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Software | Burbulator

Package Burbulator (520 Mbyte), Installation notes

for a free 14-day trial key.

Simulations of single-molecule measurements are performed by using Brownian dynamics approach [1-4].

The spatial intensity distribution of the observation volume is assumed to be:

  • 3D Gaussian [5],
  • 3D Gaussian ex & CEF,
  • Rectangular,
  • Cylindrical,
  • Gaussian-Lorentzian + pinhole,
  • Gaussian-Lorentzian + cyl. pinhole,
  • 3D Gaussian + Flow,
  • Trace.

In most of the literature, Brownian diffusion is modelled in a box with periodic boundary conditions (see e.g. [2]). In our approach instead, “molecules” diffuse freely in an “open” volume. This means that the molecules are allowed to leave the simulation volume, after which they are not further tracked. To keep the desired average number of molecules constant, new molecules are added at each time step.

The simulation includes diffusion, intensity distribution, fluorescence relaxation, background, and transitions between different by any simulation parameter states (FRET, anisotropy, brightness, etc.).

Single molecule Pulse Interleaved Excitation (PIE) data simulation recently is added where Donor channel corresponds to “green”, FRET sensitized Acceptor channel “red” (prompt window) and Acceptor direct excitation channel “yellow” (delayed window). 

TCSPC data could be saved in BH SPC-134 or PQ PTU data formats.

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