity models produce billions of data points per time step, making in situ visualization techniques extremely desirable as they mitigate I/O bottlenecks and provide computational steering capability. In this work, we present a novel high-performance scheme to couple in situ visualization with the simulation of the vocal fold inflammation and repair using little to no extra cost in execution time or computing resources. The visualization component is first optimized with an adaptive sampling scheme to accelerate the rendering process while maintaining the precision of the displayed visual results. Our software employs VirtualGL to perform visualization in situ. The scheme overlaps visualization and simulation, resulting in the optimal utilization of computing resources. This results in an in situ system biology simulation suite capable of remote simulation of 17 million biological cells and 1.2 billion chemical data points, remote visualization of the results, and delivery of visualized frames with aggregated statistics to remote clients in real-time.

SUBMITTER: Seekhao N

PROVIDER: S-EPMC5701753 | biostudies-literature | 2017 Jul-Sep

REPOSITORIES: biostudies-literature

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Publications

In Situ Visualization for 3D Agent-Based Vocal Fold Inflammation and Repair Simulation.

Seekhao Nuttiiya N JaJa Joseph J Mongeau Luc L Li-Jessen Nicole Y K NYK

Supercomputing frontiers and innovations 20170701 3

A fast and insightful visualization is essential in modeling biological system behaviors and understanding underlying inter-cellular mechanisms. High fidelity models produce billions of data points per time step, making <i>in situ</i> visualization techniques extremely desirable as they mitigate I/O bottlenecks and provide computational steering capability. In this work, we present a novel high-performance scheme to couple <i>in situ</i> visualization with the simulation of the vocal fold inflam ...[more]

PMID: 29177201

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Project description:Human voice is generated in the larynx by the two oscillating vocal folds. Owing to the limited space and accessibility of the larynx, endoscopic investigation of the actual phonatory process in detail is challenging. Hence the biomechanics of the human phonatory process are still not yet fully understood. Therefore, we adapt a mathematical model of the vocal folds towards vocal fold oscillations to quantify gender and age related differences expressed by computed biomechanical model parameters.The vocal fold dynamics are visualized by laryngeal high-speed videoendoscopy (4000 fps). A total of 33 healthy young subjects (16 females, 17 males) and 11 elderly subjects (5 females, 6 males) were recorded. A numerical two-mass model is adapted to the recorded vocal fold oscillations by varying model masses, stiffness and subglottal pressure. For adapting the model towards the recorded vocal fold dynamics, three different optimization algorithms (Nelder-Mead, Particle Swarm Optimization and Simulated Bee Colony) in combination with three cost functions were considered for applicability. Gender differences and age-related kinematic differences reflected by the model parameters were analyzed.The biomechanical model in combination with numerical optimization techniques allowed phonatory behavior to be simulated and laryngeal parameters involved to be quantified. All three optimization algorithms showed promising results. However, only one cost function seems to be suitable for this optimization task. The gained model parameters reflect the phonatory biomechanics for men and women well and show quantitative age- and gender-specific differences. The model parameters for younger females and males showed lower subglottal pressures, lower stiffness and higher masses than the corresponding elderly groups. Females exhibited higher subglottal pressures, smaller oscillation masses and larger stiffness than the corresponding similar aged male groups. Optimizing numerical models towards vocal fold oscillations is useful to identify underlying laryngeal components controlling the phonatory process.

Dataset Information

In Situ Visualization for 3D Agent-Based Vocal Fold Inflammation and Repair Simulation.

Publications

In Situ Visualization for 3D Agent-Based Vocal Fold Inflammation and Repair Simulation.

Similar Datasets

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