247 — Application of smoothed particle hydrodynamics to modeling mechanisms of biological tissue

Palyanov, Khayrulin & Larson (10.1016/j.advengsoft.2016.03.002)

Read on 24 April 2018
#neuroscience  #c-elegans  #worm  #tissue  #simulation  #OpenCL  #computational-fluid-dynamics  #fluids  #muscle  #tissue  #biomechanics 

There are a bajillion reasons why it might be interesting to simulate biotic tissue or systems of tissue and I probably don’t need to even begin to explain why. But this paper explains that one important prerequisite for simulation is a robust, computational fluid dynamics simulator. Sibernetic is just this: a physical simulator for biomechanical matter, which uses the PCISPH model for computation.

PCISPH, or Predictive Corrective Incompressible Smoothed Particle Hydrodynamics, is a solver that accomodates the simulation of fluids, proxied as large-scale particle systems for which overall volume remains consistent. Though this is a loose approximation of certain types of tissue (such as muscle), it works at small scale, and C. elegans is a small-scale organism.

The authors use Sibernetic as a proof-of-concept to simulate a basic biological system (such as a C. elegans worm). This simulation enables fine-grained control over muscle movement (since it is well known how muscles are innervated by the C. elegans nervous system) and the resultant forces on the rest of the body (based upon scans of the worm tissue).

Separate from biology entirely, the authors also demonstrate utility in this technology for simulating liquid-liquid interactions, or the interactions of phase-changes on a system over time.