Reaction Diffusion Models and Pattern Formation

Abstract. These models applications are.

Reaction-diffusion systems are models which explain the concentration of its constituents under the
influence of chemical reactions and diffusion. Many biological, geological and physical processes are
described by these models. In this project I will discuss various reaction-diffusion systems and there
applications in the biological sciences, paying particular attention to the findings of Alan Turings
landmark paper in 1952 and the work of Professor James D. Murray on pattern formation.
Examine
1.Introduction. species
2. Reaction Diffusion equations 3
Derivation, travelling wave solution, popular examples (Gray Scott, Fitzhugh nagumo,)
Sources of info: Page 399 Murray vol1 has good derivation of general Reaction Diffusion. This is then
discussed further in Jones book and this compared with the wikiwaves page might fill the rest of the
page. Look at one big example, GRAY SCOTT, or even Fitzhugh nagumo also, for sources look @
email there is plenty there.
3. Turing and Morphogenesis 4
Define morphogenesis and talk a bit, plenty in Murrays book. Give a brief spiel about Turing and his
results, try anyway, set it up to bull onto the important stuff that is pattern formations. Instability,
Bifurcations, DDI, Conditions, use the books for this. Also mention Tompkins paper on testing the
results.
4. Murray and Pattern Formation 3
Murray, and then on and on and on. Should be easy to fill
5. Other applications 1


Conclusions etc.





2. (4 to 5 pages)
A reaction-diffusion system is a model which consists of species that are converted into each other
via a chemical reaction and also transported in space by diffusion. The model can often calculate the
concentration of the species based upon this said reaction and diffusion, and often a feed and
removal rate. These models describe the fundamental process of a chemical reaction, but also result
in patterns which are interestingly similar to ones found in the real world, which we will see
in(SECTION BLAH). In this section I will examine the derivation of such systems, as well as looking at
two important reaction diffusion systems as a means of introducing there general structure to build
towards more complicated examples in following sections.
2.1 Derivation.
We will start off slowly, first looking at a simple derivation of a three dimensional system with one
chemical diffusing in space, as seen in (MURRAYS FIRST EDITION). He asks us to consider diffusion in
three spatial dimensions, with S being an arbitrary surface enclosing a volume V. The general
conservation equation says that the rate of change of the amount of material in V is equal to the
rate of flow of material across S into V plus the material created in V. Thus
(11.12)
Where J is the flux of material and f, which represents the source of material, may be a function of c,
x and t. applying the divergence theorem to the surface integral and assuming c(x, t) is continuous,
the last equation becomes
(11.13)
Since the volume V is arbitrary the integrand must be zero and so the conservation equation for c is
(11.14)
This equation holds for a general flux transport J, whether by diffusion or some other process. If
classical diffusion is the process then the generalisation of (11.5), for example, is
(11.15)
And (11.14) becomes
(11.16)
Where D may be a function of x and c and f a function of c, x and t...
Although trivial, this idea can easily be extended to more than one chemical, (PAGE 283 JONES ALSO)
and in particular, we will be paying attention to the case n=2.

Travelling Wave solutions, mention.
2.2 Gray Scott Model
The Gray Scott model is a powerful RD model looking at the interaction of 3 chemical species under
the following chemical reaction.

P is essentially an inactive product. It is assumed for simplicity that the reverse reactions do not
occur (this is a useful simplification when a constant supply of reactants prevents the attainment of
equilibrium). Because V appears on both sides of the first reaction, it acts as a catalyst for its own
production.A nonequilibrium constraint is represented by a feed term for U. Both U and V are
removed by the feed process. The resulting dimensionless equations are seen as:

Explain diffusion term, reaction rate, replenishment term, diminishment from mrob website. All
from website, need to quote paper.
popular largely due to its ability to produce a very varied number of biological looking (and
behaving) patterns, both static and constantly changing
See paper by pearson, and some very good links in email. Fill a page.
Definitely use the pretty image on xmorphia, hon


2.2Fitzhugh_naguma.

With rabbitfish picture definitely. And pick something.



Grest paper by yazdan were now at 3 pages boysh.

















Section 3.
Renowned predominantly for his contributions to computer science and code-breaking (Churchill
said that Turing made the single biggest contribution to Allied victory in WW2), Alan Turings work
on morphogenesis is often overshadowed. Less well known is that he spent the last few years of his
life developing his morphogenetic theory using reaction-diffusion systems. Only one paper was
published in his lifetime in 1952, the momentous The Chemical Basis of Morphogenesis, which
paved the way for advances in modern reaction-diffusion theory.
Morphogenesis

Turings paper
Instability, Bifurcations, DDI, Conditions, use the books for this

Verification
Section 4
Basis
Murrays model and analysis, hug the Colorado page
Butterflies
Meinhardts work (need his other papers)
Section 5
Optical Imaging (also look at shertinksy picard)