Object Type: symcompartment Description: Axially symmetric compartment. Ra is divided into two equal components across the compartment. Author: M. Wilson, Caltech (6/88) ------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------ 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