From 658e85bbcf22883cb49f8964ab80fe3bb5bd9981 Mon Sep 17 00:00:00 2001
From: Riccardo Foffi <riccardo.foffi@protonmail.com>
Date: Sun, 31 Dec 2023 16:17:31 +0100
Subject: [PATCH] add example: drift in exponential ramp with brumley model
 (#66)

---
 .../Chemotaxis/5_drift_exponential.md         | 144 ++++++++++++++++++
 examples/Chemotaxis/5_drift_exponential.jl    | 141 +++++++++++++++++
 2 files changed, 285 insertions(+)
 create mode 100644 docs/src/examples/Chemotaxis/5_drift_exponential.md
 create mode 100644 examples/Chemotaxis/5_drift_exponential.jl

diff --git a/docs/src/examples/Chemotaxis/5_drift_exponential.md b/docs/src/examples/Chemotaxis/5_drift_exponential.md
new file mode 100644
index 0000000..4c7d795
--- /dev/null
+++ b/docs/src/examples/Chemotaxis/5_drift_exponential.md
@@ -0,0 +1,144 @@
+```@meta
+EditURL = "../../../../examples/Chemotaxis/5_drift_exponential.jl"
+```
+
+# Chemotactic drift in exponential ramp with noisy sensing
+
+We will peform simulations of chemotaxis in an exponential concentration
+ramp using the `Brumley` model of chemotaxis and measure their drift velocity
+along the gradient.
+The concentration field has the form
+```math
+C(x) = C_0\exp(x/λ)
+```
+and its gradient is
+```math
+\nabla C(x) = \dfrac{C_0}{\lambda}\exp(x/\lambda)\hat{\mathbf{x}}.
+```
+
+In the `Brumley` model, the microbe estimates the local gradient in the form of
+the convective derivative of the concentration field (``U\nabla C``).
+The measurement is affected by noise, represented by an intrinsic
+noise term ``\sigma = \sqrt{3C/(\pi a D_c T^3)}`` (Mora & Wingreen (Phys Rev Lett 2010),
+where ``a`` is the microbe radius, ``T`` the chemotactic sensory timescale
+and ``D_c`` the thermal diffusivity of the chemoattractant compound)
+and a pre-factor ``\Pi`` which represents the "chemotactic precision".
+Higher values of ``\Pi`` imply higher levels of noise in chemotaxis pathway.
+
+Therefore, with each measurement the bacterium samples from a Normal distribution
+with mean ``U\nabla C`` and standard deviation ``\Pi\sigma``.
+The measurement, ``\mathcal{M}``, determines the evolution of an internal state
+``S`` which obeys an excitation-relaxation dynamics:
+```math
+\dot{S} = \kappa M -\dfrac{S}{\tau_M}.
+```
+This internal state, in turn, determines the tumbling rate.
+
+We will study how ``Pi`` affects the drift velocity of bacteria.
+
+````@example 5_drift_exponential
+using MicrobeAgents
+
+function concentration_field(pos, model)
+    x = first(pos)
+    C0 = model.C0
+    λ = model.λ
+    concentration_field(x, C0, λ)
+end
+concentration_field(x, C0, λ) = C0*exp(x/λ)
+
+function concentration_gradient(pos, model)
+    x = first(pos)
+    C0 = model.C0
+    λ = model.λ
+    concentration_gradient(x, C0, λ)
+end
+concentration_gradient(x, C0, λ) = SVector{3}(i==1 ? C0/λ*exp(x/λ) : 0.0 for i in 1:3)
+
+# wide rectangular channel confined in the z direction
+Lx, Ly, Lz = 6000, 3000, 100
+space = ContinuousSpace((Lx,Ly,Lz); periodic=false)
+dt = 0.1
+
+C0 = 10.0
+λ = Lx/2
+properties = Dict(
+    :concentration_field => concentration_field,
+    :concentration_gradient => concentration_gradient,
+    :C0 => C0,
+    :λ => λ,
+)
+model = StandardABM(Brumley{3}, space, dt; properties, container=Vector)
+
+# add n bacteria for each value of Π
+# all of them initialized at x = 0
+Πs = [1.0, 2.0, 5.0, 10.0, 25.0]
+n = 200
+for Π in Πs
