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)