Bacteria in Blender

I made this while drinking my morning coffee. I just stretched a UV Sphere, stuck two layers of hair on it (flagella, cilia) and added a few modifiers to get it bumpy. The texture is just some glass, Voronoi textures, and diffuse shaders. Meh, it's OK.

Generating n-Dimensional Lattice Coordinates

It comes up sometimes in my research that I need to generate coordinates along a lattice. For example, when generating an initial structure for a molecular dynamics simulation. I thought I share my code for this. The code works by recursively enumerating each dimension in a lattice and calling a given function each time it reaches a point. So, it could be used to execute any function along a lattice. Here's what it looks like for a 2D and 3D example. In the 3D example I didn't choose a cubic number of points on the lattice, so that it sort of stops in the middle.

Category Colors in R

I thought I'd write down the color palette I use for categories. I've seen many discussions about gradient color choices, but category colors are less often discussed. I have a function given below which generates colors where there is not meant to be an ordering to the color. It is important when data points are near, that they are easy to distinguish with the eye. It makes more sense to see it:

ggplot Style in Classic R Plots

ggplot is a highly acclaimed R package for plotting. I have had very little experience with the library because I've mostly memorized all the quirks of normal R plots. I like the ggplot default style though, so I thought write down how to replicate it in R plots. The distinctive feature of ggplot is the gray rectangle and white grid lines. This may be replicated like so:



Here's an example

DNA-Polymer Nanoparticle

DNA-Polymer nanoparticle are used to deliver DNA to cell nuclei for curing diseases at the genetic level. In my research group, we work with carboxy-betaine acrylamide polymers. I modeled an exceptionally large DNA-polymer nanoparticle below. The polymer is 80 kDa and the DNA is a single strand of 65 base pairs. After condensing it (in blender, not a true physical simulation), the nanoparticle comes out to about 15nm in diameter. 

The Accuracy of Ghose-Crippen ALogP for Peptides

I was using the Ghose-Crippen ALogP predictor implemented in CDK as a QSAR for looking at peptide solubilities. Unfortunately, this partition coefficient predictor is fit on small organic molecules and does a pretty bad job at predicting peptide partition coefficients. Here's what it looks like on single amino acids compared with experimental data.

Visualizing Size in Biochemical Systems - Update

After some helpful suggestions, I've revised the previous image I made. This time I've used the atom representation for the proteins and peptides, so atoms are used everywhere for visualization and they have the correct radii. Doesn't look as cool, but it is more consistent.