Files used to run simulations from 

Oliveira R.F., Kim M., Blackwell K.T. (2012) Subcellular Location of
PKA Controls Striatal Plasticity: Stochastic Simulations in Spiny
Dendrites.  PLoS Comput Biol 8:e1002383

These xml files are used as input to NeuroRD - java software for
computationally efficient stochastic simulation of reaction-diffusion
systems.  NeuroRD (and information on how to use it) is available for
free download from http://krasnow1.gmu.edu/CENlab/software.html.  The
version used for simulations in the publication,
stochdiff-2.0.3.3-mol.jar, is included in this tar file

Several random seeds were used for these figures, only one of the
random seeds is provided in this tar file.

A. Files to generate figures 3 - 5.  
  1. Top level model files:
    MSPNmodel_A_5DaStim_4spine_newa.xml  MSPNmodel_D_5DaStim_4spine_newa.xml
    MSPNmodel_B_5DaStim_4spine_newa.xml  MSPNmodel_E_5DaStim_4spine_newa.xml
    MSPNmodel_C_5DaStim_4spine_newa.xml  MSPNmodel_F_5DaStim_4spine_newa.xml
    Letters A-F above indicate the following:
    A: PKA and AC colocalized in the spine (Fig 3, 4)
    B: PKA in the dendrite, AC in the spine (Fig 4)
    C: AC in the spine, PKA diffusely distributed (Fig 5)
    D: PKA in the spine, AC in the dendrite (Fig 3, 4)
    E: PKA and AC colocalized in the dendrite (Fig 4)
    F: AC in the dendrite, PKA diffusely distributed (Fig 5)

Here is an example run command (for D above) for a unix system shell
prompt:

java -jar ./stochdiff-2.0.3.3-mol.jar MSPNmodel_E_5DaStim_4spine_newa.xml \
MSPNmodel_E_5DaStim_4spine_newa.out >> MSPNmodel_E_5DaStim_4spine_newa.log

  2. MSPNreactions_4spine_new.xml
    File containing the reactions.  This file is also used for the Da
    + Ca simulations (of figure 7), and the bath application (see
    below)
  3. MSPNmorph_4spinea.xml 
    file specifying the morphology. This file is also used for the Da
    + Ca simulations, the bath application, robustness simulations
    (fig 6), and also fig 8
  4. MSPNstim_5DaStim_4spine2.xml
    dopamine stimulation.
  5. Initial conditions files.  One each for cases A through F
    MSPNic_A_4spine_new.xml (Fig 3, 4)
    MSPNic_B_4spine_new.xml (Fig 4)
    MSPNic_C_4spine_new.xml (Fig 5)
    MSPNic_D_4spine_new.xml (Fig 3, 4)
    MSPNic_E_4spine_new.xml (Fig 4)
    MSPNic_F_4spine_new.xml (Fig 5)
  6. MSPNio_4spine_newmorph.xml
   This specifies the molecules to output to the -conc.txt files

B. Files used to run bath application simulations (figure 2):
  1. Top level model files: 
    MSPNmodel_AE_CaDaBath_4spine_newa.xml - calcium + dopamine
    MSPNmodel_AE_CaBath_4spine_newa2.xml - dopamine alone
  2. Same reaction files, morphology files, and io files as above
  3. Initial conditions place have of PKA and AC in the spine and half
  in the dendrite: MSPNic_AE_4spine_new.xml
  4. stimulation files:
    MSPNstim_Ca_Bath2.xml for calcium alone
    MSPNstim_CaDaBath.xml for calcium plus dopamine

C. Files used for control long dendrite + 12 spine simulations (Fig 9:
panels A,B,C,E)
  1. top level model file:
    MSPNmodel_A_5DaStim_12spine_newa50_long.xml
  2. initial conditions - multiple dendritic segments necessitates
  multiple surfaceDensity specifications.
    MSPNic_A_12spine_new_long.xml
  3. morphology (obviously must be longer)
    MSPNmorph_12spine_long.xml
  4. reactions - this has slower diffusion constant that the 4 spine
  reaction file to ensure a dopamine gradient
   MSPNreactions_12spine_new50.xml
  5. stimulation - slighly more dopamine to compensate for larger
  volume to diffuse in, also need to specify the injection site that
  corresponds to the differently numbered spines.
    MSPNstim_5DaStim_12spine_50_long.xml
  6. MSPNio_12spine_newmorph_long.xml
    fewer molecules just to save disk space

Examples of how to run simulations using NeuroRD is the NeuroRD.bat.
Examples of how to use the post-processor to extract single molecule
spatial information is in NRDpost.bat

Note the NRDpost program referred to in NRDpost.bat is built with the
command

c++ nrdpost.cpp -o NRDpost

(the most recent version of NRDpost is available at
http://krasnow1.gmu.edu/CENlab/software.html under the Postprocessing
link http://krasnow1.gmu.edu/CENlab/software/PostProcess.tar.gz)
