www.neuron.yale.edu

Jui-Yun Chang, PhD and her colleagues at Duke have studied calmodulin (CaM) and proposed a model in their 2019 paper: Chang, J. Y., Nakahata, Y., Hayano, Y., & Yasuda, R. (2019). Mechanisms of Ca2+/calmodulin-dependent kinase II activation in single dendritic spines. Nature communications, 10(1)...

I have not added a GABA receptor on the spine-head or neck because I believe they are found only on the pre-synaptic side of the synaptic cleft. Ted may disagree; I cite his 2013 paper (Chiu, C. Q., Lur, G., Morse, T. M., Carnevale, N. T., Ellis-Davies, G. C., & Higley, M. J. (2013). Compartment...

We have the best modeling minds at Yale, U Montreal and USC but no calcium influx into sensory spine-necks. I suspect that in addition to AMPA, NMDA, and VGCC model processes, there may also need to be a 5HT-2A receptor process that indirectly increases calcium influx near but not in the postsynapti...

Jean-marie Bouteiller at USC has also agreed to help me figure out why I can't get a decent calcium flow into sensory spine-necks.

Thank you Professor. That 1981 reference was an “hallucination” by BARD AI. No such reference exists, although I believe the 100 ms spine-neck duration is correct. I have written to the Montreal lab again asking if they could look at the following list of NEURON hoc file commands and see if their mo...

I asked BARD* again: Prompt: In response to a 16 ms visual stimulus, what will be the duration of visual cortex pyramidal spine neck calcium influx. BARD* Response: The duration of visual cortex pyramidal spine neck calcium influx in response to a 16 ms visual stimulus is approximately 100 ms. This ...

I asked Bard, “In my NEURON program simulation of a pyramidal neuron spine neck calcium ion concentration, which mechanisms are needed in the segment?” Bard responded: // Define the spine neck. spine_neck = compartment(name='spine_neck', length=100.0, diameter=10.0) // Define the membrane. spine_nec...

Soledad Miranda-Rottman PhD, an author and team member, has sent me the Tazerart et al 2022 reprint and will visit the Forum. Ty Soledad.

I opened ModelDB.science in my browser > entered Chiu into the filter, found Chiu et al Compartmentalization …2013 > Files > Mod folder > I found 12 mod files, some already in my spine_neck model, some I did not recognize: ca.mod, ca_a1g.mod, ca_a1h.mod, cad.mod, constant.mod, distr.mod, exp2syncur....

NEURON does seem to be the best neuronal simulator and it's shareable. The shoulders of giants! Ty sir and permit the revision 'play with your own blocks'.

I am looking forward to the research group’s input on their model. In the meantime, I note another group has reported that a single action potential generates a calcium influx into the spine of about 20 uM, Higley, M. J., & Sabatini, B. L. (2008). Calcium signaling in dendrites and spines: pract...

Just to be sure, I ran a longer train of synaptic transmissions https://docs.google.com/document/d/1Iu95s4B4xmyK1jOoXiqQn2adWchVaAyQfq8-4M9bklA/edit?usp=sharing But I still got no response in the intracellular calcium concentration. I wonder if I need voltage-gated calcium channels distributed in th...

Sensory Spine model-Araya Mitchell et al 2023, and Tazerart et al 2022 (referenced in link) describe the following mechanisms and parameters: spine-neck length 1 um. spine axial resistance, neck, head 500, 150 MΩ. spine-head volume 0.18 um3. V = ℼ* D3/6 diam = 0.7 um connected to basilar dendrite 17...

Thank you. I'm waiting to hear back from Dr. Tazerart.

Good plan. A good model of calcium in sensory spine_necks needs a good launch with a model that's recently published. I am reaching out to the team that created it.