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

Area of Science:

• Biophysics
• Cell Biology
• Computational Biology

Background:

• Intracellular environments significantly influence biochemical reaction kinetics.
• Previous work combined Fluorescence Correlation Spectroscopy (FCS) and Transmission Electron Microscopy (TEM) to study these effects.

Purpose of the Study:

• To develop a method for reconstructing realistic 3D intracellular environments from TEM images.
• To simulate and analyze the impact of these environments on biochemical reaction processes, specifically diffusion.

Main Methods:

• Reconstruction of 3D simulation spaces from Transmission Electron Microscopy (TEM) images.
• Interactive raytracing visualization for 3D structural perception.
• In silico simulation of diffusion dynamics with varying image post-processing and non-reactive obstacle (NRO) parameters.

Main Results:

• Image post-processing (denoising) critically affects simulated diffusion; noisy images create "frayed" structures that hinder diffusion more than smooth surfaces.
• Static structures induce anomalous diffusion due to confinement.
• Mobile crowding agents (NROs) do not cause anomalous diffusion at moderate levels.
• A relationship between NRO diffusion coefficient (Dnro) and tracer diffusion anomaly (α) was established, matching FCS measurements for Dnro = 21.96–44.49 μm²/s.
• Simulated NRO radius of 58 nm aligns with cellular protein complex sizes.

Conclusions:

• Accurate reconstruction of intracellular environments in silico requires careful consideration of image processing to reflect realistic reaction conditions.
• The mobility and size of crowding agents are key factors influencing diffusion anomalies within the cell.
• The developed simulation approach provides insights compatible with experimental observations of cellular diffusion.