+    for i in 1:n
+        pos = SVector{3}(0.0, rand()*Ly, rand()*Lz)
+        add_agent!(pos, model; chemotactic_precision=Π)
+    end
+end
+
+# also store Π for grouping later
+adata = [position, velocity, :chemotactic_precision]
+nsteps = 2000
+adf, = run!(model, nsteps; adata)
+
+# evaluate drift velocity along x direction
+target_direction = SVector(1.0, 0.0, 0.0)
+Analysis.driftvelocity_direction!(adf, target_direction)
+
+# we now want to first average the drift velocities in each group of Π values
+# and then average each group over time to obtain a mean drift
+# the calculation is much easier to perform with the DataFrames package
+using DataFrames, StatsBase
+gdf = groupby(adf, :chemotactic_precision)
+drift_velocities = zeros(1+nsteps, length(Πs))
+for (i,g) in enumerate(gdf)
+    for h in groupby(g, :id)
+        drift_velocities[:,i] .+= h.drift_direction
+    end
+    drift_velocities[:,i] ./= n
+end
+avg_drift = vec(mean(drift_velocities; dims=1))
+
+# we also apply a smoothing function to remove some noise
+function moving_average(y::AbstractVector, m::Integer)
+    @assert isodd(m)
+    out = similar(y)
+    R = CartesianIndices(y)
+    Ifirst, Ilast = first(R), last(R)
+    I1 = m÷2 * oneunit(Ifirst)
+    for I in R
+        n, s = 0, zero(eltype(out))
+        for J in max(Ifirst, I-I1):min(Ilast, I+I1)
+            s += y[J]
+            n += 1
+        end
+        out[I] = s/n
+    end
+    return out
+end
+smoothing_window = 51
+smooth_drift_velocities = mapslices(
+    y -> moving_average(y, smoothing_window), drift_velocities;
+    dims = 1
+)
+
+using Plots
+t = axes(smooth_drift_velocities, 1) .* dt
+plot(layout=(1,2), size=(760,440),
+    plot(t, smooth_drift_velocities, lab=Πs',
+        xlab="t (s)", ylab="drift (μm/s)"
+    ),
+    plot(Πs, avg_drift, lw=4, m=:c, ms=8, lab=false,
+        xlab="Π", ylab="avg drift (μm/s)"
+    )
+)
+````
+
+Increasing Π significantly reduces the ability of bacteria to drift
+along the gradient.
+
diff --git a/examples/Chemotaxis/5_drift_exponential.jl b/examples/Chemotaxis/5_drift_exponential.jl
new file mode 100644
index 0000000..477a0a5
--- /dev/null
+++ b/examples/Chemotaxis/5_drift_exponential.jl
@@ -0,0 +1,141 @@
+# # Chemotactic drift in exponential ramp with noisy sensing
+
+#=
+We will peform simulations of chemotaxis in an exponential concentration
+ramp using the `Brumley` model of chemotaxis and measure their drift velocity
+along the gradient.
+The concentration field has the form
+```math
+C(x) = C_0\exp(x/λ)
+```
+and its gradient is
+```math
+\nabla C(x) = \dfrac{C_0}{\lambda}\exp(x/\lambda)\hat{\mathbf{x}}.
+```
+
+In the `Brumley` model, the microbe estimates the local gradient in the form of
+the convective derivative of the concentration field (``U\nabla C``).
+The measurement is affected by noise, represented by an intrinsic
+noise term ``\sigma = \sqrt{3C/(\pi a D_c T^3)}`` (Mora & Wingreen (Phys Rev Lett 2010),
+where ``a`` is the microbe radius, ``T`` the chemotactic sensory timescale
+and ``D_c`` the thermal diffusivity of the chemoattractant compound)
+and a pre-factor ``\Pi`` which represents the "chemotactic precision".
+Higher values of ``\Pi`` imply higher levels of noise in chemotaxis pathway.
+
+Therefore, with each measurement the bacterium samples from a Normal distribution
+with mean ``U\nabla C`` and standard deviation ``\Pi\sigma``.
