MATLAB Code for Full-Wave Multiphysics Modeling of a Two-Dimensional Photonic Crystal for Spectral–Thermal Conditioning in Multiwavelength Knee Photobiomodulation

Abstract

This repository contains the complete MATLAB source code associated with the manuscript entitled “Full-Wave Multiphysics Modeling of a Two-Dimensional Photonic Crystal for Spectral–Thermal Conditioning in Multiwavelength Knee Photobiomodulation.” The code implements a unified numerical framework linking an energy-conserving, scalar E-polarized two-dimensional finite-difference frequency-domain (FDFD) model of a photonic crystal to conservative optical diffusion and transient bioheat transport in a simplified multilayer knee domain. The computational workflow includes optimization of the photonic-crystal lattice constant, rod-radius ratio, and number of rows; calculation of wavelength-dependent transmission and reflection at 660, 808, and 850 nm; homogeneous-medium and dielectric-slab validation; electromagnetic and tissue-grid convergence analyses; optical power-balance verification; regional optical-energy calculations; transient Pennes bioheat simulations; combined-spectrum analysis; optical-property and simplified-anatomy sensitivity analyses; and full-wave fabrication-tolerance evaluation. The photonic crystal is modeled as a passive spectral-conditioning layer. The code does not impose an artificial optical source at depth, reduce tissue scattering, predict macroscopic focusing within cartilage, or represent experimental or clinical validation. The model uses representative nondispersive photonic-crystal refractive indices, a simplified two-dimensional tissue geometry, diffusion-based optical transport, and effective thermal and perfusion parameters. Experimental device characterization, dispersive material data, tissue-equivalent phantom measurements, and anatomically realistic validation remain necessary before practical or clinical application. The archive includes the complete MATLAB R2015b-compatible implementation, a direct execution script, documentation, citation metadata, licensing information, and instructions for reproducing the computational workflow.