PrebioDivSim

Simulation model for prebiotic replicator (like RNAs) dynamics and evolution.

This simulation model is constructed mimicking translation-coupled RNA relpication system (TCRR system; Ichihashi et al., Nat. Commun., 2013).

Simulations

This repository (PrebioDivSim) includes two simulations, PrebioDivPreserv and PrebioDivEvo.

PrebioDivPreserv is a simulation for determining whether compartmentalized replication systems are maintained or not. Firstly a replicator network and its activity matrix are given, then the population dynamics is simulated fixed them.

PrebioDivEvo is a simulation for determining how compartmentalized replication systems evolved.

In these simulations, the concentrations of replicators in each compatment are defined as a type Lives. The entity of this type is std::vector<double>. And, the activities of replications are defined as a type Act. The entity of this type is std::vector<std::vector<double>>, then a matrix.

The entity of simulation process is a class World. For simulation, environmental parameters are unified as a class Env.

Dependency

To use these simulations, openmp and boost must be installed in environment.

And, their operations are confirmed in g++11 and c++17 and later.

Licence

Simplified BSD License (read file LICENSE)

Reference

[1] Kamiura, R., Mizuuchi, R. & Ichihashi, N. Plausible pathway for a host–parasite molecular replication network to increase its complexity through Darwinian evolution. bioRxiv 2022.01.17.476531 (2022).

[2] Ichihashi, N. et al. Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment. Nat. Commun. 4, (2013).