Erban-Othmer Model Model Class for a bacterium: Class implementing Erban-Othmer Model with exponential run and exponential tumble in the steady state, using a cartoon for the internal dynamics. More...

#include <EO_rExp_tExp.h>

Inheritance diagram for EO_rExp_tExp:

Public Member Functions
	EO_rExp_tExp ()

	EO_rExp_tExp (const EO_rExp_tExp &modello)

void	change_par (int change)

void	change_lambda_par ()

virtual double	f_lambda ()

void	stationary_dyn (double dt, std::vector< double > &m0, int changed_pos)

int	agg_dyn (double dt, double t)

void	agg_dyint (double dt, double t)

void	save_dyn (std::ofstream &file_, double t)

void	gnuplot_single (std::string names_files_Ecoli_mod, std::string &names_indice_mod, std::string names_files_tau_mod, std::string &names_file_dyn_mod, std::string names_info_mod, double T_f, Funz_C f, int save_, int con_gen_sim)

int	saveIntDyn (std::string nameFile)

void	reset_par ()

void	print_info (std::ofstream &file_save)

Public Member Functions inherited from ParameterEstimation_E_coli
	ParameterEstimation_E_coli ()

	ParameterEstimation_E_coli (const E_coli &modello)

void	s_F_lambda_r (vector< Q_tau_stat > vector_lambda, int n_vect)

void	set_GoodnessFit (int Good, double D_n, double cumD_n)

Public Member Functions inherited from E_coli
	E_coli ()

	E_coli (const E_coli &modello)

int	initial_position_ec (int j, std::array< double, 2 > x0, double Raggio, int num_dist, int &cont_dist_5, int delta_dist_cont, double Delta_delta_dist)

int	dist_iniz_ec (std::array< double, 2 > x0, double R, unsigned int num_dist)

std::array< double, 2 >	X ()

double	V ()

int	N_dyn_var ()

double	C ()

double	C_iniziale ()

double	Production_rate ()

void	setProductionRate (double _prodRate)

void	Tau_t (double tt_)

void	Get_tipo_response_c (int T_r)

void	Get_RC_0 (double Rc0)

void	Get_RC_1 (double Rc1)

void	Get_RC_q (int Rcq)

int	F_tipo_response_c ()

double	F_RC_0 ()

double	F_RC_1 ()

double	F_RC_q ()

void	set_response (int ftipo_response_c, double fRC_0, double fRC_1, int fRC_q)

void	agg_ligand (double t, Funz_C *f)

void	aggiornamento (double dt, double t, Funz_C f, int &sign_p, ofstream file_tau, std::ofstream &file_theta)

void	start_simulation (Funz_C *f)

void	response_function ()

void	save_E_coli (ofstream *file, double t)

void	save_E_coli_initial (std::ofstream *file_, double t)

void	save_run (double t, ofstream &file_salto, double dt)

void	save_tumble (double t, ofstream &file_tumble, double dt)

void	save_theta (double t, double theta, std::ofstream &file_run)

virtual void	produce (Funz_C *f_i, double dt)

virtual double	reset_barrier ()

virtual double	reset_barrier_t ()

virtual void	save_dyn (ofstream &file, double t)

virtual void	gnuplot_single_film (std::string names_files_Ecoli_mod, std::string &names_indice_mod, std::string names_files_tau_mod, std::string &names_file_dyn_mod, std::string names_info_mod, double T_f, Funz_C f, int cont_sim)

virtual void	gnuplot_single_film_gif (std::string names_files_Ecoli_mod, std::string &names_indice_mod, std::string names_files_tau_mod, std::string &names_file_dyn_mod, std::string names_info_mod, double T_f, Funz_C f, int cont_sim)
	produce the .gif film More...

virtual void	gnuplotFunzInternalDynalmic (std::string buffer, int save_, int con_gen_sim)

virtual void	gnuplot_response (std::string names_info_mod, int save_, int con_gen_sim)

virtual void	s_F_lambda_r (std::vector< Q_tau_stat > vector_lambda, int n_vect)

void	statF_lambda_r (s_lambda &vector_lambda)

virtual void	debugFunction ()

Protected Member Functions
int	writeScriptgnuplotSingle (std::string tipo, std::string names_files_Ecoli_mod, std::string names_files_tau_mod, std::string *names_info_mod, std::string &names_file_dyn_mod, double T_f, int con_gen_sim, int save_)

Protected Member Functions inherited from E_coli
void	setSeed_ec (unsigned int *seed_thread)

virtual int	writeScriptLunchgnuplotSingle (std::string tipo, int save_, int con_gen_sim)

double	Exp_dist_ec ()

double	rand_normal_ec (double stddev)

double	gamma_par_double_ec ()

double	unifRand_ec ()

double	deltaW_ec (double dt)

double	newtheta_ec (double theta)

void	setEngine_ec (std::mt19937_64 engine_thread_theta, std::mt19937_64 engine_thread_bar, std::mt19937_64 *engine_thread_altro)

Protected Attributes
double	t_e

double	t_a

int	tipo_lambda

double	A_0

double	A_1

double	A_2

double	A_3

vector< double >	m

Protected Attributes inherited from ParameterEstimation_E_coli
double	s_lambda_t

int	GoodFit

double	KS_D_n

double	KS_L1

string	distribution_I_r

double	I_tau_r [2]

string	distribution_I_t

double	I_tau_t [2]

Protected Attributes inherited from E_coli
double	production_rate

double	v

std::array< double, 2 >	x

double	theta

double	c

double	D_theta

double	lambda_r

double	lambda_t

double	tau_r

double	tau_t

int	n_dyn_var

double	barriera_r

double	barriera_t

int	salto_

double	t_t

double	t_r

int	sign_c

int	up_down

double	c_iniziale

int	tipo_response_c

double	RC_0

double	RC_1

int	RC_q

int	tipoNewTheta

unsigned int *	seed_ecoli
	pointer to a seed More...

