2.2 Simulation algorithm

The multi-agent simulation algorithm used to simulate the RP system is presented below. Each replicase and parasite is represented by a single agent in the simulation. When the agent is created, its remaining life time (RLT) is initialized random (see Eq 2), and during each simulation iteration, the time is decreased. When the complex is dissociated, the time does not have to be recalculated because of memoryless properties (see Section 2.4). There are a maximal number of allowed neighbors for each agent. If this is exceeded, the agent is removed due to a lack of resources. During each replication event, there is a certain probability of a mutation to agent properties with regard to agent affinity towards attributes or the probability of being in a folded state. The detailed algorithm is presented in the below list 1.

Algorithm 1 Our algorithm.

1: Initialize the simulation.

2:  Initialize the number and positions of the agents from a file or randomly.

3:  Initialize all replicases with equal a_R and l_R values.

4:  Initialize all parasites with equal a_P and l_P values.

5: while ((simulation time < time limit) AND (there are both parasites and replicases (complexed or uncomplexed) present)) do

6:  Increase the simulation time by Δt.

7:  Decrease the RLT time for each agent (complexes and uncomplexed).

8:  for all uncomplexed agents with the RLT = 0 do

9:   Remove the agents.

10:  end for

11:  Randomize the order of all agents.

12:  for all agent x_i do

13:   if x_i is complex AND RLT(x_i) = 0 then

14:    Dissociate agents into two uncomplexed agents with the same position as the complex.

15:   end if

16:   for all agent that overlaps x_i (see Eq 3) do

17:    Add it to the set of neighbors N

18:   end for

19:   if |N|>N_max then

20:    remove agent x_i from the simulation

21:   end if

22:   Randomize the order of N.

23:   Move x_i (see Eq 1).

24:   if x_i is complex then

25:    Decrease the replication time (TTR).

26:    if TTR = 0 then

27:     Create new agent x′ equal to the template from complex x_i.

28:     Mutate x′.

29:     Dissociate x_i:

30:      Create agents t and r based on the complexed template and replicase.

31:      Copy the position of x_i to t and r.

32:      Restore the RLT(r) and RLT(t) values from the moment when the complex was created.

33:      Remove x_i from the simulation.

34:    end if

35:   else

36:    for all n_j ∈ N do

37:     if (n_j is uncomplexed) AND (n_j OR x_i is replicase) AND CheckReactionProbability(see Eq 4) then

38:      Create complex x′.

39:      Randomly initialize TTR(x′) (see Eq 2).

40:      Randomly initialize RLT(x′) (see Eq 2).

41:      Initialize the position of x′ as the average position of n_j and x_i.

42:      Remove n_j and x_i from the simulation.

43:     end if

44:    end for

45:   end if

46:  end for

47: end while