ca.go

// Copyright (c) 2021 The Emergent Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.

package main

import (
	"github.com/emer/emergent/chem"
	"github.com/emer/etable/etable"
	"github.com/emer/etable/etensor"
)

// CaState records the Ca levels
// 2 state vars total
type CaState struct {
	Cyt float64 `desc:"in cytosol"`
	PSD float64 `desc:"in PSD"`
}

func (cs *CaState) Init() {
	cs.Cyt = chem.CoToN(0.05, CytVol)
	cs.PSD = chem.CoToN(0.05, PSDVol)
}

func (cs *CaState) Zero() {
	cs.Cyt = 0
	cs.PSD = 0
}

func (cs *CaState) Integrate(d *CaState) {
	chem.Integrate(&cs.Cyt, d.Cyt)
	chem.Integrate(&cs.PSD, d.PSD)
}

func (cs *CaState) Log(dt *etable.Table, row int) {
	dt.SetCellFloat("Cyt_Ca", row, chem.CoFmN(cs.Cyt, CytVol))
	dt.SetCellFloat("PSD_Ca", row, chem.CoFmN(cs.PSD, PSDVol))
}

func (cs *CaState) ConfigLog(sch *etable.Schema) {
	*sch = append(*sch, etable.Column{"Cyt_Ca", etensor.FLOAT64, nil, nil})
	*sch = append(*sch, etable.Column{"PSD_Ca", etensor.FLOAT64, nil, nil})
}

// CaParams manages Ca parameters including soft buffering dynamics of calcium
type CaParams struct {
	CytBuffer chem.Buffer  `desc:"Ca buffering in the cytosol"`
	PSDBuffer chem.Buffer  `desc:"Ca buffering in the PSD"`
	Diffuse   chem.Diffuse `desc:"Ca diffusion between Cyt and PSD"`
	InjectCa  CaState      `desc:"extra Ca injection values in N terms -- see SetInject for concentration -- be sure to zero or update as needed"`
	Clamp     bool         `desc:"clamp ca by fixed values"`
	ClampCa   CaState      `desc:"clamped Ca values -- in N terms -- see SetClamp for concentration"`
}

func (cp *CaParams) Defaults() {
	// note: verified constants from initial_routines/Ca2_efflux.g
	// using showmsg /efflux_PSD / cytosol and showfield /efflux_PSD *
	// and doing the math.. replicates corresponding behavior in model
	cp.CytBuffer.SetTargVol(0.05, CytVol)
	cp.CytBuffer.K = (1.0426e5 * 0.8) / 12
	cp.PSDBuffer.SetTargVol(0.05, PSDVol)
	cp.PSDBuffer.K = (1.7927e5 * 0.8) / 12

	cp.Diffuse.SetSym(600.0 / 0.0225)
	cp.Clamp = false
}

func (cp *CaParams) Init() {
	cp.InjectCa.Zero()
}

// SetBuffTarg sets buffered target level of calcium in terms of concentrations
func (cp *CaParams) SetBuffTarg(cyt, psd float64) {
	cp.CytBuffer.SetTargVol(cyt, CytVol)
	cp.PSDBuffer.SetTargVol(psd, PSDVol)
}

// SetClamp sets clamped calcium levels in terms of concentrations
func (cp *CaParams) SetClamp(cyt, psd float64) {
	cp.Clamp = true
	cp.ClampCa.Cyt = chem.CoToN(cyt, CytVol)
	cp.ClampCa.PSD = chem.CoToN(psd, PSDVol)
}

// SetInject sets injected calcium levels in terms of concentrations
func (cp *CaParams) SetInject(cyt, psd float64) {
	cp.InjectCa.Cyt = chem.CoToN(cyt, CytVol)
	cp.InjectCa.PSD = chem.CoToN(psd, PSDVol)
}

func (cp *CaParams) Step(c *CaState, d *CaState) {
	if cp.Clamp {
		*c = cp.ClampCa
		d.Zero()
		return
	}
	d.PSD += cp.InjectCa.PSD
	d.Cyt += cp.InjectCa.Cyt
	cp.CytBuffer.Step(c.Cyt, &d.Cyt)
	cp.PSDBuffer.Step(c.PSD, &d.PSD)
	cp.Diffuse.Step(c.Cyt, c.PSD, CytVol, PSDVol, &d.Cyt, &d.PSD)
}