PSICS - the Parallel Stochastic Ion Channel Simulator
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Ion Channels

The KSChannel object encompasses all the allowed formats for ion channel definitions. The "KS" prefix indicates that it is focused on kinetic schemes, but it also allows multi-complex channels which enables Hodgkin-Huxley style models to be included within the same formalism. A single complex scheme is one where any state is connected to all other states directly or indirectly by channel transitions. A multi-complex scheme is one where the states fall into disjoint groups, or gating complexes. Each gating complex behaves independently and the relative conductance of the whole channel is the product of the relative conductances of each complex. A typical Hodgkin-Huxley model has three or four independent two-state complexes.

For stochastic calculations, multi-complex schemes are internally converted to the equivalent single-complex scheme. For deterministic calculations either form may be used, depending which is more efficient. Further details on the stochastic channel algorithm can be found in the numerical methods section of the user guide.

A channel is specified as a collection of states and transitions. There are two types of state, OpenState or ClosedState, and rather more types of transition. Each state should have an id that is unique within the channel definition. The transitions then refer to states by this id in their from and to attributes specifying the start and end states. There are a number of different parameterizations provided for the transitions themselves, but in general models should use the VHalfTransition for all voltage-dependent transitions. The other transition types are provided so that PSICS can exactly express certain legacy channel models for validation purposes but do not necessarily have much biophysical justification.

For multi-complex channels, the states and transitions for each complex should be embedded within KSComplex objects. This is not strictly required (PSICS can work out what the sub-complexes are just from the transition start and end points) but is good practice. It is required if there are multiple instances of a certain complex and you do not want to list all the states and transitions explicitly. In that case you can define them once and set the instances attribute to say how many instances of the complex there are in the channel. This is primarily useful for representing Hodgkin-Huxley style models where the powers on the gating variables can be interpreted as the number of instances of a two-state gate.

KSChannel

An ion channel represented by a kinetic scheme

Standalone model

Also known as a Markov model,the schem defines the possible states (configurations) of the channel and the transitions between them. If the scheme falls into disjoint sub-schemes these are interpreted as independent serial gating complexes and the effective relative conductance os the product of the relative conductances of separate complexes. This enables Hodgkin Huxley styleto be economically represented as a collection of separate two-state complexes

Attributes

NameTypeDefinitionUnitsRangeRequired
ididentifierIdentifier (name) for the element; unique within the modelyes
permeantIonidentifier referenceThe permeant ion (Ion) yes
gSingleFloating point valueSingle channel conductance. Separate open states canspecify their relative conductance as a fraction of this quantity.pS(0.1, 100)yes

Elements

Element typeRole
OpenState, ClosedStatelist of states
FixedRateTransition, VHalfTransition, VRateTransition, ExpLinearTransitionlist of transitions
KSComplexgating complexes
OhmicConductanceModelConductance model - just one per channel
CodedTransitionFunction(deprecated) Additional coded functions, if any, needed for coded transitions.
FunctionAdditional functions, if any, needed for transitions.
AboutExtended textual information about the model
ParameterParameters that can be used within the component

ClosedState

non-permeable configuration of an ion channel

within: KSChannel

Attributes

NameTypeDefinitionUnitsRangeRequired
ididentifierIdentifier (name) for the state; unique within this channelyes
xFloating point valueposition for visualization of state diagramnone(-1, 1)
yFloating point valueposition for visualization of state diagramnone(-1, 1)

Elements - No child elements are allowed

Example

<ClosedState id="C" />

OpenState

Permeable configuration of an ion channel

within: KSChannel

The conductance is specified relative to the maximum conductance for the channel. Different states can have different conductances, but other permeation properties are assumed to be the same for all open states.

Attributes

NameTypeDefinitionUnitsRangeRequired
ididentifierIdentifier (name) for the state; unique within this channelyes
gRelFloating point valuerelative conductance for this state compared to the channel conductancenone(0, 1)yes
xFloating point valueposition for visualization of state diagramnone(-1, 1)
yFloating point valueposition for visualization of state diagramnone(-1, 1)

Elements - No child elements are allowed

Example

<OpenState id="O" grel="1.0" />

FixedRateTransition

A transition between states of a kinetic scheme with fixed forward and reverse rates

within: KSChannel

A fixed-rate transition, sometimes known as a time-dependent transition, is one where the probability of the transition occuring in a given time interal is always the same, independent of external factors such as the membrane potential.

