Abdul Binmahfuth's Personal Blog

In the first article ( here ), we have explored what Turing patterns means in a biological sense by given examples of how it occurs in nature.  The series of the articles is building up to genetically modifying organisms to forward engineer Turing patterns. But first, a clear understanding of genes and gene regulatory networks must be given. Gene Anatomy At a crude level, in any living organisms –with some rare few exceptions–, The DNA acts as the blueprint for computations performed in the cell. It consists of nucleic acid monomers linked together to form polymer chains . There are four main types of nucleic acids, adenine (A), guanine (G) cytosine (C), and thymine (T) [3]. DNA molecules usually come in double-helix strands of polymer chains, as shown in figure 1. The two polymer chains are linked together via hydrogen bonds in the given structure: an adenine (A) base is always linked to a thymine (T) base, and cytosine base (C) is always linked to a guanine (G) b...

As of today, most countries are on lockdown; a strategy devised by governments to help slow down the spread of the novel coronavirus COVID-19. Moreover, officials use the term flattening the curve to help the healthcare system cope with the expected large amount of patients, but what does that mean mathematically? I will go on an overview of how to construct a useful toy mathematical model to get a qualitative view of the dynamics of the virus. This is a typical SIR model appearing a lot lately in the media. I will go further to explain how to develop such a model and explain the power and limitations of such models. How to construct SIR models SIR stands for Susceptible, Infectious and Recovered (or Removed) agents. In our example, the agents are humans spreading the disease to each other. To simplify things, we model an agent as a node and the links between nodes represent social connections, as seen in the picture below: Figure 1: Modelling humans as nodes...

What is this post about? This post will cover an overview of pattern formation, specifically Turing pattern formation in a non-mathematical way. The whole point here is to appreciate the beauty of what can Turing's reaction-diffusion model describe. If you are excited enough about the topic and want to cover some technicalities, a subsequent post will cover my Master's thesis work on the design of genetic circuits from first principles that makes use of Turing's reaction-diffusion model. Pattern formation in Biology It is best to start by explaining pattern formation in biology. The easiest and most obvious way to see patterns is within animals. Zebras; fish; cheetahs are some of the few animal examples that exhibit pigment patterns on their skin [1]. If you accept the fact that pigments are no more than proteins expressed within a group of cells [2], one can reasonably ask the question: How can cells determine their relative position to other cells so they end up ex...