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Figure 1 | BMC Bioinformatics

Figure 1

From: Quantitative fluorescence loss in photobleaching for analysis of protein transport and aggregation

Figure 1

Simulation of homogenous diffusion and fitting with the StrExp function. A, Sketch of the FLIP experiment with the cell attached to a surface and filled with eGFP (green) and the cylindrical laser beam focused in the cell center (yellow). B, Geometry of the analytical model for the reaction diffusion system in Eq. 6 to model the FLIP experiment. The cell is assumed to be a flat cylinder with a radius, r2 = 12 μm. The central bleached region with radius r1 = 3 μm is also cylindrical covering the whole cell height (grey shaded area). C-E, The model was solved analytically and simulated for two positions outside the bleached area at a distance of 5 μm (red dot in B and red symbols in C-E) and 10 μm (blue dot in B and blue symbols in C-E) from the origin, respectively. Simulations were performed with a rate constant for the intended bleaching process of k = 10 sec-1 and diffusion constants of D = 0.1 μm2/sec (C), D = 1 μm2/sec (D) and D = 10 μm2/sec (E). A non-linear regression with the StrExp function (black lines) was performed in SigmaPlot (upper panels) including the residuals of the fit (lower panels). F, G, time courses were simulated for D = 0.1 μm2/sec as a function of distance from the origin and fitted to the StrExp function. Fitted parameters including standard deviation of the fit are plotted for the rate constant (‘kfit’; F) and stretching parameter (‘hfit’; G). H, rate coefficients calculated according to Eq. S4 for the parameters in panels F, G as function of distance from bleach ROI (starting at 4 μm from origin and indicated as ‘r’ on the ordinate in H) over time. The scale bar shows rate coefficients color-coded using a FIRE-LUT

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