Attributes

NameTypeDefinitionUnitsRangeRequired
ididentifierIdentifier (name) for the transition; unique within this channelyes
fromidentifier referenceThe originating state of the transition (ClosedState, OpenState) yes
toidentifier referenceThe destination state of the transition (ClosedState, OpenState) yes
forwardFloating point valueForward rate, transitions per msper_ms(0.01, 1000)yes
reverseFloating point valueReverse rate, transitions per msper_ms(0.01, 1000)yes
baseTemperatureFloating point valueBase temperature for Q10Celsius(5,40)
q10Floating point valueTemperature dependence of rates: rate change for a rise of ten degreesnone(0,4)

Elements - No child elements are allowed

Example

<FixedRateTransition forward="1.2per_ms" reverse="0.3per_ms" />

VHalfTransition

Voltage dependent transition defined by its midpoint

within: KSChannel

This is one of two ways of expressing a first order Boltzmann transition with one or two extra term(s) to make the rates saturate rather than become indefinitely large for extreme potentials. This form uses the mid-pint potential, vHalf at which forward and reverse rates are equal, and the timescale (reciprocol of the rate) at that point. The saturation timescale can be expressed either as tauMin, or separately for the forward and reverse rates as tauMinFwd and tauMinRev.

Attributes

NameTypeDefinitionUnitsRangeRequired
ididentifierIdentifier (name) for the transition; unique within this channelyes
fromidentifier referenceThe originating state of the transition (ClosedState, OpenState) yes
toidentifier referenceThe destination state of the transition (ClosedState, OpenState) yes
vHalfFloating point valuePotential at which the forward and reverse rates are equalmV(-80, -20)yes
zFloating point valueEquivalent gating charg in electronic charge unitse(-4, 4)yes
gammaFloating point valueGating assymetry: relative position of potential peak in the transit of gating particlenone[0,1]yes
tauFloating point valuetransition timescale (reciprocol ofthe rate at vHalf)ms(0.001, 1)yes
tauMinFloating point valueminimum transition timescale (saturation of rate for extreme potentials) - must either set tauMin or the forward and reverse timescales separatelyms(1.e-5, 1.)
tauMinFwdFloating point valueminimum transition timescale for forward transition (if tauMin is not set)ms(1.e-5, 1.)
tauMinRevFloating point valueminimum transition timescale for reverse transition (if tauMin is not set)ms(1.e-5, 1.)
baseTemperatureFloating point valueBase temperature for Q10Celsius(5,40)
q10Floating point valueTemperature dependence of rates: rate change for a rise of ten degreesnone(0,4)

Elements - No child elements are allowed

Example

<VHalfTransition from="C3" to="O" vHalf="-45mV" z="3.5e" gamma="0.8" tau="1.2ms" tauMin="0.02ms" />

VRateTransition

Voltaqe dependent transition defined by forward and reverse rates are v=0

within: KSChannel

This is one of two ways of expressing a first order Boltzmann transition with one or two extra term(s) to make the rates saturate rather than become indefinitely large for extreme potentials. This version requires the forward and reverse rates for a membrane potential of zero. Internally, these transitions are converted into exactly the same form as is used for the VHalfTransition.

Attributes

NameTypeDefinitionUnitsRangeRequired
ididentifierIdentifier (name) for the transition; unique within this channelyes
fromidentifier referenceThe originating state of the transition (ClosedState, OpenState) yes
toidentifier referenceThe destination state of the transition (ClosedState, OpenState) yes
forwardFloating point valueForward rate at zero potential differenceper_ms(0.01, 1000)yes
reverseFloating point valueReverse rate at zero potential differenceper_ms(0.01, 1000)yes
zFloating point valueEquivalent gating chargee(-5, 5)yes
gammaFloating point valueGating assymetrynone[0., 1.]yes
tauMinFloating point valueSaturation time constantms(0.0001, 1)yes
baseTemperatureFloating point valueBase temperature for Q10Celsius(5,40)
q10Floating point valueTemperature dependence of rates: rate change for a rise of ten degreesnone(0,4)

Elements - No child elements are allowed

Example

<VRateTransition from="C3" to="O" forward="3.2per_ms" reverse="0.2per_ms" z="2.3e" gamma="0.8" tauMin="0.02ms" />

ExpLinearTransition

HH style one-way exponential-linera transition

within: KSChannel, KSComplex

A one-way transition expressed in the form A x / (1 - exp(-x)) where x = (v - v0) / B. The parameters are the rate, A, the modpoint, v0, where x = 0, and the voltage scale, scale, which divides both the midpoint and v0. Note that this expression has numerous variants, so published parameters may not map directly onto the rate, midpoint and scale. Most often the signs of the rate and scale are reversed or the scale dependence of the numerator is wrapped into the rate, in a form sucha as alpha (v - v0) / (exp (beta (v - v0)) - 1).

