Celani Shimitzu Vergassola Molecular Model Class for a bacterium. More...

#include <Molecular_rExp_tExp.h>

Inheritance diagram for Molecular_rExp_tExp:

Public Member Functions
	Molecular_rExp_tExp ()

	Molecular_rExp_tExp (const Molecular_rExp_tExp &modello)

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

void	change_par (int change)

void	change_molecular ()

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

void	print_info (std::ofstream &file_save)

void	reset_par ()

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 int	saveIntDyn (std::string nameFile)

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	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 (string tipo, string names_files_Ecoli_mod, string names_files_tau_mod, string *names_info_mod, 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	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	a_m

double	m_0

double	K_off

double	K_on

double	n_a

double	M_max

double	A_max

double	L_max

double	y_max

double	K_R

double	K_B

double	kCheR

double	kCheB

double	y_0

double	k_a

double	k_z

double	H

double	meth

double	a

double	y

double	p_r

double	factor_prob

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...

Friends
double	F_CSV (Molecular_rExp_tExp *batterio, double m_s, double L_use)

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

Celani Shimitzu Vergassola Molecular Model Class for a bacterium.

Class implementing Celani Shimitzu Vergassola Molecular model

This model is taken from CSV11 [A. Celani, T.S. Shimizu and M. Vergassola, Molecular and functional aspects of bacterial chemotaxis, J. Stat. Phys. 144, 219-240 (2011).], and implement the mean field approximation for the molecular-base model of the internal dynamic of the bacterium. The generalization to the Inverse gaussian and exponential-inverse gaussian is straightforward.

The chemotactic transduction pathway is conveniently modeled by the following set of mean-field equations:

$\begin{align} a&=G(m,L),\\ \frac{d}{dt}m&=F(a,m),\\ \frac{d}{dt}y&=k_a a(1-y)-k_zy,\\ \frac{d}{dt}p_r&=\frac{1-\frac{p_r}{h(y)}}{\tau_t}. \end{align}$

The detailed expressions for the functions that appear above are

$\begin{align*} G(m,L)&=\frac{1}{1+e^{f(m,L)}},\\ f(m,L)&=n_a\alpha_m(m_0-m)+n_a\ln\frac{1+\frac{L}{K_{off}}}{1+\frac{L}{K_{on}}},\\ F(a,m)&=k_r[\textrm{CheR}](1-a)\frac{M-a}{M-m+K_R}-k_b[\textrm{CheB}]a\frac{m}{m+K_B};\\ h(y)&=\frac{1}{1+\Big(\frac{y}{y_0}\Big)^H}. \end{align*}$

Constructor & Destructor Documentation

Molecular_rExp_tExp::Molecular_rExp_tExp ( )

Molecular_rExp_tExp::Molecular_rExp_tExp ( const Molecular_rExp_tExp & modello )

Member Function Documentation

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

virtual

update internal dynamic

Reimplemented from E_coli.

int Molecular_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 Molecular_rIG_tExp.

void Molecular_rExp_tExp::change_molecular ( )

void Molecular_rExp_tExp::change_par ( int change )

virtual

set parameters model

Reimplemented from E_coli.

Reimplemented in Molecular_rIG_tExp.

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

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

virtual

print info for LateX report

Reimplemented from E_coli.

void Molecular_rExp_tExp::reset_par ( )

virtual

reset defolt parametes model

Reimplemented from E_coli.

Reimplemented in Molecular_rExpIG_tExp, and Molecular_rIG_tExp.

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

void Molecular_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 Molecular_rExp_tExp::writeScriptgnuplotSingle	(	string	tipo,
		string *	names_files_Ecoli_mod,
		string *	names_files_tau_mod,
		string *	names_info_mod,
		string &	names_file_dyn_mod,
		double	T_f,
		int	con_gen_sim,
		int	save_
	)

protected

Friends And Related Function Documentation

double F_CSV	(	Molecular_rExp_tExp *	batterio,
		double	m_s,
		double	L_use
	)

friend

Function to calculate stationary state in CV model see paper [Celani Schimizu Vergassola] E_coli "something" 2011

Member Data Documentation

double Molecular_rExp_tExp::a

protected

Internal variable: see model in detailed description

double Molecular_rExp_tExp::a_m

protected

see model in detailed description

double Molecular_rExp_tExp::A_max

protected

see model in detailed description

double Molecular_rExp_tExp::factor_prob

protected

factor to adjust initial value for probability rate, it's make stable the process, it's like play with y_0

double Molecular_rExp_tExp::H

protected

see model in detailed description

double Molecular_rExp_tExp::k_a

protected

see model in detailed description

double Molecular_rExp_tExp::K_B

protected

see model in detailed description

double Molecular_rExp_tExp::K_off

protected

see model in detailed description

double Molecular_rExp_tExp::K_on

protected

see model in detailed description

double Molecular_rExp_tExp::K_R

protected

see model in detailed description

double Molecular_rExp_tExp::k_z

protected

see model in detailed description

double Molecular_rExp_tExp::kCheB

protected

see model in detailed description

double Molecular_rExp_tExp::kCheR

protected

see model in detailed description

double Molecular_rExp_tExp::L_max

protected

see model in detailed description

double Molecular_rExp_tExp::m_0

protected

see model in detailed description

double Molecular_rExp_tExp::M_max

protected

see model in detailed description

double Molecular_rExp_tExp::meth

protected

Internal variable methalination level: see model in detailed description

double Molecular_rExp_tExp::n_a

protected

see model in detailed description

double Molecular_rExp_tExp::p_r

protected

Internal variable: see model in detailed description

double Molecular_rExp_tExp::y

protected

Internal variable: see model in detailed description

double Molecular_rExp_tExp::y_0

protected

see model in detailed description

double Molecular_rExp_tExp::y_max

protected

see model in detailed description

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

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation