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PyBroMo 0.1: A simulator for single molecule FRET experiments of freely diffusing particles

Antonino Ingargiola

PyBroMo is an open-source simulator for Brownian-motion diffusion and photon emission of fluorescent particles excited by a diffraction limited laser spot. PyBroMo allows to simulate timestamps of photons emitted during smFRET experiments, including sample background and detectors dark counts.

PyBromo simulates 3-D Brownian motion trajectories and emission of an arbitrary number of particles freely diffusing in a simulation volume (a box). Inside the simulation box a laser excitation volume (thePSF of the objective lens) is defined numerically or analytically (Gaussian shape). Molecules diffusing through the excitation volume emit photons at a rate proportional to the local excitation intensity.

A precomputed numerical PSF is included and used by default. The included numerical PSF is computed through rigorous vectorial electromagnetic computations using the PSFLab software. The user can provide a different numerical PSF or, alternatively, use an analytical Gaussian-shaped PSF.

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