ecoli.processes.chromosome_replication

Chromosome Replication

Performs initiation, elongation, and termination of active partial chromosomes that replicate the chromosome.

First, a round of replication is initiated at a fixed cell mass per origin of replication and generally occurs once per cell cycle. Second, replication forks are elongated up to the maximal expected elongation rate, dNTP resource limitations, and template strand sequence but elongation does not take into account the action of topoisomerases or the enzymes in the replisome. Finally, replication forks terminate once they reach the end of their template strand and the chromosome immediately decatenates forming two separate chromosome molecules.

class ecoli.processes.chromosome_replication.ChromosomeReplication(parameters=None)

Bases: PartitionedProcess

Chromosome Replication PartitionedProcess

calculate_request(timestep, states)

defaults: Dict[str, Any]

{   'D_period': array([], dtype=float64),
    'basal_elongation_rate': 967,
    'criticalInitiationMass': 975 [fg],
    'dntps': [],
    'emit_unique': False,
    'get_dna_critical_mass': <function ChromosomeReplication.<lambda> at 0x7f82414c1c60>,
    'make_elongation_rates': <function ChromosomeReplication.<lambda> at 0x7f82414c1d00>,
    'max_time_step': 2.0,
    'mechanistic_replisome': True,
    'no_child_place_holder': -1,
    'nutrientToDoublingTime': {},
    'polymerized_dntp_weights': [],
    'ppi': [],
    'replication_coordinate': array([], dtype=float64),
    'replichore_lengths': array([], dtype=float64),
    'replisome_monomers_subunits': [],
    'replisome_protein_mass': 0,
    'replisome_trimers_subunits': [],
    'seed': 0,
    'sequences': array([], dtype=float64)}

evolve_state(timestep, states)

name = 'ecoli-chromosome-replication'

ports_schema()

topology

{   'active_replisomes': ('unique', 'active_replisome'),
    'bulk': ('bulk',),
    'chromosome_domains': ('unique', 'chromosome_domain'),
    'environment': ('environment',),
    'full_chromosomes': ('unique', 'full_chromosome'),
    'listeners': ('listeners',),
    'oriCs': ('unique', 'oriC'),
    'timestep': ('timestep',)}