CONICET | Buscador de Institutos y Recursos Humanos

Fluorescence correlation spectroscopy (FCS) and related techniques are powerful methods to unveil the dynamical organization of cells.For simple cases such as molecules passively moving in a homogeneous media, the FCS analysis yields analytical functions that can befitted to the experimental data in order to recover the phenomenological rate parameters. Unfortunately, many dynamical processes incells do not follow these simple models and in many instances it is not possible to obtain an analytical function through the theoreticalanalysis of a more complex model. In those cases, the experimental analysis can be combined with Monte Carlo simulations to help withthe interpretation of the data. In this work, we present FERNET, a new toolkit designed to simulate a variety of FCS-based techniques. Thistool works in combination with MCell-Blender platform which was designed to treat the reaction-diffusion problem under realistic scenar-ios. The new program allows setting complex, user-defined geometries of the simulation space and distributing the molecules betweendifferent compartments as desired. Also, the platform includes the possibility of defining reactions among the species considered in thesimulations; the user only needs to set the kinetic constants, diffusion coefficient and brightness of each species. We illustrate the possibil-ities opened by FERNET showing its application to the simulation of single and multiple point FCS and photon counting histogram analysis, raster image correlation spectroscopy and two-color fluorescence crosscorrelation spectroscopy. We also demonstrate how these simulations can aid in the interpretation of FCS data obtained from complex systems, such as transcription factor dynamics in living mouse em-bryos.

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