+The measurement, ``\mathcal{M}``, determines the evolution of an internal state
+``S`` which obeys an excitation-relaxation dynamics:
+```math
+\dot{S} = \kappa M -\dfrac{S}{\tau_M}.
+```
+This internal state, in turn, determines the tumbling rate.
+
+We will study how ``\Pi`` affects the drift velocity of bacteria.
+=#
+
+using MicrobeAgents
+
+function concentration_field(pos, model)
+    x = first(pos)
+    C0 = model.C0
+    λ = model.λ
+    concentration_field(x, C0, λ)
+end
+concentration_field(x, C0, λ) = C0*exp(x/λ)
+
+function concentration_gradient(pos, model)
+    x = first(pos)
+    C0 = model.C0
+    λ = model.λ
+    concentration_gradient(x, C0, λ)
+end
+concentration_gradient(x, C0, λ) = SVector{3}(i==1 ? C0/λ*exp(x/λ) : 0.0 for i in 1:3)
+
+## wide rectangular channel confined in the z direction
+Lx, Ly, Lz = 6000, 3000, 100
+space = ContinuousSpace((Lx,Ly,Lz); periodic=false)
+dt = 0.1
+
+C0 = 10.0
+λ = Lx/2
+properties = Dict(
+    :concentration_field => concentration_field,
+    :concentration_gradient => concentration_gradient,
+    :C0 => C0,
+    :λ => λ,
+)
+model = StandardABM(Brumley{3}, space, dt; properties, container=Vector)
+
+## add n bacteria for each value of Π
+## all of them initialized at x = 0
+Πs = [1.0, 2.0, 5.0, 10.0, 25.0]
+n = 200
+for Π in Πs
+    for i in 1:n
+        pos = SVector{3}(0.0, rand()*Ly, rand()*Lz)
+        add_agent!(pos, model; chemotactic_precision=Π)
+    end
+end
+
+## also store Π for grouping later
+adata = [position, velocity, :chemotactic_precision]
+nsteps = 2000
+adf, = run!(model, nsteps; adata)
+
+## evaluate drift velocity along x direction
+target_direction = SVector(1.0, 0.0, 0.0)
+Analysis.driftvelocity_direction!(adf, target_direction)
+
+## we now want to first average the drift velocities in each group of Π values
+## and then average each group over time to obtain a mean drift
+## the calculation is much easier to perform with the DataFrames package
+using DataFrames, StatsBase
+gdf = groupby(adf, :chemotactic_precision)
+drift_velocities = zeros(1+nsteps, length(Πs))
+for (i,g) in enumerate(gdf)
+    for h in groupby(g, :id)
+        drift_velocities[:,i] .+= h.drift_direction
+    end
+    drift_velocities[:,i] ./= n
+end
+avg_drift = vec(mean(drift_velocities; dims=1))
+
+## we apply a smoothing function to remove some noise for better visualization
+function moving_average(y::AbstractVector, m::Integer)
+    @assert isodd(m)
+    out = similar(y)
+    R = CartesianIndices(y)
+    Ifirst, Ilast = first(R), last(R)
+    I1 = m÷2 * oneunit(Ifirst)
+    for I in R
+        n, s = 0, zero(eltype(out))
+        for J in max(Ifirst, I-I1):min(Ilast, I+I1)
+            s += y[J]
+            n += 1
+        end
+        out[I] = s/n
+    end
+    return out
+end
+smoothing_window = 51
+smooth_drift_velocities = mapslices(
+    y -> moving_average(y, smoothing_window), drift_velocities;
+    dims = 1
+)
+
+using Plots
+t = axes(smooth_drift_velocities, 1) .* dt
+plot(layout=(1,2), size=(760,440),
+    plot(t, smooth_drift_velocities, lab=Πs',
+        xlab="t (s)", ylab="drift (μm/s)"
+    ),
+    plot(Πs, avg_drift, lw=4, m=:c, ms=8, lab=false,
+        xlab="Π", ylab="avg drift (μm/s)"
+    )
+)
+
+#=
+Increasing Π significantly reduces the ability of bacteria to drift
+along the gradient.
+=#