virionspread.py

import random

# time
t = 0
# how likely is replication to be successful
replication_success_ratio = 0.7
# estimate time for rna in a cell to reach a replication center,
# we'll also repurpose it as how long it takes a viable strand to
# start itself replicating (which is generous),
# and how long the virions in a dead cell take to find new cells.
replication_cycle = 3 * 60
# how many virions from a dead cell are viable and find another
viable_escape_ratio = .2
# how many virions from a dead cell find a unique cell:
unique_cell_arrivals = .3
# how many virions in a cell causes it to die?
lethal_population = 400



class Cell:
    def __init__(self, live_virions):
        self.live_virions = live_virions
        self.dead = False

    def cycle(self):
        if random.random() <= replication_success_ratio:
            self.live_virions += max(int(self.live_virions * replication_success_ratio), 1)
        self.dead = self.live_virions >= lethal_population
        if self.dead:
            self.live_virions = int(self.live_virions * viable_escape_ratio)
        
        return not self.dead


class Body:
    # track live cells that are infected
    infected_cells = None
    # track cells that have died whose virions need to find new homes
    dead_cells = []

    # counters
    cells_died = 0
    active_virions = 0
    transit_virions = 0

    def cycle(self):
        # infect new cells from the died cells
        if self.infected_cells is None:
            self.infected_cells = [Cell(1)]
        else:
            new_infections = []
            new_cells = []
            for cell in self.dead_cells:
                escapees = cell.live_virions
                for i in range(1, 5):
                    infecting = max(int(escapees * unique_cell_arrivals), 1)
                    new_cells.extend([Cell(i) for _ in range(infecting)])
                    escapees -= infecting

            self.dead_cells = [c for c in self.infected_cells if not c.cycle()]
            self.cells_died += len(self.dead_cells)
            self.infected_cells[:] = [c for c in self.infected_cells if not c.dead] + new_cells

        self.active_virions = sum(c.live_virions for c in self.infected_cells)
        self.transit_virions = sum(c.live_virions for c in self.dead_cells)

body = Body()
for i in range(60):
    body.cycle()
    print(
            "T+%02dh:%02dm:%02ds infected cells: %9d, total virions: %9d, active virions: %9d, cells killed:%9d"
            % (
             int(t/3600), int((t/60)%60), t % 60,
             len(body.infected_cells),
             body.active_virions + body.transit_virions,
             body.active_virions,
             body.cells_died
            )
    )
    t += replication_cycle
print("Fin")