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This program implements a model for determining phase behavior for a binary mixture of two charged colloid particles phase separates. The target application is a mixture of globular RNA with negative charge and proteins with positive charge.

*** Compilation:

g++ -O3 -o phasesep phasesep.c

*** Requirements:

radial distribution functions 
provided are RDFs for RNA-RNA, RNA-protein, protein-protein interactions from CG simulations

*** Usage:

phasesep [options]
  -verbose                            // provide extra output
  -highres                            // output with more digits
  -tag <name>                         // add tag to output
  -temp <value>                       // temperature in K
  -n <rnavalue> <posvalue>            // number of molecules (can be fractional)
  -nrna <value> -npos <value>        
  -c <rnavalue> <posvalue>            // concentrations in mM   
  -crna <value> -cpos <value> 
  -len <value>                        // system size: len*len*len
  -kappa <value>                      // salt screening; typical: 0.5-2.0 

  -fcharge <value>                    // effective charge screening parameter, model 1, typical: 10-30
  -abcharge <value> <value>           // effective charge screening parameter, model 2, typical: 2 0.6 
  -maxvol <value>                     // maximum allowable macromolecular volume fraction in condensate, 
                                      // typical: 0.3-0.5
 
  -q <rnavalue> <posvalue>            // charges
  -qrna <value> -qpos <value>
  -r <rnavalue> <posvalue>            // radii
  -rrna <value> -rpos <value> 
  -epsilon <value>                    // model parameter; default: 4.0
  -a0 <value>                         // model parameter; default: 3.0

  -rnarna <name>                      // name for alternative RNA-RNA RDF profile
  -rnapos <name>                      // name for alternative RNA-POS RDF profile
  -posrna <name>                      // name for alternative POS-RNA RDF profile
  -pospos <name>                      // name for alternative POS-POS RDF profile
  -rdfcut <value>                     // cutoff for RDF beyond which it is set to 1
  -maxrad <value>                     // radial integration limit 

  -thresh <value>                     // numerical error tolerance; default: 0.0005
  -vfac <value>                       // multiplier when scanning for volume; default: 0.9995
  -nrscale <value>                    // step size when scanning for concentration; default: 0.02

*** Example:

1. RNA with trypsin at sufficiently high concentration:
   ./phasesep -qrna -46 -rrna 1.47 -qpos 6 -rpos 1.81 -crna 0.4 -cpos 0.3 -kappa 1.3
      phasesep       :[rna_mM]: 0.243405 16.25 :[pos_mM]: 0.059332 24.66 :[clusterrad_nm]: 13.27 :[volfrac]: 0.13 0.37


2. RNA with trypsin at a concentration that is too low:     
   ./phasesep -qrna -46 -rrna 1.47 -qpos 6 -rpos 1.81 -crna 0.4 -cpos 0.05 -kappa 1.3
      disperse       :[rna_mM]: 0.400000  0.40 :[pos_mM]: 0.050000  0.05 :[clusterrad_nm]: 62.04 :[volfrac]: 0.00 0.00

3. RNA with trypsin with alternative effective charge model and using a reduced maximum macromolecular volume fraction:
   ./phasesep -qrna -46 -rrna 1.47 -qpos 6 -rpos 1.81 -crna 0.4 -cpos 0.3 -kappa 1.17 -abcharge 2.0 0.6 -maxvol 0.3
      phasesep       :[rna_mM]: 0.306871  8.62 :[pos_mM]: 0.133601 14.98 :[clusterrad_nm]: 13.88 :[volfrac]: 0.07 0.22

*** Citation:

Bercem Dutagaci, Grzegorz Nawrocki, Joyce Goodluck, Ali Akbar Ashkarran, Charles G. Hoogstraten, Lisa Lapidus, Michael Feig: 
Charge-Driven Condensation of RNA and Proteins Suggests Broad Role of Phase Separation in Cytoplasmic Environments
bioRxiv(2020)

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