PyGBe

PyGBe computes localized surface plasmon resonance (LSPR) responses and wavelength‑dependent extinction cross sections of metallic nanoparticles by solving continuum electrostatics with a boundary element formulation in the long‑wavelength (electrostatic) limit to enable geometric modeling of biosensors and analytes while approximating the full Maxwell equations.

Key Features:

• Electrostatic Approximation: Implements continuum electrostatics in the long‑wavelength (electrostatic) limit to model nanoparticle–analyte interactions for LSPR simulations.
• Algorithmic Acceleration: Integrates a Barnes‑Hut treecode with a GMRES solver to achieve O(N log N) complexity per iteration for N unknowns in boundary element computations.
• GPU Acceleration: Utilizes NVIDIA GPUs via CUDA kernels and PyCUDA to accelerate simulations involving millions of boundary elements.
• Extinction Cross Section Computation: Extends the continuum electrostatics solution to compute wavelength‑dependent extinction cross sections of metallic nanoparticles in the presence of molecular targets.

Scientific Applications:

• LSPR Biosensing Analysis: Models spherical silver nanoparticles interacting with bovine serum albumin (BSA) proteins and captures resonance frequency redshift at nanometer‑scale separations to evaluate biosensor sensitivity.

Methodology:

Represents target molecules as surface meshes derived from crystal structures, solves boundary element formulations in the electrostatic limit, computes LSPR responses and extinction cross sections across wavelengths, demonstrates grid convergence, and scales to systems with ≥500,000 boundary elements.