Topics › Biochemistry

pH, pKa, pI and protein charge

What is acidity?

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.

Project:

Cell Simulation

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

Project:

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.