title: Exploring the dynamics of cell processes through simulations of fluorescence microscopy experiments.
abstract: Fluorescence correlation spectroscopy (FCS) methods are powerful tools for unveiling the dynamical organization of cells. For simple cases, such as molecules passively moving in a homogeneous media, FCS analysis yields analytical functions that can be fitted to the experimental data to recover the phenomenological rate parameters. Unfortunately, many dynamical processes in cells do not follow these simple models, and in many instances it is not possible to obtain an analytical function through a theoretical analysis of a more complex model. In such cases, experimental analysis can be combined with Monte Carlo simulations to aid in interpretation of the data. In response to this need, we developed a method called FERNET (Fluorescence Emission Recipes and Numerical routines Toolkit) based on Monte Carlo simulations and the MCell-Blender platform, which was designed to treat the reaction-diffusion problem under realistic scenarios. This method enables us to set complex geometries of the simulation space, distribute molecules among different compartments, and define interspecies reactions with selected kinetic constants, diffusion coefficients, and species brightness. We apply this method to simulate single- and multiple-point FCS, photon-counting histogram analysis, raster image correlation spectroscopy, and two-color fluorescence cross-correlation spectroscopy. We believe that this new program could be very useful for predicting and understanding the output of fluorescence microscopy experiments.
authors.affiliation: Departamento de Química Biológica-IQUIBICEN, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
authors.forename: Juan
authors.initials: J
authors.lastname: Angiolini
authors.affiliation: European Molecular Biology Laboratory, Australian Regenerative Medicine Institute, Monash University, Victoria, Australia; Institute of Molecular and Cell Biology, A(∗)STAR, Singapore.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Plachta
authors.affiliation: Departamento de Computación, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina; Centro de Simulación Computacional p/Aplicaciones Tecnológicas, CSC-CONICET, Buenos Aires, Argentina. Electronic address: emocskos@dc.uba.ar.
authors.forename: Esteban
authors.initials: E
authors.lastname: Mocskos
authors.affiliation: Departamento de Química Biológica-IQUIBICEN, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina. Electronic address: vlevi12@gmail.com.
authors.forename: Valeria
authors.initials: V
authors.lastname: Levi
mesh_terms: D002477:Cells / Q000166:cytology*; D004058:Diffusion; D008856:Microscopy, Fluorescence; D009010:Monte Carlo Method