This example can be found in the directory examples/rec-frap. The full list of directories in examples/rec-frap includes:

This example is a SDAMM-type simulation with 9000 particles. The particles are in a simulation box of 1100 Å^3 at a concentration of 110 mM.

The simulation uses Periodic Boundary Conditions (PBC) in all three directions. The solutes are interacting through soft-core (LJ) repulsion only.

You can run exec.sh or execute the steps below.

1. Decompress the directory part2 (first download it as seen in the script exec.sh)
2. Access the directory part1: cd part1

3. Generate a simulation box with a Gaussian distribution of fluorescent particles in the border of the bleached area.

   Bleaching is assumed to occur in the xy plane, and the center of the bleached area corresponds to the center of the box.

   python box-dist2.py

   The following input files are required:

   • restart.ascii: file with particle positions in the simulation box. For instructions on how to generate this file, please see the tool genbox in SDA. The following parameters must be specified in box-dist2.py:
     • boxedge: length of box edge
     • rbleach: radius of bleached region (xy plane)
     • npart: number of particles in the box
     • func: type of distribution of fluorescent particles: 1-step function; 2-Gaussian distribution
     • fileinp1: name of input file with particle positions
     • fileout1: name of output file with particle positions, with particles separated in bleached and fluorescent
     • fileout2: name of output file with number of fluorescent and bleached particles
     • center: center of bleached area
     The following output files are generated:
     • restart-new.ascii: output file with particle positions, with particles separated in bleached and fluorescent.
     • recount: number of fluorescent and bleached particles in the simulation box. The first N particles of type 1 in restart-new.ascii are fluorescent particles, and the last M particles of type 2 are bleached particles.
     • prob-box.txt: probability distribution of fluorescent particles according to the distance from the center of the bleached area. This distribution is expected to resemble a Gaussian (if func=2 in the script), and have value equal to 0 at short distances and equal to 1 at large distances.
     Examples of output files are available in the directory 'sample-output'.
   • Access the directory 'part2': cd .. ; cd part2
   • Compute the fraction of fluorescent particles in the analysis area in a trajectory obtained using Brownian dynamics.python fraction-flu2-2y.py The following input files are required:
     • trajectory1: trajectory of particles obtained using Brownian dynamics. For information on how to perform Brownian dynamics simulations, please see the documentation of SDA.
     • boxedge: length of box edge
     • dimx: length of the analysis area in the x axis
     • dimy: length of the analysis area in the y axis
     • dimz: length of the analysis area in the z axis
     • npart: number of particles in the box
     • nbleach: number of bleached particles in the box (should be the same number specified in the file 'recount')
     • fileinp1: name of input file containing the trajectory of particles
     • fileout1: name of output file containing the fraction of fluorescent particles in the analysis area along time
     • fileout2: name of output file containing the total number of particles in the analysis area along time
     • center: center of bleached area
     The following output files are generated:
     • count-flu-2y.xvg: fraction of fluorescent particles in the analysis area (second column) as a function of simulation time steps (first column).
     • count-total-2y.xvg: total number of particles in the analysis area (second column) as a function of simulation time steps (first column).
     Examples of output files for a longer trajectory are available in the directory 'sample-output'.

This simulation is described in detail in: D. Dey, S. Marciano, A. Nunes-Alves, V. Kiss., R. C. Wade, G. Schreiber (2021). Line-FRAP, a versatile method to measure diffusion rates in vitro and in vivo. J. Mol. Biol. https://www.sciencedirect.com/science/article/abs/pii/S0022283621000929

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