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rbmatlab
1.16.09
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rbmatlab
1.16.09
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model of the human follicle growth More...
Go to the source code of this file.
Functions | |
| function model = | follicle_rect_model (params) |
| model of the human follicle growth More... | |
| function A = | folliclerectmodel>A_func (model, model_data) |
| function Acomp = | folliclerectmodel>A_components (model, model_data) |
| function Acoeff = | folliclerectmodel>A_coefficients (model) |
| function B = | folliclerectmodel>B_func (model, model_data) |
| function Bcomp = | folliclerectmodel>B_components (model, model_data) |
| function Bcoeff = | folliclerectmodel>B_coefficients (model) |
| function C = | folliclerectmodel>C_func_separatrix (model, model_data) |
| function C = | folliclerectmodel>C_func_expectation_M (model, model_data) |
| function C = | folliclerectmodel>C_func_expectation_N (model, model_data) |
| function Ccomp = | folliclerectmodel>C_components_separatrix (model, model_data) |
| function Ccomp = | folliclerectmodel>C_components_expectation_M (model, model_data) |
| function Ccomp = | folliclerectmodel>C_components_expectation_N (model, model_data) |
| function Ccoeff = | folliclerectmodel>C_coefficients (model) |
| function D = | folliclerectmodel>D_func (model, model_data) |
| function x0 = | folliclerectmodel>x0_func (model, model_data) |
| function x0comp = | folliclerectmodel>x0_components (model, model_data) |
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function
x0coeff = | folliclerectmodel>x0_coefficients (model) |
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function
model_data = | folliclerectmodel>my_ds_gen_model_data (model) |
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function
detailed_data = | folliclerectmodel>my_ds_gen_detailed_data (model, model_data) |
| function p = | folliclerectmodel>plot_state_probabilities (model, model_data, sim_data, params) |
| function p = | folliclerectmodel>my_plot_slice (model, model_data, sim_data, params) |
| function cm = | folliclerectmodel>my_transformed_colormap () |
model of the human follicle growth
Definition in file follicle_rect_model.m.
| function model = follicle_rect_model | ( | params | ) |
model of the human follicle growth
two chemical components are assumed to be characteristic for the growth of human follicles.
A deterministic model for the two species is given by a positive feedback loop, a bistable switch, i.e. 2-d nonlinear ODE.
An approximation to the Chemical Master Equation gives a linear dynamical system.
here, the state vector is the probability of states (pair of number of two chemical components) and the matrix A describes the change in these probabilities over time. The number of states is p = (range+1)*(range+1) hence rectangular domain
separatrix: an average over a subset of states, the ones below the diagonal "separatrix", which are assumed to be still "in rest", i.e. waiting for their growth specified by model.output_range expectation_M: the expectation of M state is computed expectation_N: the expectation of N state is computed| params | params |
| model | model |
range — range output_range — output range init_range — init range reg_epsilon — reg epsilon output_type — output type output_plot_indices — output plot indices estimate_bounds — estimate boundsdata_const_in_time — data const in time verbose — flag indicating the verbosity level of informative output debug — flag indicating wether debug output shall be turned on M1 — M1 h — h M2 — M2 range — range output_range — output range init_range — init range reg_epsilon — reg epsilon u1 — u1 u2 — u2 k1fact — k1fact V1fact — V1fact V2fact — V2fact mu_names — a string array containing the symbolic names of the parameter vector \(\mu\) mu_ranges — matrix storing the admissable ranges for parameter vector components. Each two dimensional column vector represents a range for a component specified by model.mu_names. T — end time for evolution problems nt — number of time steps for evolution discretizations affinely_decomposed — affinely decomposed A_function_ptr — A function ptr B_function_ptr — B function ptr C_function_ptr — C function ptr D_function_ptr — D function ptr x0_function_ptr — x0 function ptr u_function_ptr — u function ptr G_matrix_function_ptr — G matrix function ptr gen_model_data — gen model data gen_detailed_data — gen detailed data plot_sim_data_state — plot sim data state plot_slice — plot slice axis_tight — axis tight orthonormalize — orthonormalize dim_x — dim x dim_y — dim y output_plot_indices — output plot indices theta — theta enable_error_estimator — enable error estimator state_bound_constant_C1 — state bound constant C1 output_bound_constant_C2 — output bound constant C2 estimate_lin_ds_nmu — estimate lin ds nmu estimate_lin_ds_nX — estimate lin ds nX estimate_lin_ds_nt — estimate lin ds nt inner_product_matrix_algorithm — function pointer to a function computing a inner product matrix \(W\), such that \(u^t W v = <u, v>\). An example is fv_inner_product_matrix(). error_algorithm — error algorithm RB_stop_timeout — RB stop timeout RB_stop_epsilon — RB stop epsilon RB_error_indicator — RB error indicator RB_stop_Nmax — RB stop Nmax RB_generation_mode — RB generation mode RB_numintervals — RB numintervals RB_detailed_train_savepath — RB detailed train savepath RB_save_temp_detailed_data — RB save temp detailed data RB_extension_algorithm — RB extension algorithm save_detailed_simulations — save detailed simulations transformed_colormap — transformed colormap Definition at line 17 of file follicle_rect_model.m.
1.8.8