Attributes

NameTypeDefinitionUnitsRangeRequired
ididentifierIdentifier (name) for the transition; unique within this channelyes
fromidentifier referenceThe originating state of the transition (ClosedState, OpenState) yes
toidentifier referenceThe destination state of the transition (ClosedState, OpenState) yes
rateFloating point valueRate at inflectionper_ms(0.01, 1000)yes
midpointFloating point valuePotential of inflection between exponential and linear dependieciesmV(-80, -20)yes
scaleFloating point valuePotential scalingmV(-80, 40)yes
baseTemperatureFloating point valueBase temperature for Q10Celsius(5,40)
q10Floating point valueTemperature dependence of rates: rate change for a rise of ten degreesnone(0,4)

Elements - No child elements are allowed

Example

<ExpLinearTransition rate="1.2ms" midpoint="-45.0mV" scale="12mV" />

ExpTransition

Exponential HH style rate

within: KSChannel

A one-way transition as used in the original HH model, giving the rate, beta, as beta = rate exp((v - midpoint)/ vscale)

Attributes

NameTypeDefinitionUnitsRangeRequired
ididentifierIdentifier (name) for the transition; unique within this channelyes
fromidentifier referenceThe originating state of the transition (ClosedState, OpenState) yes
toidentifier referenceThe destination state of the transition (ClosedState, OpenState) yes
rateFloating point valueRate at v = midpointper_ms(0.01, 1000)yes
scaleFloating point valueScale factor for voltage termmV(0.0, 100)yes
midpointFloating point valuePotential of inflection between exponential and linear dependieciesmV(-80, -20)yes
baseTemperatureFloating point valueBase temperature for Q10Celsius(5,40)
q10Floating point valueTemperature dependence of rates: rate change for a rise of ten degreesnone(0,4)

Elements - No child elements are allowed

Example

<ExpTransition rate="1.2ms" midpoint="-45.0mV" scale="12mV" />

SigmoidTransition

Exponential HH style rate

within: KSChannel

A one-way transition as used in the original HH model, giving the rate, beta, as beta = rate / (1 + exp(-(v - midpoint)/ vscale))

Attributes

NameTypeDefinitionUnitsRangeRequired
ididentifierIdentifier (name) for the transition; unique within this channelyes
fromidentifier referenceThe originating state of the transition (ClosedState, OpenState) yes
toidentifier referenceThe destination state of the transition (ClosedState, OpenState) yes
rateFloating point valueRate at v = midpointper_ms(0.01, 1000)yes
scaleFloating point valueScale factor for voltage termmV(0.0, 100)yes
midpointFloating point valuePotential of midpoint of curve, where the rate is half its maximum valuemV(-80, -20)yes
baseTemperatureFloating point valueBase temperature for Q10Celsius(5,40)
q10Floating point valueTemperature dependence of rates: rate change for a rise of ten degreesnone(0,4)

Elements - No child elements are allowed

Example

<SigmoidTransition rate="34.2per_ms" scale="12.3mV" midpoint="-30mV" />

KSComplex

a single complex within a kinetic scheme channel

Standalone model or within: KSChannel

KSComplexes provide an optional grouping of states within a channel. The effect is the same as specifying transitions between top-level that implicitly define separate gating complexes, with the exception that the complex also allows an instances attribute that can be used to specify that the channel has more tna one sequential instance of the same complex. This is primarily useful for the economical representation of Hodgkin-Huxley style channels that have multiple independent, but identically gated, two-state complexes.

Attributes

NameTypeDefinitionUnitsRangeRequired
ididentifierIdentifier (name) for the complexyes
instancesWhole numbernumber of complexes of this type in the channel, equivalentto the power used in HH models[1,4)

Elements

Element typeRole
OpenState, ClosedStatelist of states
FixedRateTransition, VHalfTransition, VRateTransition, ExpLinearTransitionlist of transitions

TauInfCodedTransition

Voltaqe dependent transition defined by a fragment of code

within: KSChannel

This

Attributes

NameTypeDefinitionUnitsRangeRequired
ididentifierIdentifier (name) for the transition; unique within this channelyes
fromidentifier referenceThe originating state of the transition (ClosedState, OpenState) yes
toidentifier referenceThe destination state of the transition (ClosedState, OpenState) yes
baseTemperatureFloating point valueBase temperature for Q10Celsius(5,40)
q10Floating point valueTemperature dependence of rates: rate change for a rise of ten degreesnone(0,4)
tauvarplain textThe name of the output variable for the time constant.
infvarplain textThe name of the output variable for the equilbrium gate position.

Elements

Element typeRole
Constant

Example

<VHalfTransition from="C3" to="O" vHalf="-45mV" z="3.5e" gamma="0.8" tau="1.2ms" tauMin="0.02ms" />

TauInfTransition

Voltaqe dependent transition defined by functions for Tau and m-infinity

within: KSChannel

Attributes

NameTypeDefinitionUnitsRangeRequired
ididentifierIdentifier (name) for the transition; unique within this channelyes
fromidentifier referenceThe originating state of the transition (ClosedState, OpenState) yes
toidentifier referenceThe destination state of the transition (ClosedState, OpenState) yes
baseTemperatureFloating point valueBase temperature for Q10Celsius(5,40)
q10Floating point valueTemperature dependence of rates: rate change for a rise of ten degreesnone(0,4)

Elements

Element typeRole
Constant
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