simul.evol.enz.one: Simulation of enzyme evolution

In SimEvolEnzCons: Simulation of Evolution of Enzyme Under Constraints

Description

This function simulates evolution of enzyme concentrations under constraints

Usage

simul.evol.enz.one(E_ini_fun, kin_fun, Keq_fun, N_fun, correl_fun, 
beta_fun=NULL, X_fun=1, pasobs=250, npt=500, max_mut_size_E=1, max_mut_size_A=1,
pmutA=0, typ_E=1, typ_A=1, use.old.mut=FALSE)

Arguments

E_ini_fun	Numeric vector of the initial concentrations
kin_fun	Numeric vector of the initial kinetic parameters
Keq_fun	Numeric vector of equilibrium constants
N_fun	Numeric. Population size
correl_fun	Character string indicating the abbreviation of the constraint applied on the system
beta_fun	Matrix of co-regulation coefficients
X_fun	Numeric. Numerator of function flux. Default is 1
pasobs	Numeric. Number of time steps between two successive observations of the system. Default is 250
npt	Numeric. Number of observations. Default is 500
max_mut_size_E	Numeric. Maximum absolute size of mutation for enzyme concentrations. Default is 1
max_mut_size_A	Numeric. Maximum absolute size of mutation for kinetic parameters. Default is 1
pmutA	Numeric. Mutation probability of kinetic parameters. Higher pmutA, higher the mutation probability of kinetic parameters compared to enzyme concentrations. Default is 0, i.e. no mutation of kinetic parameters
typ_E	Numeric for mutation method. Authorized values: 1 or 2. Default is 1.
typ_A	Numeric for mutation method. Default is 1. See details in mut.kin.
use.old.mut	Logical. If FALSE (default), use mut.E.direct mutation method, else use mut.E.old mutation method if TRUE

Details

Time step is defined between appearance of two mutation.

Time step is simulated with function simul.next.resident, which gives values of resident after a time step.

To reduce size of result matrix, certain results only are conserved. State of simulation is observed every pasobs time steps. There is npt observations, so result matrix has npt rows. In total, a simulation includes pasobs*npt time steps. By default, there is 125 000 time steps.

Chosen equilibrium for pred_enzsim and pred_contsim are the theoretical equilibrium for constraints "SC", "Comp" and "RegPos", and the effective one for constraints "RegNeg", "CRPos" and "CRNeg". If there are regulation groups (1<sum(1/B)<n), the equilibrium is not computed, and pred_ returns NA.

Value

Invisible list of 4 elements:

• $res_sim: numeric matrix of npt rows and 3*n+3 columns. Each row corresponds to state at each observation step (i.e. after pasobs mutations), and columns are respectively concentrations (1:n), kinetic parameters (n+1:2n), total concentration (2n+1), total kinetic (2n+2), flux/fitness (2n+3), activities (2n+4:3n+3);

• $pred_enzsim: numeric matrix of npt rows and n columns, corresponding to relative concentrations at equilibrium, for each observation step (in rows);

• $pred_contsim: same as $pred_enzsim, but for response coefficients

• $param: list of input parameters:

  • n: number of enzymes,

  • E0: numeric vector of initial concentrations,

  • kin: numeric vector of initial kinetic parameters,

  • Keq: numeric vector of constant equilibrium,

  • beta: matrix of co-regulation coefficients,

  • B: numeric vector of global co-regulation coefficients,

  • correl: character string indicating the constraint abbreviation,

  • N: population size,

  • pasobs: number of steps between two system observations,

  • npt: number of system observations,

  • X: parameter for flux computation,

  • pmutA: probability for activity mutation,

  • other input parameters

Note that n is the number of enzymes, which is the length of E_ini_fun.

See Also

See function simul.next.resident to see how works each time steps.

Use function simul.evol.enz.multiple to compute several simulations.

SimEvolEnzCons documentation built on Oct. 29, 2021, 1:07 a.m.