Chapter 5

using Startup

using OrdinaryDiffEq
using ModelingToolkit
using ModelingToolkit: t_nounits as t, D_nounits as D
using Plots
Plots.gr(linewidth=1.5)

function meshgrid(xrange, yrange)
    xx = [x for y in yrange, x in xrange]
    yy = [y for y in yrange, x in xrange]
    return xx, yy
end

"Get the gradients of the vector field of an ODE system at a grid of points in the state space."
function get_gradient(prob, xsym, ysym, xx, yy; t = nothing)
    # The order of state variables (unknowns) in the ODE system is not guaranteed. So we may need to swap the order of x and y when calling ∂F.
    swap_or_not(x, y; xidx=1) = xidx == 1 ? [x, y] : [y, x]
    ∂F = prob.f
    ps = prob.p
    sys = prob.f.sys
    xidx = ModelingToolkit.variable_index(sys, xsym)
    yidx = ModelingToolkit.variable_index(sys, ysym)
    dx = map((x, y) -> ∂F(swap_or_not(x, y; xidx), ps, t)[xidx], xx, yy)
    dy = map((x, y) -> ∂F(swap_or_not(x, y; xidx), ps, t)[yidx], xx, yy)
    return (dx, dy)
end

function normalize_gradient(dx, dy, xscale, yscale; transform=cbrt)
    maxdx = maximum(abs, dx)
    maxdy = maximum(abs, dy)
    dx_norm = @. transform(dx / maxdx) * xscale
    dy_norm = @. transform(dy / maxdy) * yscale
    return (dx_norm, dy_norm)
end

function model510(; name=:model510, simplfy=true)
    hil(x, k=one(x)) = x / (x + k)
    hil(x, k, n) = hil(x^n, k^n)
    @parameters begin
        K_AHC= 0.1
        Adenosine = 1.0
        v_MATI_max = 561.0
        Met = 48.5
        K_MATI_m = 41.0
        K_MATI_i = 50.0
        v_MATIII_max = 22870.0
        K_MATIII_m2 = 21.1
        v_GNMT_max = 10600.0
        K_GNMT_m = 4500.0
        K_GNMT_i = 20.0
        v_MET_max = 4544.0
        A_over_K_MET_m2 = 0.1
        alpha_d = 1333.0
    end
    @variables AdoMet(t)=10 AdoHcy(t)=10
    @variables Hcy(t) v_MATI(t) v_MATIII(t) K_MATIII_m1(t) v_GNMT(t) K_MET_m1(t) v_MET(t) v_D(t)

    eqs = [
        Hcy ~ AdoHcy * K_AHC / Adenosine,
        v_MATI ~ v_MATI_max * hil(Met * hil(K_MATI_i, AdoMet), K_MATI_m),
        v_MATIII ~ v_MATIII_max * hil(Met, K_MATIII_m1 * hil(K_MATIII_m2, Met)),
        K_MATIII_m1 ~ 20000 / (1 + 5.7 * hil(AdoMet, 600)^2),
        v_GNMT ~ v_GNMT_max * hil(AdoMet, K_GNMT_m, 2.3) * hil(K_GNMT_i, AdoHcy),
        K_MET_m1 ~ 10 + 2.5 * AdoHcy,
        v_MET ~ v_MET_max * hil(AdoMet, K_MET_m1) * hil(A_over_K_MET_m2),
        v_D ~ alpha_d * Hcy,
        D(AdoMet) ~ (v_MATI + v_MATIII) - (v_GNMT + v_MET),
        D(AdoHcy) ~ (v_GNMT + v_MET - v_D) * hil(Adenosine, K_AHC)
    ]

    sys = ODESystem(eqs, t; name)
    return mtkcompile(sys; simplify)
end

@time "Build system" sys = model510()

tend = 5.0
@time "Build problem" prob510 = ODEProblem(sys, [], (0.0, tend))
@time "Solve problem" sol510 = solve(prob510, KenCarp47())

plot(sol510, title="Fig. 5.10", xlabel="Time (s)", ylabel="Concentration (μM)")

xrange = range(0, 1200, 101)
yrange = range(0, 6, 101)
xx, yy = meshgrid(xrange, yrange)
@unpack AdoMet, AdoHcy = prob510.f.sys
dx, dy = get_gradient(prob510, AdoMet, AdoHcy, xx, yy)

xx_sp = xx[1:5:end, 1:5:end]
yy_sp = yy[1:5:end, 1:5:end]
dx_sp = dx[1:5:end, 1:5:end]
dy_sp = dy[1:5:end, 1:5:end]
dx_sp_norm, dy_sp_norm = normalize_gradient(dx_sp, dy_sp, step(xrange) * 4 , step(yrange) * 4)

quiver(xx_sp, yy_sp, quiver=(dx_sp_norm, dy_sp_norm), color=:gray)
contour!(xrange, yrange, dx, levels=[0], line=(:black, :solid), colorbar=false)
plot!([], [],  line=(:black, :solid), label="AdoMet nullcline")
contour!(xrange, yrange, dy, levels=[0],  line=(:black, :dash), colorbar=false)
plot!([], [], line=(:black, :dash), label="AdoHcy nullcline")
plot!(title="Fig. 5.11 (A)", xlabel="AdoMet (μM)", ylabel="AdoHcy (μM)", legend=:bottomright, size=(800, 600), xlims=(0, 1200), ylims=(0, 6))

prob511b = remake(prob510, p=[sys.Met => 51.0])

xrange = range(0, 1200, 101)
yrange = range(0, 6, 101)
xx, yy = meshgrid(xrange, yrange)
@unpack AdoMet, AdoHcy = prob511b.f.sys
dx, dy = get_gradient(prob511b, AdoMet, AdoHcy, xx, yy)

xx_sp = xx[1:5:end, 1:5:end]
yy_sp = yy[1:5:end, 1:5:end]
dx_sp = dx[1:5:end, 1:5:end]
dy_sp = dy[1:5:end, 1:5:end]
dx_sp_norm, dy_sp_norm = normalize_gradient(dx_sp, dy_sp, step(xrange) * 4 , step(yrange) * 4)

quiver(xx_sp, yy_sp, quiver=(dx_sp_norm, dy_sp_norm), color=:gray)
contour!(xrange, yrange, dx, levels=[0], line=(:black, :solid), colorbar=false)
plot!([], [],  line=(:black, :solid), label="AdoMet nullcline")
contour!(xrange, yrange, dy, levels=[0],  line=(:black, :dash), colorbar=false)
plot!([], [], line=(:black, :dash), label="AdoHcy nullcline")
plot!(title="Fig. 5.11 (B)", xlabel="AdoMet (μM)", ylabel="AdoHcy (μM)", legend=:bottomright, size=(800, 600), xlims=(0, 1200), ylims=(0, 6))