From microscopy data to in silico environments for in vivo-oriented simulations

The complex physical structure of the cytoplasm has been a long-standing topic of interest [1,2]. The physiological environment of intracellular biochemical reactants is not one of well diluted, homogeneous space. This fact is in contradiction with the basic assumption underlying the standard theories for reaction kinetics [3]. The difference may render actual in vivo reaction processes deviate from those in vitro or in silico. Lately, we showed the results of a combined investigation of Fluorescence Correlation Spectroscopy (FCS) and Transmission Electron Microscopy (TEM) [4,5]. We examined the effects of intracellular crowding and inhomogeneity on the mode of reactions in vivo by calculating the spectral dimension (ds) which can be translated into the reaction rate function. We compared estimates of the anomaly parameter, obtained from FCS data, with the fractal dimension from an analysis with transmission electron microscopy images. Therefrom we estimated a value of ds=1.34±0.27. This result suggests that the in vivo reactions run faster at initial times when compared to the reactions in a homogeneous space. The result is compatible with the result of our Monte Carlo simulation. Also, in our further investigation, we confirmed by the simulation that the above-mentioned in vivo like properties are different from those of homogeneously concentrated environments. Also other simulation results indicated that the crowding level of an environment affects the diffusion and reaction rate of reactants [6-9]. Such knowledge of the spatial condition enables us to construct realistic models for in vivo diffusion and reaction systems.The novel points of this study are the following three:(i) we investigated the influence of the mobility of non-reactive obstacles (NRO) on the anomaly coefficient,(ii) we investigated the influence of the size of the NROs, and(iii) we reconstructed the static simulation space based on TEM images and run diffusion tests in these virtual volumes a