SpringSaLaD: A Spatial, Particle-Based Biochemical Simulation Platform with Excluded Volume

Main text

(Biophysical Journal 110, 523–529; February 2016)

In the originally published article, the sentence at the end of the first partial paragraph on page 527 is not correct. The sentence reads as follows: “In practice, only ratio $k/\xi$ is required, and in SpringSaLaD this ratio is the same for all bonds and links, namely $k/\xi$ = 10⁸ s^–1; this allows us to use time steps of ∼1–100 ns for biologically relevant diffusion coefficients.” The correct sentence should read as follows: “In practice, only $k/\xi$ is required, where $\xi =D/k_{B}T$ ($D$ is a site’s diffusion coefficient, $k_B$ is the Boltzmann constant, and $T$ is absolute temperature), and $k/k_{B}T={10}^2{\text{nm}}^{-2}$ is the same for all bonds and links; this allows us to use time steps of ∼1–100 ns for biologically relevant diffusion coefficients.”