Base Class for a bacterium: It implements the virtual function to evolve the dynamic of the bacterium. More...

#include <E_Coli.h>

Inheritance diagram for E_coli:

Public Member Functions
	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	change_par (int change)

virtual void	reset_par ()

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

virtual int	agg_dyn (double dt, double t)

virtual int	saveIntDyn (std::string nameFile)

virtual void	agg_dyint (double dt, double t)

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 (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 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	print_info (std::ofstream &file_save)

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	set_GoodnessFit (int Good, double D_n, double cumD_n)

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 ()

Public Attributes
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

Protected Member Functions
void	setSeed_ec (unsigned int *seed_thread)

virtual 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_)

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	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...

Detailed Description

Base Class for a bacterium: It implements the virtual function to evolve the dynamic of the bacterium.

Constructor & Destructor Documentation

E_coli::E_coli ( )

E_coli::E_coli ( const E_coli & modello )

Member Function Documentation

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

virtual

update internal dynamic

Reimplemented in CV_rExp_tExp, Molecular_rExp_tExp, and EO_rExp_tExp.

int E_coli::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 in CV_rExp_tExp, Molecular_rExp_tExp, EO_rExp_tExp, CV_rIG_tExp, EO_rIG_tExp, and Molecular_rIG_tExp.

void E_coli::agg_ligand	(	double	t,
		Funz_C *	f
	)

update ligand concentration

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

update all the parameters of the bacterium during the simulation

double E_coli::C ( )

return current ligand concentration

double E_coli::C_iniziale ( )

return initial ligand concentration

void E_coli::change_par ( int change )

virtual

set parameters model

Reimplemented in CV_rExp_tExp, Molecular_rExp_tExp, EO_rExp_tExp, CV_rIG_tExp, EO_rIG_tExp, and Molecular_rIG_tExp.

void E_coli::debugFunction ( )

virtual

Reimplemented in CV_rExp_tExp, and CV_rIG_tExp.

double E_coli::deltaW_ec ( double dt )

protected

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

double E_coli::Exp_dist_ec ( )

protected

double E_coli::F_RC_0 ( )

return 1st coefficient

double E_coli::F_RC_1 ( )

return 2nd coefficient

double E_coli::F_RC_q ( )

return 3rd coefficient

int E_coli::F_tipo_response_c ( )

return current type of response

double E_coli::gamma_par_double_ec ( )

protected

void E_coli::Get_RC_0 ( double Rc0 )

set 1st coefficient

void E_coli::Get_RC_1 ( double Rc1 )

set 2nd coefficient

void E_coli::Get_RC_q ( int Rcq )

set 3rd coefficient

void E_coli::Get_tipo_response_c ( int T_r )

set type of response

Parameters

tt_	type of response

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

virtual

plot response: empty function ... not yet implemented

Empty function

void E_coli::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 in CV_rExp_tExp, and EO_rExp_tExp.

void E_coli::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

save and produce film of single tracking

void E_coli::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
	)

virtual

produce the .gif film

save and produce film of single tracking in .gif

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

virtual

plot internal dynamic

int E_coli::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
	)

This function set the initial position. What it does is: if the distribution is the n. 5, then update the new center, otherwise it calls dist_iniz(x,x0,Raggio,num_dist).

Parameters

x[]	position of pacterium (to be set)
x0[]	initial position, set in the menu
R	radius distribution
type	of distribution, see menu

Returns: if the initial position change return 1, otherwise 0. If the position didn't change the initial condition for this bacterium are the same as the previous one, so we don't have to perform initial-condition calculation.

int E_coli::N_dyn_var ( )

return number of internal variables in the current model

double E_coli::newtheta_ec ( double theta )

protected

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

virtual

print info for LateX report

Reimplemented in CV_rExp_tExp, Molecular_rExp_tExp, EO_rExp_tExp, ParameterEstimation_CV_rExp_tExp, EO_rIG_tExp, CV_rIG_tExp, CV_rExpIG_tExp, and EO_rExpIG_tExp.

void E_coli::produce	(	Funz_C *	f_i,
		double	dt
	)

virtual

update concentration ligand after production (in interacting mode)

double E_coli::Production_rate ( )

retun rate of production of new ligand concentration by the bacterium

double E_coli::rand_normal_ec ( double stddev )

protected

double E_coli::reset_barrier ( )

virtual

reset trashold for the run

Reimplemented in EO_rIG_tExp, CV_rIG_tExp, Molecular_rIG_tExp, CV_rExpIG_tExp, Molecular_rExpIG_tExp, and EO_rExpIG_tExp.

double E_coli::reset_barrier_t ( )

virtual

reset trashold for the tumble

void E_coli::reset_par ( )

virtual

reset defolt parametes model

Reimplemented in CV_rExp_tExp, Molecular_rExp_tExp, EO_rExp_tExp, EO_rIG_tExp, CV_rIG_tExp, CV_rExpIG_tExp, Molecular_rExpIG_tExp, EO_rExpIG_tExp, and Molecular_rIG_tExp.

void E_coli::response_function ( )

update the current concentration via the response function

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

virtual

initialize and save the empirical satisfaction index (function lambda)

void E_coli::save_dyn	(	ofstream &	file,
		double	t
	)

virtual

save internal dynamic in a file

void E_coli::save_E_coli	(	ofstream *	file,
		double	t
	)

save position, concentration and direction to file

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

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

save time and duration of a run

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

function used to save the angle at the moment of a tumble.

