biophysics/MarkovSolverBase.h

Go to the documentation of this file.

/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
** Copyright (C) 2003-2011 Upinder S. Bhalla. and NCBS
** It is made available under the terms of the
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/
#ifndef _MARKOVSOLVERBASE_H
#define _MARKOVSOLVERBASE_H

//Class : MarkovSolverBase
//Author : Vishaka Datta S, 2011, NCBS
//Description : Base class for all current Markov solver(s) (and future ones,
//hopefully).
//
//After the setup of the MarkovRateTable class, where the user has entered
//the lookup tables for the various transition rates, we have enough
//information to compute all the exponential matrices that correspond to the 
//solution of the kinetic equation at each time step. 
//
//Before the channel simulation is run, the setup of the MarkovSolver requires
//that a table of matrix exponentials be computed and stored. In general, 
//this would require a 2D lookup table where each exponential is index by
//([L],V) where [L] = ligand concentration and V = membrane voltage.  
//In the case all rates are either ligand or voltage dependent, not both, a 1D
//lookup table of exponentials suffices. 
//
//The above computations are achieved by going through the lookup tables 
//of the MarkovRateTable class. In a general case, the number of divisions 
//i.e. step sizes in each lookup table will be different. We choose the smallest
//such step size, and assume that rates with bigger step sizes stay constant
//over this time interval. By iterating over the whole range, we setup the
//exponential table. 
//
//The MarkovSolverBase class handles all the bookkeeping for the table of matrix
//exponentials. It also handles all the above-mentioned interactions with the 
//remaining MOOSE classes.  
//
//Any MarkovSolver class that derives from this one only need implement
//a ComputeMatrixExponential() function, which handles the actual computation
//of a the matrix exponential given the Q_ matrix.
//

//SrcFinfos

class MarkovSolverBase {
    public : 
    MarkovSolverBase();

    virtual ~MarkovSolverBase();

    //Set-get stuff.
    Matrix getQ() const ;
    Vector getState() const;
    Vector getInitialState() const;
    void setInitialState( Vector );

    //Lookup table related stuff. Have stuck to the same naming
    //used in the Interpol2D class for simplicity.
    void setXmin( double );
    double getXmin() const;
    void setXmax( double );
    double getXmax() const;
    void setXdivs( unsigned int );
    unsigned int getXdivs() const;
    double getInvDx() const;

    void setYmin( double );
    double getYmin() const;
    void setYmax( double );
    double getYmax() const;
    void setYdivs( unsigned int );
    unsigned int getYdivs() const;
    double getInvDy() const;
    
    //Lookup table related stuff.
    
    //Fills up lookup table of matrix exponentials.
    void innerFillupTable( vector< unsigned int >, string, 
                                               unsigned int, unsigned int );
    void fillupTable();

    //This returns the pointer to the exponential of the Q matrix.
    virtual Matrix* computeMatrixExponential();
    
    //State space interpolation routines.
    Vector* bilinearInterpolate() const;
    Vector* linearInterpolate() const;

    //Computes the updated state of the system. Is called from the process
    //function.
    void computeState();    

    //MsgDest functions.
    void reinit( const Eref&, ProcPtr );
    void process( const Eref&, ProcPtr );

    //Handles information about Vm from the compartment. 
    void handleVm( double ); 

    //Handles concentration information.
    void handleLigandConc( double );

    //Takes the Id of a MarkovRateTable object to initialize the table of matrix
    //exponentials. 
    void init( Id, double );

    static const Cinfo* initCinfo();
    
    //Unit test
    #ifdef DO_UNIT_TESTS
    friend void testMarkovSolverBase();
    #endif

    protected : 
    //The instantaneous rate matrix.
    Matrix *Q_;

    #ifdef DO_UNIT_TESTS
    //Allows us to set Vm_ and ligandConc_ for the state space interpolation
    //unit test in the MarkovSolver class.
    void setVm( double );
    void setLigandConc( double );
    #endif

    private :
    //Helper functions.
    
    //Sets the values of xMin, xMax, xDivs, yMin, yMax, yDivs.
    void setLookupParams();

    //Lookup table related stuff.
    /*
    * Exponentials of all rate matrices that are generated over the 
    * duration of the simulation. The idea is that when copies of the channel
    * are made, they will all refer this table to get the appropriate 
    * exponential matrix. 
    *
    * The exponential matrices are computed over a range of voltage levels 
    * and/or ligand concentrations and stored in the appropriate lookup table.
    *
    * Depending on whether
    * 1) All rates are constant,
    * 2) Rates vary with only 1 parameter i.e. ligand/votage,
    * 3) Some rates are 2D i.e. vary with two parameters,
    * we store the table of exponentials in the appropriate pointers below.
    *
    * If a system contains both 2D and 1D rates, then, only the 2D pointer 
    * is used. 
    */
    //Used for storing exponentials when at least one of the rates are 1D and
    //none are 2D.
    vector< Matrix* > expMats1d_;

    Matrix* expMat_;

    //Used for storing exponentials when at least one of the rates are 2D.
    vector< vector< Matrix* > > expMats2d_;

    double xMin_;
    double xMax_;
    double invDx_;
    unsigned int xDivs_;
    double yMin_;
    double yMax_;
    double invDy_;
    unsigned int yDivs_;

    //Miscallenous stuff
    
    //Pointer to the MarkovRateTable object. Necessary to glean information
    //about the properties of all the transition rates.
    MarkovRateTable* rateTable_;

    //Instantaneous state of the system.
    Vector state_;

    //Initial state of the system.
    Vector initialState_;

    //Stands for a lot of things. The dimension of the Q matrix, the number of 
    //states in the rate table, etc which all happen to be the same.
    unsigned int size_;

    //Membrane voltage.
    double Vm_;
    //Ligand concentration.
    double ligandConc_;

    //Time step in simulation. The state at t = (t0 + dt) is given by
    //exp( A * dt ) * [state at t = t0 ].
    double dt_;
};
//End of class definition.
#endif

---