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parameters.xml
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parameters.xml
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<?xml version="0.0" encoding="UTF-8" ?>
% free speckles diffusing and fusion, random motion
<simulation>
<time_step> 0.01 </time_step>
<final_time> 10000 </final_time>
<nb_output> 100 </nb_output>
<initial_time> 0 </initial_time>
<equilibre_nsteps> 5000 </equilibre_nsteps>
<openmp> 8 </openmp>
<activity> 0.5 </activity>
</simulation>
<sphere_prop>
<mode_diffusion> 0 </mode_diffusion>
<minimal_mobility> 0.03 </minimal_mobility> % 0.03
<alpha> 0.11 </alpha> %0.11
<name> nucleolus </name>
<maximal_distance> 0 </maximal_distance>
<friction> 1 </friction>
<membrane_repulsion> 20 </membrane_repulsion>
<sphere_repulsion> 1 </sphere_repulsion>
<dna_repulsion> 0 </dna_repulsion>
<dna_sticker> 0 </dna_sticker>
<dna_source> 1 </dna_source>
<dna_escape_rate> -1 </dna_escape_rate>
</sphere_prop>
<sphere_prop>
<mode_diffusion> 0 </mode_diffusion>
<minimal_mobility> 0.03 </minimal_mobility>
<alpha> 0.11 </alpha>
<name> speckle </name>
<membrane_repulsion> 20 </membrane_repulsion>
<sphere_repulsion> 1 </sphere_repulsion>
<sphere_attraction> 1 </sphere_attraction>
<maximal_distance> 0.1 </maximal_distance>
<friction> 0.1 </friction>
<dna_repulsion> 0 </dna_repulsion>
<dna_sticker> 0 </dna_sticker>
<dna_source> 0 </dna_source>
<dna_escape_rate> -1 </dna_escape_rate>
</sphere_prop>
<space>
<geometry> 0 </geometry>
<radius> 12 </radius>
<write> 0 </write>
</space>
<init_config>
<add_nucleolus>
<number> 1 </number>
<radius_mean> 4.5 </radius_mean>
<radius_std> 0.25 </radius_std>
<distrib_mode> 2 </distrib_mode>
<distrib_length> 12 </distrib_length>
</add_nucleolus>
<add_speckle>
<number> 50 </number>
<radius_mean> 0.55 </radius_mean>
<radius_std> 0.01 </radius_std>
<distrib_mode> 2 </distrib_mode>
<distrib_length> 12 </distrib_length>
<dna_contact_prop> 1 </dna_contact_prop>
</add_speckle>
</init_config>