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

save time and duration of a tumble

Parameters

dt	time-step in the simulation

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

virtual

Reimplemented in CV_rExp_tExp, EO_rExp_tExp, EO_rIG_tExp, and CV_rIG_tExp.

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

virtual

save outpot of goodness fit test

Reimplemented in ParameterEstimation_E_coli.

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

set response function

Parameters

type	and coefficient (from 1st to last)

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

protected

void E_coli::setProductionRate ( double _prodRate )

set production rate (it is a static variable, once for all!)

void E_coli::setSeed_ec ( unsigned int * seed_thread )

protected

void E_coli::start_simulation ( Funz_C * f )

set initial data for the simulation

void E_coli::statF_lambda_r ( s_lambda & vector_lambda )

void E_coli::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 in CV_rExp_tExp, Molecular_rExp_tExp, and EO_rExp_tExp.

void E_coli::Tau_t ( double tt_ )

set time start of a tumble

Parameters

tt_	time in sec.

double E_coli::unifRand_ec ( )

protected

double E_coli::V ( )

inline

return speed bacterium

int E_coli::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 in CV_rExp_tExp, and EO_rExp_tExp.

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

protectedvirtual

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

return position bacterium

Member Data Documentation

double E_coli::barriera_r

protected

threshold for lambda_r (when lambda_r crosses it, tumble starts)

double E_coli::barriera_t

protected

threshold for lambda_t (when lambda_r crosses it, run starts)

double E_coli::c

protected

Ligand concentration

double E_coli::c_iniziale

protected

initial concentration of Ligand

int E_coli::codice_batterio

double E_coli::D_theta

protected

Diffusion coefficient direction

std::mt19937_64* E_coli::engine_altro

std::mt19937_64* E_coli::engine_barrier

std::mt19937_64* E_coli::engine_theta

pointer to a engine (if I want to use std::uniform_real_distribution<double>)

double E_coli::lambda_r

protected

probability rate to tumble

double E_coli::lambda_t

protected

probability rate to run

int E_coli::n_dyn_var

protected

number internal variables

double E_coli::production_rate

protected

Production rate bacterium

double E_coli::RC_0

protected

1st paramter in the response function

double E_coli::RC_1

protected

2nd paramter in the response function

int E_coli::RC_q

protected

3rd paramter in the response function: esponent in th Hill function

s_lambda E_coli::s_lambda_r

estimated parameter for the function lambda

int E_coli::salto_

protected

variable identifying in which state I'm in run_fase == 1, tumble_fase == 2, jump_instant == 0, tumble_fase == -1

unsigned int* E_coli::seed_ecoli

protected

pointer to a seed

The idea is the following: At the beginning of every simulation I seed the extra-thread

if I use a nomal 1-thread then nothing change from the 'basic implmentation', I just move the random generation function inside the class E_coli.
if I use multi-thread, for each thread I create a new seed_ecoli, which I pass to rand_r(&seed_ecoli) in this case I have independent sereis of Random Numebr for every thread.

int E_coli::sign_c

protected

sign of the "temporal gradient": c(now) - c(now-dt)

int E_coli::simulation

MODE of simulation:

simulation = 0 -> MODE simulation,
simulation = 1 -> MODE statistical_Simulation ...

double E_coli::t_r

protected

time began run

double E_coli::t_t

protected

time began tumble

double E_coli::tau_r

protected

mean of a run in the steady state

double E_coli::tau_t

protected

mean of a tumble in the steady state

double E_coli::theta

protected

Direction

std::string E_coli::Tipo_batterio

Name of the model used
the format in as follows: [Name Model]_r[Name Distribution run]_t[Name Distribution tumble]

int E_coli::tipo_response_c

protected

Type of reponse function between the available

int E_coli::tipoNewTheta

protected

This variable take track of the for of the distribution of the new theta

int E_coli::up_down

protected

variable that keep track if I'm going up or down the gradient

double E_coli::v

protected

Speed bacterium

std::array<double,2> E_coli::x

protected

Position

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

include/Ecoli/E_Coli.h
src/Ecoli/E_Coli.cpp
src/Ecoli/Internal_dynamic.cpp
src/Ecoli/Reset_barriera.cpp
src/LateX/print_and_open_info.cpp
src/Statistics/s_F_lambda_r.cpp
src/Varie/funzioni_risposta.cpp
src/Visualization/gnuplot_single_3.cpp
src/Visualization/gnuplot_single_film.cpp
src/Visualization/gnuplotFunzInternalDynalmic.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation