Smectodynamics of Dividing Cells

Taylor Womack*, Tyler Shendruk†, Joost de Graaf‡

April 12, 2024

* Utrecht University — Masters Student of Theoretical Physics

† Universityof Edinburgh — Institute of Condensed Matter and Complex Systems
‡ Utrecht University — Institute of Theoretical Physics

1
CONTENTS CONTENTS

Contents

1 Introduction 4

2 Density Functional Theory 4

2.1 Chemical Potential . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

2.2 Dynamic Density Functional Theory . . . . . . . . . . . . . . . . . . . . . . 5

2.3 A Note on Functional Derivatives . . . . . . . . . . . . . . . . . . . . . . . . 5

3 Energy of Rodlike Cells 6

3.1 The Cahn-Hilliard Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

3.2 The Ground State of the Natural Wavenumber . . . . . . . . . . . . . . . . 7

3.3 The Rodlike Cells’ Free Energy Functional . . . . . . . . . . . . . . . . . . . 7

3.4 Dynamics of the Smectic Ordering Functional . . . . . . . . . . . . . . . . . 8

4 Relaxation Dynamics 9

4.1 The Dominant Mode of Smectic Phase Decomposition . . . . . . . . . . . . 9

4.2 The Cubic Term . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

4.3 Nonlinear SH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

5 Phase Diagram 11

6 Numerical Methods 11

2
CONTENTS CONTENTS

6.1 Pystencils . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

6.2 Discretization Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

6.3 Important Implementation Details . . . . . . . . . . . . . . . . . . . . . . . 14

6.4 Initialization Scheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

7 Validation 15

8 Growth 16

8.1 Non-dimensionalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

9 Miscellaneous 18

Bibliography 18

3
 2 DENSITY FUNCTIONAL THEORY

1 Introduction

2 Density Functional Theory

Density Functional Theory (hereby referred to as DFT) allows for the determination of
the equilibrium properties of a classical fluid even if these properties are non-uniform in
space (e.g. an ideal fluid in the presence of some non-uniform external field). That is to
say that DFT provides the theoretical tools to solve for the density ρ(r, t) and chemical
potential µ(r, t) fields given the free energy functional of the fluid F [ρ(r, t)].

The free energy functional is defined for some free energy density f (ρ(r, t)) dependent
on the local density. That is

ż
F [ρ(r, t)] = dr f (ρ(r, t)) (2.1)

As a well known example, the energy density of an ideal gas takes the form f id (ρ(r, t) =
k B Tρ(r, t)(ln[ρ(r, t)Λ3 ] ´ 1) where Λ is the de Broglie thermal wavelength.

2.1 Chemical Potential

In bulk thermodynamics, we recall the Helmholtz free energy F for a system in equilib-
rium changes as
BF
µ= . (2.2)
BN
The chemical potential is a measurement of the change in free energy due to the addition
of particles N into the system. DFT provides an analogous relation. It can be shown
(which is beyond the scope of the present manuscript) for some external field Vext (r )
that the equilibrium density profile ρ0 (r ) of a thermodynamic system with free energy
functional F satisfies
ˇ ˇ
δF [ρ(r )] ˇˇ B f (ρ(r )) ˇˇ
= = µ ´ Vext (r ) (2.3)
δρ(r ) ˇρ(r)=ρ0 (r) Bρ(r ) ˇρ(r)=ρ0 (r)

4
2.2 Dynamic Density Functional Theory 2 DENSITY FUNCTIONAL THEORY

δF [ρ(r )]
where δρ(r )
is the functional derivative of free energy with respect to the density field.
Here the bulk chemical potential and external field both contribute to the change in free
energy from changes in local density. We now turn to apply this theory to dynamical,
non-equilibrium systems.

2.2 Dynamic Density Functional Theory

We presume our system has a near-but-out-of-equilibrium density profile ρ(r, t), with ho-
mogeneous bulk equilibrium density ρh . We now introduce the Landau order parameter
field ϕ(r, t) := ρ(r, t)/ρh . We can now rewrite the free energy functional of our system as
dependent on the phase-field F [ϕ(r, t)] (Should I include the derivation of phase-field
crystal methods??). Doing so, we find a local, time-dependent, and out-of-equilibrium
chemical potential as

δF [ϕ(r, t)]
µ(r, t) = (2.4)
δϕ(r, t)
where this takes into account external fields and interactions.

Now Fick’s first law tells us that the order-field flux vector diffuses as

Jϕ = ´D ∇µ(r, t) (2.5)

for some mobility (diffusion) constant D. Furthermore, since our order parameter charac-
terizes mass, it is conserved and thus obeys the continuity equation
Bϕ(r, t)
= ´∇ ¨ Jϕ (2.6)
Bt

Putting these together we find a self-contained equation that governs the dynamical
evolution of our order-field
δF [ϕ(r, t)]
 
Bϕ(r, t)
= D ∇2 (2.7)
Bt δϕ(r, t)

2.3 A Note on Functional Derivatives

In Eq. 2.3 we have already shown that the functional derivative of the free energy
functional with respect to the field is equivalent to the partial derivative of the free energy

5
 3 ENERGY OF RODLIKE CELLS

density with respect to the field. However, in order to characterize interfacial phases
- or layering - the free energy density will also be dependent on the gradients of the
order-field. That is ż
F [ϕ(r, t)] = dr f (ϕ, ∇ϕ, ∇2 ϕ, ...) (2.8)

In this case we find that the functional derivative can be written to

δF [ϕ(r, t)]
 
Bf Bf 2 Bf
= ´∇¨ +∇ + ...
δϕ(r, t) Bϕ B (∇ϕ) B (∇2 ϕ)
8 (2.9)
ÿ Bf
= (´1)n ∇n ¨
B (∇n ϕ)
n =0

(I plan to show the derivation of this explicitly up to the Laplace term, but I still need
to work out the finer details through the more “physics” approach rather than strict
variational definition of functional derivatives, which I feel is too mathematical for my
project.)

3 Energy of Rodlike Cells

During division and growth, we expect rodlike cells to order in a smectic liquid crystal
pattern, with natural, energetically favorable wavelengths roughly corresponding to the
length of the cells l, for which we define a natural wavenumber q0 = 2π/l. We would
like to physically motivate the free energy of such a system

3.1 The Cahn-Hilliard Model

The Cahn-Hilliard model is a phase field theory that describes the spinodal phase de-
composition of a binary alloy mixture. The free energy density is described by two terms
f CH = f bulk + f int , a bulk phase separation term

1 2 u 1 4
     
α
f bulk = ´ 2 ϕ´ + 2 ϕ´ (3.1)
2 2 4 2

and an interfacial term

λ
f int = |∇ϕ|2 (3.2)
2

6
3.2 The Ground State of the Natural Wavenumber 3 ENERGY OF RODLIKE CELLS

The parameter α = ( Tc ´ T )/Tc drives the separation of the double well in the bulk
term when the system is quenched below the critical temperature. This induces the
phase separation into the void phase (ϕ = 0) and the cellular presence phase (ϕ = 1).
The interfacial term induces a cost for the presence of phase interfaces and thus drives
accumulation of one phase into a local region of the domain. λ determines the interfacial
length.

3.2 The Ground State of the Natural Wavenumber

As described, the smectic ordering of the cells should produce wave patterns with void
regions (ϕ = 0) at the troughs and cellular presence (ϕ = 1) at the peaks. This means that
the ground state is
ϕ0 (r ) = C1 eiq0 ¨r + C2 e´iq0 ¨r (3.3)

for complex Cn . We can now define the covariant derivative to the ground state pattern as

D := ∇ + iq0 . (3.4)

Since D: Dϕ0 := D2 ϕ0 = (∇2 + q20 )ϕ0 = 0, we can leverage the covariant derivative to
construct the free energy functional without inducing an energy cost for the ground state.

3.3 The Rodlike Cells’ Free Energy Functional

The nature of wave-like patterns is to have recurrent interfaces between the void and
cellular phases, so the interfacial term for rodlike cells must be negative (i.e., ´ λ2 |∇ϕ|2 ),
thus inducing nearby phase coexistence. However, in order to prevent interfaces from
forming everywhere in the domain, there must be some cost to interface formation.
This can be achieved by adding the higher order term λ|∇2 ϕ|2 which prevents runaway
interfacial growth.

Inside the free energy functional, we use integration by parts to rewrite the free energy
density’s gradient terms as
ż
λ λ
Fgrad [ϕ(r, t)] = dr (´ |∇ϕ|2 + |∇2 ϕ|2 )
2 2
ż (3.5)
λ λ
= dr ( ϕ∇2 ϕ + ϕ∇4 ϕ) .
2 2

7
3.4 Dynamics of the Smectic Ordering Functional 3 ENERGY OF RODLIKE CELLS

Finally, by taking D4 = ( D: D )2 = q40 + 2q20 ∇2 + ∇4 we can use the covariant derivative

to construct
λ λ
ϕD4 ϕ = ϕ(q20 + ∇2 )2 ϕ .
f rods = (3.6)
2 2
Combined with the bulk term, the total free energy density is

1 2 u 1 4 λ
     
α
f cells = ´ 2 ϕ´ + 2 ϕ´ + ϕ(q20 + ∇2 )2 ϕ (3.7)
2 2 4 2 2

Here, the typical double well potential that characterizes spinodal decomposition models
such as Cahn-Hilliard (hereby referred to as CH) has been combined with the fourth
order SH layering terms. a ą 0 and represents system periodicty, q0 is the dominant
wave-number that minimizes the system’s energy as previously described, and u ą 0,
λ are other physical parameters. ∆0 = Tc ´ T is the quench parameter in which Tc is
the critical temperature, below which the double well actually separates, favoring phase
separation.

3.4 Dynamics of the Smectic Ordering Functional

We now proceed using the techniques of dynamic DFT to determine the time evolution of
our system defined by the functional given in Eq. ??. We proceed by applying Eq. 2.9 and
find
δF [ϕ(r, t)]
    
B 2 B 4 B
= µ(r, t) = +∇ +∇ f (ϕ, ∇2 ϕ, ∇4 ϕ) (3.8)
δϕ(r, t) Bϕ B (∇2 ϕ) B (∇4 ϕ)

with energy density

ϕ2 ϕ4 λ λ
f (ϕ, ∇2 ϕ, ∇4 ϕ) = ´a∆0 + u + q40 ϕ2 + λq20 ϕ ¨ ∇2 ϕ + ϕ ¨ ∇4 ϕ (3.9)
2 4 2 2
This results in
µ(r, t) = ´a∆0 ϕ + uϕ3 + λq40 ϕ + 2λq20 ∇2 ϕ + λ∇4 ϕ (3.10)

So now by applying both Fick’s Law and continuity of mass, we find the dynamical
evolution of the order-field as

Bϕ(r, t)
= D ∇2 (´a∆0 ϕ + uϕ3 + λ(q20 + ∇2 )2 ϕ) (3.11)
Bt

8
 4 RELAXATION DYNAMICS

b
Finally, by non-dimensionalizing our dynamical variables as ϕ̃ = ϕ u/(λq40 ), t̃ = tDλq60 ,
and ∇˜ = ∇/q0 and defining ϵ = ( a∆0 )/(λq4 ) we find
0

B ϕ̃ 
˜ 2 [´ϵ + (1 + ∇
˜ 2 )2 ]ϕ̃ + ϕ̃3

=∇ (3.12)
B t̃

4 Relaxation Dynamics

We refer back to the one-parameter non-dimensionalized equation that we ended the last
section with (Eq. 3.12). For the curious reader, this equation is known as a conserved form
of the Swift-Hohenberg equation with a specified non-linear term. The Swift-Hohenberg
equation is a dynamical equation of a scalar field that is known to generate lamellar
patterning and has been well explored in the literature. For simplicity, we remove the
tildes from

Bϕ(r, t)
= ∇2 [´ϵϕ + ϕ3 + (1 + ∇2 )2 ϕ] . (4.1)
Bt

4.1 The Dominant Mode of Smectic Phase Decomposition

In order to inspect the nature of the patterns formed by our dynamical equation, we can
perform a Fourier transform on the linear portion of the equation. We transform
ż
ϕ(r, t) = dk ϕ q(k, t)eik¨x , (4.2)

and put this into

Bϕ(r, t)
= ∇2 [´ϵϕ + (1 + ∇2 )2 ϕ] (4.3)
Bt
thus disregarding the nonlinear, cubic term. Due to linearity of integration, we can write
a new dynamical equation
 2 
q(k, t)
Bϕ 2

2
= |k| ϵ ´ 1 ´ |k| q(k, t)
ϕ (4.4)
Bt

q(k, t). Note the extra minus signs on the squared terms
in terms of the k-space function ϕ
is due to a factor of 2 resulting from ∇2 eik¨x . This equation is now a classic exponential

9
4.2 The Cubic Term 4 RELAXATION DYNAMICS

growth system and is solved by

"   2  *
ϕ q(k, 0) exp |k|2 ϵ ´ 1 ´ |k|2
q(k, t) = ϕ t . (4.5)

The mode determines the character of the exponential prefactor. Specifically, since the
1 ´ |k|2 term is squared, the modes will decay for most values of k. However, if ϵ ą 0,



2
then the modes for which 1 ´ |k|2 ă ϵ grow. The mode with the highest growth factor
depends subtlety on ϵ and is found as
?
2+ 1 + 3ϵ
|k|max = , (4.6)
3
so this mode grows the fastest and emerges as the dominant wave mode. Note also that
the wave mode |k| = 0 remains constant. This corresponds to the infinite wavelength (the
entire domain) and is consistent with the conservation built into this dynamical system.
The exponential prefactor is plotted for several values of ϵ in figure

4.2 The Cubic Term

In our model of rod-like cell relaxation, we find a conserved Swift-Hohenberg dynamics

which induces an additional two spatial derivatives on the right hand side of the equation

Bϕ(r, t)
= ∇2 [ϵϕ + (q20 + ∇2 )2 ϕ]
Bt
(4.7)

4.3 Nonlinear SH

By introducing a nonlinear cubic term f (ϕ) = ´ϕ3 , we restrict otherwise unlimited

growth of the lamellar patterns so that locally dominant modes outcompete others and a
specific direction wins k = k i . This allows for complex layering and defects to develop.

10
 6 NUMERICAL METHODS

5 Phase Diagram

6 Numerical Methods

Recall our model of smectic binary phase separation is driven by

Bϕ(r, t)
= ∇2 [´ϵϕ + ϕ3 + (1 + ∇2 )2 ϕ] (6.1)
Bt
driving the dynamics of the phase order parameter field ϕ(r, t). Therefore, we employ a
numerical approach to simulate it. This means that our continuum field is approximated
by a domain broken into discrete grid points, and we use the local neighbors of each
point to find a discretized approximation of the local values of the derivatives.

Therefore, we will need to execute a program that calculates local values for every field
point in a discretized grid using the values of those points neighbors. These are also
known as stencil calculations.

6.1 Pystencils

Pystencils [3] is a python module designed to run stencil code to simulate physical pro-
cesses on fields. Specifically, Pystencils can run stencil code much faster than traditional
python scripts because it compiles all calculations under the hood as a C script, and it
allows this C code to be called as if it were a native Python function.

Pystencils also leverages the SymPy module [2] so that all equations can be viewed
symbolically by users to ensure they represent the correct physical system that users
would like to simulate.

All results presented in this manuscript were computed using Pystencils.

6.2 Discretization Methods

In order to help with numerical stability, Pystencils is built to handle the dynamics of
conserved phase order parameter fields as two separate fields, each of which influence

11
6.2 Discretization Methods 6 NUMERICAL METHODS

the other’s dynamics. These two fields are the phase order parameter field itself ϕ, and
the chemical potential field µ as defined in Eqn. 2.4. In this way our numerics are broken
into
Bϕ(r, t)
= ∇2 [µ(r, t)] (6.2)
Bt
and
µ(r, t) = ´ϵϕ(r, t) + [ϕ(r, t)]3 + (1 + ∇2 )2 ϕ(r, t) . (6.3)
Now, we do not need to discretize a 6th order PDE, but a 4th order and a 2nd order
one. This technique of rewriting the PDE into 2 is especially useful for avoiding the
discretization of derivatives on nonlinear terms such as ∇2 [ϕ(r, t)]3 . In this manuscript,

we will compute the dynamics of ϕ(r, t) up to a maximum of two spatial dimensions,

so that is the number of dimensions that we will show the explicit discretization for.
Accordingly, we write r = (r x , ry ) and define the discretization steps between points in
time, the first spatial dimension, and the second spatial dimension to be ∆t, ∆x, and ∆y,
respectively. We also simplify our notation by denoting f (r x , ry , t) = f (i∆x, j∆y, k∆t) ”
k.
f i,j

Beginning with the diffusive Eqn. 6.2, we can separate the spatial dimensions as
Bϕ(r, t)
= Bx2 [µ(r, t)] + By2 [µ(r, t)] , (6.4)
Bt
and subsequently implement a straightforward 2nd order, centered discretization for the
spatial dimensions and a 1st order, forward discretization for time. This method leads to
k +1 k
ϕi,j ´ ϕi,j µik+1,j ´ 2µi,j
k + µk
i´1,j
k
µi,j k k
+1 ´ 2µi,j + µi,j´1
= + . (6.5)
∆t ∆x2 ∆y2
In the case that ∆x = ∆y (as will always be true throughout this manuscript), we can
simplify to
k +1 k
ϕi,j ´ ϕi,j µik+1,j + µi,j
k k k k
+1 ´ 4µi,j + µi,j´1 + µi´1,j
= (6.6)
∆t ∆x2
which solves for the new value of ϕ in terms of the old value and the chemical potential
field as
k +1 k ∆t  k k k k k

ϕi,j = ϕi,j + µ i +1,j + µ i,j+1 ´ 4µ i,j + µ i,j´1 + µ i´1,j . (6.7)
∆x2

As for discretizing Eqn. 6.3, while the form of the equation is more complicated than
mere diffusion, the lack of time derivatives means that the chemical potential field only
depends on the same-time spatial distribution of ϕ(r, t) throughout the domain. First we
foil out the gradient operators and separate the differently ordered differential terms as

µ(r, t) = [(1 ´ ϵ)ϕ + ϕ3 ] + [2∇2 ϕ] + [∇4 ϕ] . (6.8)

12
6.2 Discretization Methods 6 NUMERICAL METHODS

The zero order terms do not need to be discretized. The second order term can be
discretized the same as in Eqn. 6.6 as
2  k k k k k

2∇2 ϕ(r, t) ÝÑ ϕi +1,j + ϕi,j+1 ´ 4ϕi,j + ϕi,j´1 + ϕi´1,j . (6.9)
∆x2
The fourth order term requires a centered, fourth order method to properly discretize.
The quartic gradient operator can be written as

∇4 ϕ(r, t) = Bx4 ϕ(r, t) + 2Bx2 By2 ϕ(r, t) + By4 ϕ(r, t) , (6.10)

and the subsequent discretizations of these three terms are

ϕik+2,j ´ 4ϕik+1,j + 6ϕi,j
k ´ 4ϕk k
i´1,j + ϕi´2,j
Bx4 ϕ(r, t) ÝÑ (6.11)
∆x4
and
k k k k k
ϕi,j +2 ´ 4ϕi,j+1 + 6ϕi,j ´ 4ϕi,j´1 + ϕi,j´2
By4 ϕ(r, t) ÝÑ (6.12)
∆y4
and (discretizing one dimension at a time)
k k k
!
ϕi,j +1 ´ 2ϕi,j + ϕi,j´1
2Bx2 By2 ϕ(r, t) ÝÑ 2Bx2
∆y2

2 ϕik+1,j+1 ´ 2ϕi,j
k k
+1 + ϕi´1,j+1
ÝÑ (6.13)
∆y2 ∆x2
´2ϕik+1,j + 4ϕi,j
k ´ 2ϕk ϕik+1,j´1 ´ 2ϕi,j
k k
!
i´1,j ´1 + ϕi´1,j´1
+ + .
∆x2 ∆x2
By again imposing ∆x = ∆y, we can simplify the entire fourth order term to
1 h k
∇4 ϕ(r, t) ÝÑ ϕi+2,j + ϕik´2,j + ϕi,j
k k
+2 + ϕi,j´2
∆x 4

+ 2 ϕik+1,j+1 + ϕik´1,j+1 + ϕik+1,j´1 + ϕik´1,j´1 (6.14)
  i
´ 8 ϕik+1,j + ϕik´1,j + ϕi,j
k k k
+1 + ϕi,j´1 + 20ϕi,j .

We can finally write the entire discretization of Eqn. 6.3 (combining zero order terms with
Eqns 6.9 and 6.14) as
 3
k k k
µi,j = (1 ´ ϵ)ϕi,j + ϕi,j
1 h  k  i
+ 2 ϕi+1,j + ϕik´1,j + ϕi,jk k
+1 + ϕi,j´1 ´ 8ϕi,j
k
∆x 2
1 h k (6.15)
+ ϕ + ϕik´2,j + ϕi,j
k k
+2 + ϕi,j´2
∆x4 i+2,j  
+ 2 ϕik+1,j+1 + ϕik´1,j+1 + ϕik+1,j´1 + ϕik´1,j´1
  i
´ 8 ϕik+1,j + ϕik´1,j + ϕi,jk
+1 + ϕ k
i,j´1 + 20ϕ k
i,j .

13
6.3 Important Implementation Details 6 NUMERICAL METHODS

6.3 Important Implementation Details

Since Pystencils is built from the ground up to simulate the evolution of physical pa-
rameters, there are several tutorials that are premade and ready to simulate well-known
processes such as solute advection-diffusion and Cahn-Hilliard phase-field spinodal
decomposition (Eqns 3.1 and 3.2). The Cahn-Hilliard tutorial was adapted for this project.

Pystencils has several prebuilt functions to help handle the free energy density f (ϕ) and
the subsequent functional derivative of the free energy functional which determines the
dynamics of ϕ. There are also functions that handle the discretization of differential
equations. However, these functions were not built to handle differential equations with
mixed partial derivative terms nor terms with higher order than a squared gradient.
ş
Therefore, the functional derivative of dr f cells (ϕ) has to be written manually. Moreover,
the discretization of the quartic gradient term has to be found by discretizing recursively
on each successive squared derivative operators until the desired fourth order terms are
achieved. That is, for a centered discretization operator D

D(∇4 ϕ) = D[(Bx4 + 2Bx2 By2 + By4 )ϕ] (6.16)

is not possible and results in an error. However discretizing recursively as

! h  i) ! h  i) ! h  i)
D Bx2 D Bx2 ϕ + 2D By2 D Bx2 ϕ + D By2 D By2 ϕ (6.17)

is permitted and achieves the discretization schemes outlined in subsection 6.2. It is very
important to use the prebuilt discretization methods in Pystencils since they symbolically
define the necessary stencil equations that are used to build and compile the C code that
runs the actual computation of evolving each of our fields.

A final important detail of our implementation is regarding the periodic boundary con-
ditions of our system. Due to the quartic gradient term in the equation of µ (Eqn. 6.3),
the discretization schemes implement stencil operations that need information about
the neighbors up to two steps away from any given field point. In order to handle sten-
cil operations for field points on the border of the domain while maintaining periodic
boundary conditions, Pystencils implements extra layers beyond the domain called ghost
layers. By default, each field has now ghost layer associated with it at each edge of the
domain. However, our system needs two ghost to evolve properly. A non-default number
of ghost layers must be explicitly declared when initializing a field for the first time or
when initializing values in a field.

14
6.4 Initialization Scheme 7 VALIDATION

6.4 Initialization Scheme

7 Validation

In this section we show the results of our numerical method of simulation and com-
pare them with results from the literature. Examples of our method using Pystencils is
compared with data from [1] in Figures 1 and 2.

Figure 1: The 1D system at a value of ϕ0 = ´0.5 and ϵ = 0.9. We compare the results
from our Pystencils simulation (orange) to a similar steady state found in [1] (blue) at the
same point in phase space.

15
 8 GROWTH

Figure 2: The 1D system at a value of ϕ0 = ´0.625 and ϵ = 0.9. Our results using
Pystencils (orange) are compared with results from [1] (blue) at the same state point. In
the 1D case, this phase coexistence can be interpreted as the presence of a single cell in
the domain.

Since we are interested in using our continuum phase order field to model cellular
division, we want to find a steady state which corresponds to one cell in the domain,
which we can use as the initial state for subsequent growth. This means that we are
looking for a phase coexistence point in which only a single period of the periodic phase
is present in a domain of otherwise uniform void phase, such as the coexistence point
shown in figure 2

8 Growth

Here we propose
"       *
Bϕ W W
= g tanh S ϕ ´ C + tanh S ´ϕ + C + +1 (8.1)
Bt 2 2
as the growth term to account for division of our cells. By the multiplication of a sigmoid
with it’s own reflection, we have facilitated no growth in both the void phase and when

16
8.1 Non-dimensionalization 8 GROWTH

the cellular phase becomes too densely packed. g is the growth rate. A modulates the
sharpness of the growth drop offs, which we expect to be sharp when there is insufficient
cellular material as well as when there is too much cellular packing (I still need to search
the literature to see a physiological justification for this!). B modulates the location of
the region of nonzero growth in phase space, and C regulates the size of the region of
nonzero growth.

A sample plot is shown in figure 3.

Figure 3: Growth-phase plot from two hyperbolic tangent sigmoids multiplied, with one
reflected. This growth pattern exhibits what we expect from physiological conditions in
which lack of cells and overpacking of cells leads sharply to no growth.

8.1 Non-dimensionalization

The full dynamics are

Bϕ(r, t)
= D ∇2 (´a∆0 ϕ + uϕ3 + λ(q20 + ∇2 )2 ϕ) + gttanh[ A(ϕ ´ B)] tanh[ A(C ´ (ϕ ´ B))] + 1u .
Bt
(8.2)
Here we can nondimensionalize
b the system by performing the same steps as in Subsection
3.4 defining ϕ̃ = ϕ u/(λq ), t̃ = tDλq6 , and ∇
4 ˜ = ∇/q0 and defining ϵ = ( a∆0 )/(λq4 )
0 0 0

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 BIBLIOGRAPHY

in addition to setting B = (2 ´ C )/2 in order to center the region of growth about ϕ = 1.

Then the nondimensionalized dynamics are

B ϕ̃ 
˜ 2 [´ϵ + (1 + ∇˜ 2 )2 ]ϕ̃ + ϕ̃3

=∇
B t̃ # " c !# " c !# + (8.3)
2 λ C C λ
+ g̃ tanh A ϕ̃q0 + ´1 tanh A + 1 + ϕ̃q20 +1 ,
u 2 2 u
? ?
where g̃ := g u/( Dλq80 λ).

Figure 4: Here g = 0.075, ϵ = 0.1 (from the non-dimensionalized conserved phase-field

crystal dynamics), but the other constants are as in figure 3
. Here the initial conditions are set to a sine wave and the boundary conditions are set to
void phase (ϕ = ´1), with the first and second spatial derivatives of ϕ also being 0 at the
boundaries.

The control parameter will be

!3
λq40 2
g (8.4)
u

9 Miscellaneous

4th order numerical FTCS

uin+1 ´ uin un ´ 4uin+1 + 6uin ´ 4uin´1 + uin´2

= α i +2 (9.1)
∆t ∆x4

Bibliography

[1] Uwe Thiele et al. “Localized states in the conserved Swift-Hohenberg equation
with cubic nonlinearity”. In: Phys. Rev. E 87 (4 Apr. 2013), p. 042915. DOI: 10.1103/
PhysRevE.87.042915. URL: https://link.aps.org/doi/10.1103/PhysRevE.87.
042915.

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BIBLIOGRAPHY BIBLIOGRAPHY

[2] Aaron Meurer et al. “SymPy: symbolic computing in Python”. In: PeerJ Computer
Science 3 (Jan. 2017), e103. ISSN: 2376-5992. DOI: 10 . 7717 / peerj - cs . 103. URL:
https://doi.org/10.7717/peerj-cs.103.
[3] PyStencils. https://pycodegen.pages.i10git.cs.fau.de/pystencils/index.
html. Accessed: April 9, 2024.

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