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conductance

This document describes the "conductance" C++ class. This class describes objects that are conductances, or populations of ion channels.

This is an abstract class, and concrete implementations of ion channel types need to inherit from this class and define certain attributes like their activation functions.

Abstract can contain contained in
yes nothing compartment

Properties

container

type default user-accessible
compartment* NULL no

gbar

type default user-accessible
double 0 yes

The maximal conductance of this channel type (in ). This is typically exposed to the user as a parameter to set and modify.

gbar_next

type default user-accessible
double 0 no

g

type default user-accessible
double 0 no

The instantaneous conductance of this channel type. This is a product of gbar and the activation and inactivation variables.

E

type default user-accessible
double 0 yes

The reversal potential of this channel type.

m

type default user-accessible
double 0 no

The activation variable of this channel type.

h

type default user-accessible
double 1 no

The inactivation variable of this channel type.

verbosity

type default user-accessible
double 0 no

A flag that tells this channel how verbose it should be. This should not be exposed to the user, since it it broadcast to all components from xolotl.verbosity.

Methods

buildLUT

Function Signature

void buildLUT(double approx_channels) 

Description

This method constructs a look up table (LUT) that is used to estimate and other functions of the voltage. Since these functions are repeatedly evaluated, it is often faster to compute them for some values of the voltage once, store these values in a table, and use this table subsequently. This is an approximation since the voltage is rounded off to the nearest value in the look-up table, uses a little more memory, but can be much faster.

Code

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fast_pow

Function Signature

inline double fast_pow(double x, int a) 

Description

This method is a dirty hack to speed up computing exponents in C++. This requires that the power that a number is raised to be an integer (0-8)

Code

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fast_exp

Function Signature

inline double fast_exp(double x) 

Description

This method constitutes a dirty hack which is a faster way to compute exp(x) but is less precise

Code

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getCurrent

Function Signature

double getCurrent(double V) 

Description

The method returns the current that flows through this channel at this moment.

Code

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checkSolvers

Function Signature

void checkSolvers(int solver_order) 

Description

Code

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mdot

Function Signature

double mdot(double V, double Ca, double m_) 

Description

This method defines the rate of change of the m variable of this conductance. This definition is used when integrateMS is used.

Code

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hdot

Function Signature

double hdot(double V, double Ca, double h_) 

Description

This method defines the rate of change of the h variable of this conductance. This definition is used when integrateMS is used.

Code

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m_inf

Function Signature

double m_inf(double V, double Ca)

Description

This method defines the activation curve of this channel. This is a virtual method, and is meant to be defined in the channel object.

Code

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h_inf

Function Signature

double h_inf(double V, double Ca)

Description

This method defines the inactivation curve of this channel. This is a virtual method, and is meant to be defined in the channel object.

Code

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tau_m

Function Signature

double tau_m(double V, double Ca)

Description

This method defines the dependence of the timescale of the activation variable on the voltage of this channel. This is a virtual method, and is meant to be defined in the channel object.

Code

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tau_h

Function Signature

double tau_h(double V, double Ca)

Description

This method defines the dependence of the timescale of the inactivation variable on the voltage of this channel. This is a virtual method, and is meant to be defined in the channel object.

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gaussrand

Function Signature

double gaussrand() 

Description

This method implements a very fast Gaussian random number generator. This is much faster than the built-in generators in the C++ <random> header, and is copied from Knuth and Marsaglia.

For the original source, see "A Convenient Method for Generating Normal Variables" SIAM Rev., 6(3), 260–264.

Code

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connect

Function Signature

void connect(compartment *pcomp_) 

Description

This method "connects" a conductance object to a compartment object. This sets the container property of the conductance, so the channel knows which compartment contains it.

Code

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integrate

Function Signature

void integrate(double V, double Ca) 

Description

This method integrates the conductance object using the exponential Euler method. This is the default integration method used by xolotl. If an exact solution is to be calculated (i.e.,approx_m = 0 and approx_h=0) then m and h are updated using the exponential Euler equation using function evaluations of the activation functions at this voltage and Calcium.

Otherwise, the lookup table is used to update m and h in this channel.

Note that this method is defined as virtual, so it can be overridden by integration methods specified in a specific conductance.

See Also

Code

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integrateLangevin

Function Signature

void integrateLangevin(double V, double Ca) 

Description

This method integrates the conductance object using the Euler-Maruyama method. The integration method used here is consistent with the methods used in Goldwyn and Shea-Brown 2011 and with Sengupta, Laughlin and Niven

Briefly, this method follows the approximate Langevin formulation of the underlying stochastic system formed by N independent channels that have independent gating kinetics. It can be thought of as the deterministic ODE, with an additive noise term whose variance scales with the inverse square root of the number of channels. The number of channels is computed automatically from the channel density and the area of the compartment.

Code

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integrateMS

Function Signature

void integrateMS(int k, double V, double Ca) 

Description

This method integrates a channel object using a multi-step solver (MS = "multi-step"). The "sub-step" is indicated in the integer k, which is the first input to this method.

The multi-step solver that is used here is a Runge-Kutta 4th order solver. Thus, k can have values up to 4.

Based on k, different elements of the arrays k_m and k_h are calculated and stored. At each step, the derivative functions mdot and hdot are computed.

See Also

Code

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