Additional Inherited Members
Public Attributes inherited from E_coli
std::mt19937_64 *	engine_theta
	pointer to a engine (if I want to use std::uniform_real_distribution<double>) More...

std::mt19937_64 *	engine_barrier

std::mt19937_64 *	engine_altro

int	simulation

std::string	Tipo_batterio

int	codice_batterio

s_lambda	s_lambda_r

Detailed Description

Erban-Othmer Model Model Class for a bacterium: Class implementing Erban-Othmer Model with exponential run and exponential tumble in the steady state, using a cartoon for the internal dynamics.

$\begin{equation} \begin{aligned} \frac{d}{dt}y_{1}(t)&=\frac{G(c(t,x))-(y_{1}+y_{2})}{\tau_{a}}\\ \frac{d}{dt}y_{2}(t)&=\frac{G(c(t,x))-y_{2}}{\tau_{e}} \end{aligned} \end{equation}$

Constructor & Destructor Documentation

EO_rExp_tExp::EO_rExp_tExp ( )

EO_rExp_tExp::EO_rExp_tExp ( const EO_rExp_tExp & modello )

Member Function Documentation

void EO_rExp_tExp::agg_dyint	(	double	dt,
		double	t
	)

virtual

update internal dynamic

Reimplemented from E_coli.

int EO_rExp_tExp::agg_dyn	(	double	dt,
		double	t
	)

virtual

update dynamic to control run/tumble
It controll the hitting time $\tau_{n+1}$ of the inernal variable lambda_[...] Heuristically we have:

if the distribution is exponential we have
- $\int_{\tau_{n}}^{\tau_{n+1}}\Lambda^*(s)ds\sim Exp(1)$
if the distribution is IG we have
- $\tau_{n+1}=\inf\{s>\tau_n:\Lambda(s)ds\geq const\}$
if the distribution is Exp_IG we have
- $\tau_{n+1}=\inf\{s>\tau_n:\Lambda(s)ds\geq Exp(1)\}$

Where in general we can write: $d\Lambda(s)=\lambda(s)dt+\sigma(s)dW(t)$ .
note $\sigma(s)=0$ in the first case above.

Reimplemented from E_coli.

Reimplemented in EO_rIG_tExp.

void EO_rExp_tExp::change_lambda_par ( )

void EO_rExp_tExp::change_par ( int change )

virtual

set parameters model

Reimplemented from E_coli.

Reimplemented in EO_rIG_tExp.

double EO_rExp_tExp::f_lambda ( )

virtual

void EO_rExp_tExp::gnuplot_single	(	std::string *	names_files_Ecoli_mod,
		std::string &	names_indice_mod,
		std::string *	names_files_tau_mod,
		std::string &	names_file_dyn_mod,
		std::string *	names_info_mod,
		double	T_f,
		Funz_C *	f,
		int	save_,
		int	con_gen_sim
	)

virtual

plot via gnuplot trajectory and data for single tracking

Reimplemented from E_coli.

void EO_rExp_tExp::print_info ( std::ofstream & file_save )

virtual

print info for LateX report

Reimplemented from E_coli.

Reimplemented in EO_rIG_tExp, and EO_rExpIG_tExp.

void EO_rExp_tExp::reset_par ( )

virtual

reset defolt parametes model

Reimplemented from E_coli.

Reimplemented in EO_rIG_tExp, and EO_rExpIG_tExp.

void EO_rExp_tExp::save_dyn	(	std::ofstream &	file_,
		double	t
	)

int EO_rExp_tExp::saveIntDyn ( std::string nameFile )

virtual

Reimplemented from E_coli.

Reimplemented in EO_rIG_tExp.

void EO_rExp_tExp::stationary_dyn	(	double	dt,
		std::vector< double > &	m0,
		int	changed_pos
	)

virtual

calculate stationary dynamics for the initial condition

Parameters

m0	are the initial condition for the internal variables: if changed_pos says that the initial condition are not changed, for example if the initial distribution for the population is a delta dirac, then we just use the old values, and do not recalculate them

Reimplemented from E_coli.

int EO_rExp_tExp::writeScriptgnuplotSingle	(	std::string	tipo,
		std::string *	names_files_Ecoli_mod,
		std::string *	names_files_tau_mod,
		std::string *	names_info_mod,
		std::string &	names_file_dyn_mod,
		double	T_f,
		int	con_gen_sim,
		int	save_
	)

protectedvirtual

write the script for the gnuplot of single bacterium

Reimplemented from E_coli.

Member Data Documentation

double EO_rExp_tExp::A_0

protected

double EO_rExp_tExp::A_1

protected

double EO_rExp_tExp::A_2

protected

double EO_rExp_tExp::A_3

protected

vector<double> EO_rExp_tExp::m

protected

double EO_rExp_tExp::t_a

protected

double EO_rExp_tExp::t_e

protected

int EO_rExp_tExp::tipo_lambda

protected

The documentation for this class was generated from the following files:

include/Ecoli/EO_rExp_tExp.h
src/Ecoli/EO_rExp_tExp.cpp
src/Ecoli/Internal_dynamic.cpp
src/LateX/print_and_open_info.cpp
src/Visualization/gnuplot_single_3.cpp
src/Visualization/gnuplotFunzInternalDynalmic.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation