Cube-Sphere Intersection Volume

This week's math problem was particularly difficult. I wanted to know the intersection volume between a cube and a sphere. Imagine a sphere contained in a cube. The sphere will first touch the cube when its radius is equal to half the width of the cube. Until that point, its volume is just the formula for the volume of a sphere. Once the sphere's radius is 2 sqrt(3) times the width of the cube, then it completely engulfs the cube and the intersection of the 2 objects is just the volume of a cube. In between, I've found it looks like this:

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.

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.

Visualizing Size in Biochemical Systems

I decided to waste a few hours and make a Blender image based on my post on the relative size of common elements in biochemical systems. Using 1 blender unit = 1 nm, I modeled a gold nanoparticle, an antibody, albumin, an iron oxide nanoparticle, a 10 amino acid length peptide, and salicylic acid.

Changing Image Size in Tachyon in VMD

I always forget how to change the image size for rending molecular images in VMD using the (external) Tachyon rendering engine, so I thought I'd write down the steps here:

In the TCL console, get the aspect ratio correct for the image. So, for example to make a nice 1920x1080 image, we'll make the view at half of that:

 
display resize 960 540

Now, add simply add -res 1920 1080 to the end of the render command in the file render controls window. Here's an example of one of my render commands:

 
"$HOME/VMD/tachyon_LINUXAMD64" -aasamples 12 %s -format TARGA -o %s.tga  -res 1920 1080

Here's the result of one my renders:

Making nanoparticles in Blender

Today I made some nanoparticles in Blender. I used the node compositor to create the fluorophore effect. Making science in Blender is fun!

Making Proteins and Polymer in Blender

I was messing around in Blender and decided to create some artwork related to a recent paper published in my current research group. The idea is to create a two layers of polymer. One layer is to make a biosensor resistant to noise from non-target molecules adsorbing on the sensor surface. A second longer layer of polymer is used to attach anti-body to the sensor. The anti-body allows the sensor to target very specific molecules. Here's the image I made using Blender's cycles render engine: