Search found 55 matches

by adamjhn
Tue Aug 15, 2023 3:17 pm
Forum: Reaction-diffusion in NEURON
Topic: MultiCompartmentReaction across sections
Replies: 6
Views: 13145

Re: MultiCompartmentReaction across sections

You are right about multi-compartment reactions, they are used for reactions between regions of a section or with the extracellular space. A possible solution to the problem of diffusion between a pre- and post-synaptic section is to use the node.include_flux. For example; Diffusion across a synapse...
by adamjhn
Wed Aug 02, 2023 3:38 pm
Forum: Reaction-diffusion in NEURON
Topic: Integrating RxD Ca reactions with MOD mechanisms
Replies: 5
Views: 12128

Re: Integrating RxD Ca reactions with MOD mechanisms

Ted is right, CaDynamics_E2 writes to cai but it is then overwritten by rxd. Looking at the mod file it looks like it does a couple of things; calcium accumulation and restoration to minCa. RxD already handles accumulation, but unlike the mod file it uses the segment's area and volume to calculate t...
by adamjhn
Wed May 10, 2023 12:47 pm
Forum: Reaction-diffusion in NEURON
Topic: Can rxd.Rate() intrinsically keep track of currents?
Replies: 1
Views: 10025

Re: Can rxd.Rate() intrinsically keep track of currents?

Sorry for the late reply. RxD will keep track of concentrations and update Nernst potentials of the `rxd.Species` in your model. It can also generate currents, but only when a charge carrier movers across a membrane, which can be defined with a `rxd.MultiCompartmentReaction`. Here is an example of t...
by adamjhn
Wed May 10, 2023 12:42 pm
Forum: Reaction-diffusion in NEURON
Topic: Recording individual fluxes on a species that includes multiple mechanisms
Replies: 4
Views: 11152

Re: Recording individual fluxes on a species that includes multiple mechanisms

Sorry for the late reply. Current for MultiCompartmentReaction aren’t stored so cannot be directly recorded from. However by recording the contributing states, concentrations, etc. it is possible to calculate the current for any MultiCompartmentReaction. Here is an example comparing NEURON’s Hodgkin...
by adamjhn
Thu Feb 10, 2022 10:53 am
Forum: Reaction-diffusion in NEURON
Topic: Plotting Ca current through different types of VDCC's
Replies: 6
Views: 15181

Re: Plotting Ca current through different types of VDCC's

Sorry, Ted is right. It should be;

Code: Select all

cavec = h.Vector().record(soma(0.5)._ref_cai)
for calcium concentration. I've edited my previous post.
by adamjhn
Thu Feb 03, 2022 3:08 pm
Forum: Reaction-diffusion in NEURON
Topic: Different initial concentration and potential in different cells
Replies: 2
Views: 7968

Re: Different initial concentration and potential in different cells

I would define a species once for all the regions and then set the initial concentration using a function of the rxd.node. As you have several species, I would define a function for initialization, that checks the node attributes to determine which initial value to use. Also, I agree with Ted, 6e-3 ...
by adamjhn
Thu Feb 03, 2022 2:39 pm
Forum: Reaction-diffusion in NEURON
Topic: Plotting Ca current through different types of VDCC's
Replies: 6
Views: 15181

Re: Plotting Ca current through different types of VDCC's

The f_rate and b_rate are the forwards and backward rates of the reaction, provided you are using mass_action=False, they are usually third and fourth positional arguments to rxd, (the backward rate is optional and None by default), for example; k_current = rxd.MultiCompartmentReaction(ki, ko, gk * ...
by adamjhn
Wed Jan 12, 2022 10:23 am
Forum: Reaction-diffusion in NEURON
Topic: Plotting Ca current through different types of VDCC's
Replies: 6
Views: 15181

Re: Plotting Ca current through different types of VDCC's

Hi, Sorry for the delay. The flux from rxd multi compartment reactions are not stored so can not be directly recorded. However it is possible to infer them by recording the relevant rxd states and species and substituting them into the the f_rate and b_rate. Here is an example rxd Hodgkin–Huxley mod...
by adamjhn
Tue Nov 23, 2021 3:00 pm
Forum: Reaction-diffusion in NEURON
Topic: How to refer to numeric value of crxd.v?
Replies: 3
Views: 7793

Re: How to refer to numeric value of crxd.v?

