Topics › Biochemistry

Proteins that look like enzymes but aren't

This essay is taken from the introduction to my thesis, which is pretty much the only part of my thesis I was pleased with. It described way it's not always easy to assign a function to a protein and was used as the basis for my first paper Moonlighting enzymes in parasitic protozoa.

pH, pKa, pI and protein charge

What is acidity?

Most people know that pH is a measure of acidity, but what is acidity? Well, the Brønsted-Lowry theory states that an acid is a chemical that donates a proton (H+), while a base is a chemical that accepts a proton. The Lewis theory defines acids as chemicals that accept electrons, which is often, but not always, the same thing. For our purposes, acids are chemicals that can donate a proton, while bases (or alkaline substances) are chemicals that accept a proton.

Amino acids in Chinese

Table of amino acids in Chinese

When looking up the word for acid in Chinese, I came across the Chinese for the amino acids. Since I've previously written about DNA and the bases in Chinese, it seemed logical to compile a list of the Chinese amino acids. Working out the logic behind the Chinese words took quite a lot of research, but was very rewarding. Hopefully the effort will help me remember the words.

Macrophage chemotaxis

I updated my macrophage simulation to use my Python particle module, which I describe here. I was pleased how straight forward it was to effectively re-create my previous simulation from scratch using a few simple commands. There are a few changes I'd like to make so creating new simulations will be even quicker in future.


Cell Simulation

A simulation of single celled organisms and their evolution with the focus on metabolic and regulatory pathways.


Heterocyst Simulation

An old simulation of a type of cyanobacterium and its evolution, which was originally written in QBASIC. Includes analysis of the results from this simulation

Molecular dynamics simulation

I wanted to write about a Java molecular simulation that I made a while ago, before I became entranced by Python. The program is a simple 2D physics simulation, with circles representing billiard ball-style atoms. The idea before the simulation was initially an attempt to create a virtual lava lamp. In its first incarnation, there were two types of atom. Each atom was attracted to nearby atoms of the same type (with a force proportional one over distance squared). If the distance between any two atoms was below a threshold then the two atoms repel each other.

Short cell simulation update

Once again I’ve been neglecting my blog. I think I have a good excuse, which is that I was writing my thesis. That hasn’t stopped me from doing the odd spot of programming however. I’ve made some progress with my microbe simulation, notably, making a GUI to visualise where on the DNA various proteins bind. I have also started a separate microbe simulation, which is more of a game to see who can evolve the fittest microbe in the primordial soup. The game elements are all there, but the program is ugly and the game limited; a bit more work is required to make it fun to play.