Finite Element Model of Calcium Diffusion in Amphibian Muscle Sarcoplasmic Reticulum

A computational model of calcium ion diffusion within the sarcoplasmic reticulum of amphibian skeletal muscle during excitation-contraction coupling. The model, authored by Katherine J.-X. Lin and uploaded to figshare in 2026, utilizes established muscle anatomy and calcium buffering parameters to simulate concentration gradients over millisecond to second timescales.

Use Cases

• Simulating calcium concentration gradients based on described sarcoplasmic reticulum geometry and calsequestrin buffering.
• Modeling the effects of calsequestrin on calcium diffusion patterns and flux decays as detailed in the results.
• Analyzing the impact of longitudinal SR geometry on one-dimensional axial calcium gradients over time.
• Investigating the negligible role of background SERCA activity on calcium patterns as reported in the findings.

Strengths

• Model is based on quantifiable SR anatomy with specific dimensions (15 nm radius, 1800 nm length).
• Simulates both free and total calcium concentrations over defined timescales (0-20 ms, up to 2 seconds).
• Explicitly models the effects of calsequestrin buffering and its dissociation constants.
• Released under a permissive CC-BY-4.0 license.

Limitations

• The dataset is a 403.6 KB PDF document; underlying simulation data or code is not provided.
• Row count and column-level documentation are unknown, limiting direct analysis.
• The model is specific to amphibian skeletal muscle anatomy, which may limit generalizability.

Provenance

Source

figshare

Collection Method

Computational finite element modeling based on established anatomical and biochemical parameters.

Time Range

Simulation timescales from 0-20 milliseconds to under 2 seconds.

Freshness

Last updated 2026-04-28 04:29:15.

Geography

Model is based on amphibian (likely frog) skeletal muscle anatomy.