# Finding Steady States through Homotopy Continuation

The steady states of a dynamical system ${dx \over dt} = f(x)$ can be found by solving $0 = f(x)$. This is typically a hard problem, and generally, there is no method that guarantees to find all steady states for a system that has multiple ones. However, most CRNs generate polynomial systems (the main exception is when Hill functions with non-integer exponents are used). The roots of these can reliably be found through a homotopy continuation algorithm. This is implemented in Julia through the HomotopyContinuation.jl package. In this tutorial, we will demonstrate how homotopy continuation can be used to find the steady states of a CNR implemented in Catalyst.

## Basic Example

For this tutorial, we will use a model from the Wilhem (2009) paper (which demonstrates bistability in a small CRN). We declare the model and the parameter set for which we want to find the steady states:

using Catalyst
wilhelm_2009_model = @reaction_network begin
k1, Y --> 2X
k2, 2X --> X + Y
k3, X + Y --> Y
k4, X --> 0
end k1 k2 k3 k4
p = [:k1 => 8.0, :k2 => 2.0, :k3 => 1.0, :k4 => 1.5]
4-element Vector{Pair{Symbol, Float64}}:
:k1 => 8.0
:k2 => 2.0
:k3 => 1.0
:k4 => 1.5

Next, we will need to extract the actual equations from our model. In addition, we will substitute in our parameter values.

ns = convert(NonlinearSystem,wilhelm_2009_model)
subs = Dict(Pair.(ModelingToolkit.parameters(ns),last.(p)))
new_eqs = map(eq -> substitute(eq.rhs,subs), equations(ns))
2-element Vector{SymbolicUtils.Add{Real, Int64, Dict{Any, Number}, Nothing}}:
X(t)^2 - 8.0Y(t)
16.0Y(t) - (X(t)^2) - 1.5X(t) - X(t)*Y(t)

Finally, we use the as_polynomial function to read our symbolic expression as a polynomial, within it, we can apply homotopy continuation's solve command to find the roots. In addition, we use the real_solutions to filter away imaginary roots (as CRNs' states typically are non-imaginary):

using HomotopyContinuation
sols = real_solutions(as_polynomial((f, x...) -> HomotopyContinuation.solve(collect(x)), new_eqs...))

While it is not the case for this CRN, we note that some solutions with negative species concentrations may still appear. Typically, these will need to be filtered away as well.

## Rational Polynomial Systems

It is not uncommon for CRNs to generate systems corresponding to rational multivariate polynomials (e.g. through Hill functions). The roots of these can also be found using homotopy continuation. An expanded tutorial for this will be published once some awaited improvements to the as_polynomial function are completed.

## Systems with Conservation Laws

Finally, some systems are underdetermined, and have an infinite number of possible steady states. These are typically systems containing a conservation law, e.g.

using Catalyst
two_state_model = @reaction_network begin
(k1,k2), X1 <--> X2
end k1 k2
\begin{align*} \require{mhchem} \ce{ X1 &<=>[k1][k2] X2} \end{align*}

However, the conservation laws can be computed using the conservationlaws function. By supplying these, as well as fixed concentrations (in this case the total amount of X, that is X1+X2), steady states can be found. First, we set the default values of the system's initial conditions and steady states. This will allow the system to automatically find the conserved amounts.

setdefaults!(two_state_model, [:X1 => 1.0, :X2 => 1.0, :k1 => 2.0, :k2 => 1.0])

Next, we create a NonlinearSystem, while also removing the redundant equation.

ns = convert(NonlinearSystem,two_state_model; remove_conserved=true)
\begin{align} 0 =& k2 \left( - \mathrm{X1}\left( t \right) + _{ConLaw_1} \right) - k1 \mathrm{X1}\left( t \right) \end{align}

Again, we will create the dictionary for parameter values that we will sub in. However, we will do it slightly differently so that the conserved quantitites are accoutned for.

const MT = ModelingToolkit
subs = Dict(MT.parameters(ns) .=> MT.varmap_to_vars([], MT.parameters(ns); defaults=MT.defaults(ns)))
Dict{SymbolicUtils.Symbolic{Real}, Float64} with 3 entries:
k2         => 1.0
k1         => 2.0
_ConLaw => 2.0

We now extract the equation produced by the conservation law, and then sub in the parameter values creating a final set of equations (like previously). Unlike previously, we have to do eq.rhs-eq.lhs, as cons_eq may contain important information on both the lhs and rhs.

cons_eq = conservedequations(two_state_model)
new_eqs = map(eq -> substitute(eq.rhs-eq.lhs,subs), [equations(ns)...;cons_eq...])
2-element Vector{SymbolicUtils.Add{Real, Float64, Dict{Any, Number}, Nothing}}:
2.0 - 3.0X1(t)
2.0 - X1(t) - X2(t)

Finally, we compute the solution:

using HomotopyContinuation
sols = real_solutions(as_polynomial((f, x...) -> HomotopyContinuation.solve(collect(x)), new_eqs...))