File contents

Object Type:    symcompartment

Description:    Axially symmetric compartment. Ra is divided into
		two equal components across the compartment.

Author:         M. Wilson, Caltech (6/88)

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ELEMENT PARAMETERS

DataStructure:  symcompartment_type  [in src/segment/seg_struct.h]

Size:           132 bytes

Fields:         Rm              total membrane resistance
                Cm              total membrane capacitance
                Em              membrane resting potential
                Ra              axial resistance
                inject          injected current in membrane
                dia             compartment diameter
                len             compartment length              
                Vm              voltage across the membrane
                previous_state  Vm at previous time step
                Im              approximation to the total membrane current
                initVm          initial value to set Vm on reset

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SIMULATION PARAMETERS

Function:       SymCompartment  [in src/segment/symcompartment.c]

Classes:        segment
                membrane

Actions:        INIT            assign previous_state = Vm
                PROCESS         update Vm, calculate Im
                RESET           assign Vm = Em, set internal constants
                                depending on the types of incoming messages.
                CHECK           make sure Rm>0, Cm>0, Ra>0
                SAVE2
                RESTORE2

Messages:       CHANNEL Gk Ek   delivers the conductance and equilibrium
                                potential of channel within the compartment
                INJECT inject   sets the inject field to the message value
                EREST Em        sets the Em  field to the message value

                CONNECTHEAD   Ra Vm  used to connect to the child compartment
                CONNECTTAIL   Ra Vm  used to connect to the parent compartment
                CONNECTCROSS  Ra Vm  used to cross-connect the first
                                     compartments after a  binary or multiple
                                     branch.
                RAXIAL Ra Vm    alias for CONNECTTAIL
                AXIAL Ra Vm     alias for CONNECTHEAD; note that for the
                                asymmetric compartment, AXIAL only receives Vm.
                RAXIAL2 Ra Vm   alias for CONNECTHEAD
                RAXIALC Ra Vm   alias for CONNECTCROSS

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Notes:          Like the compartment object, the symcompartment simulates
                a section of passive membrane or cable. The potential across
                the membrane is given by Vm. There is a leakage path for
                current through the resistance Rm. This resistance is in
                series with a leakage battery Em, and there is a membrane
                capacitance in parallel with Rm and Em. This compartment can
                be coupled to other compartments with an axial resistance Ra,
                which is divided into two pieces of resistance Ra/2 on either
                side of the point having the potential Vm.  In most respects,
                the symcompartment is similar to the asymetric compartment
                object, and its use is more fully described in the
                documentation for compartment.  However, the division of Ra
                requires different messages to be used when linking
                symcompartments.

                For linear chains of symmetric compartments, all of the
                connection messages are equivalent, and all compartments may
                be linked by exchanging RAXIAL messages.  However, for
                branched structures, the the incoming current must be
                calculated differently, depending on whether it is from a
                parent, child, or connected sibling in the tree of
                compartments, using the messages described above.  Because of
                this added complexity, it is best to use the readcell routine
                with a cell parameter file when constructing cells with
                symcompartments.  This will link the compartments with the
                proper messages.

                Prior to GENESIS version 2.2, the CONNECTSPHERE message was
                use to connect a cylinder to a sphere, assuming that all the
                dendrites are distributed perfectly over the soma/sphere.
                This is now performed automatically by readcell, and this
                message is no longer needed.  Using CONNECTHEAD or CONNECTTAIL
                instead connects all denrites to one point on the soma/sphere.

                A note on spherical compartments by Erik De Schutter:  If you
                use readcell, spherical compartments will have zero length (a
                GENESIS convention) and the Ra field will NOT be zero.  This
                means that the (small) resistive component of the spherical
                compartment will be used in computing the axial current
                between the spherical soma and dendrite.  This is very
                different from the asymmetric case (where the connections are
                usually arranged to go through the larger Ra of the adjacent
                dendritic cylinder instead of the small soma Ra).  This may
                look strange for the case of a single dendrite.  It makes more
                sense in the case of an apical and basal dendrite: if synaptic
                current flows from one to the other, one imagines that the
                soma has some effect.  Note also that whether you use a
                CONNECTCROSS message between cylindrical compartments onto the
                same sphere really should depend on their topological
                relation.  For example, basal dendrites should probably be
                cross-connected to each other but not to an apical one.
                readcell will issue all the possible CONNECTCROSS messages
                automatically, so you may want to delete some which are not
                consistent with your intended topology.

                The compartment Im is the sum of axial currents and injected
                current only.  The (transmembrane) channel currents or the
                leakage current are not included.  For a multicompartment
                cell, under a quasistatic approximation (C*dV/dt is small), Im
                is approximately equal to the sum of the channel and leakage
                currents, due to charge conservation.  This approximation is
                used in the efield object (see efield.doc) to allow Im to be
                used to calculate external field potentials.  The exception to
                this is when Im is calculated with hsolve in chanmode 4.  In
                that case, Im is directly calculated as the sum of the channel
                currents and leakage current though Rm.

                As of GENESIS version 2.2, symcompartments may be used
                with the hsolve method, allowing the use of fast implicit
                numerical integration methods.

Example:        Use the showmsg command to examine the messages to and from
                /CA3/soma, /CA3/apical_10, /CA3/basal_8, etc. in the traub91
                simulation.

See also:       compartment, readcell