Sorry, it looks like an issue with how `abs` is compiled in rxd reactions.
A simple workaround is to use the rxdmath fabs in your reaction scheme;

Code: Select all

from neuron.rxd.rxdmath import fabs
Let me know if you have any further problems.
by adamjhn
Fri Nov 19, 2021 10:28 am
Forum: Reaction-diffusion in NEURON
Topic: How to refer to numeric value of crxd.v?
Replies: 3
Views: 7793

Re: How to refer to numeric value of crxd.v?

Hi, The problem is rxdmath.v is not a number, it is a symbol that is mapped to the membrane potential of a segment at runtime, so if-statements in the reaction scheme are not supported. However you can represent something like the if-statement using a thresholds; https://neuron.yale.edu/neuron/docs/...
by adamjhn
Thu Oct 14, 2021 11:41 am
Forum: Reaction-diffusion in NEURON
Topic: Adding a Rate to an Ion based on the flux of another Reaction function
Replies: 1
Views: 11913

Re: Adding a Rate to an Ion based on the flux of another Reaction function

Hi, If I have understood your question, you have something like; pump_current_na = rxd.MultiCompartmentReaction(nai, nao, 3.0*pump, mass_action=False, membrane=mem, membrane_flux=True) Where `nai` and `nai` are rxd Species on an intracellular and extracellular region and `pump` is the rate of the Na...
by adamjhn
Tue Apr 27, 2021 10:07 am
Forum: Reaction-diffusion in NEURON
Topic: Glutamate in the synaptic cleft
Replies: 1
Views: 7234

Re: Glutamate in the synaptic cleft

Thanks, you are right, the extracellular space was designed to be used at a macroscopic scale. The average volume that would be excluded in brain tissue is used to give the `volume_fraction` (typically 0.2) where substances are free to diffusion rather than excluding any particular voxel. However it...
by adamjhn
Mon Nov 16, 2020 10:18 am
Forum: Reaction-diffusion in NEURON
Topic: Issue with larger and more equations in Reaction
Replies: 1
Views: 7345

Re: Issue with larger and more equations in Reaction

Sorry for the late reply. 1. This is a great question, your workaround sounds reasonable. I don’t think it’s necessary to split the axon into multiple sections, just set nseg as required. An alternative solution is to use node.include_flux, here is a toy example using an nmodl mechanism to allow a l...
by adamjhn
Mon Oct 12, 2020 10:01 pm
Forum: Reaction-diffusion in NEURON
Topic: Help measuring/plotting the cytoplasmic Ca flux (nM/s) as function of Ca concentration
Replies: 2
Views: 7341

Re: Help measuring/plotting the cytoplasmic Ca flux (nM/s) as function of Ca concentration

If `pmp_thr` is the only rxd mechanism producing a membrane flux for calcium then simply recording the calcium current (as you have `ca_cur`) is sufficient. Unfortunately if this is not the case the contribution of the current resulting from a particular MulticompartmentReaction is not directly acce...
by adamjhn
Tue Jul 14, 2020 9:12 am
Forum: Reaction-diffusion in NEURON
Topic: Connecting rxd to custom mechanism where custom mechanism models production/secretion
Replies: 8
Views: 10537

Re: Connecting rxd to custom mechanism where custom mechanism models production/secretion

Sorry for the delay, you're right about not using charge=0. Rxd reads the currents and then (if they have a charge or valence) divides it by the charge and scale it appropriately to determine the change in concentration. Unfortunately this does not work with charge=0. As you have found, to work arou...