Monday, April 15, 2013

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.

The nanoparticles were created using dupliverts on Icospheres in Blender. Albumin and the Antibody were created by rendering them as STL files in VMD using the surf representation. Once imported into Blender, a decimate modifier followed by remesh (octree depth of 7, smooth) fixed the STL meshes nicely. A 5 iteration smooth modifier fixed any artifacts after the remeshing. Make sure to turn on smooth shading. The peptide and salicylic acid were made the same way, except using the VDW representation instead of the surf. No remeshing is necessary, other than enabling smooth shading. Rendering was done at 150% with 75 samples and the image was scaled down in GIMP to 100% using cubic interpolation (a ghetto denoising technique that works well). Finally, the annotations were added in Inkscape. Here's a zoom of the smaller elements.


  1. Very nice work! I love to see blender being used in scientific visualizations! I use it all the time in my own work too, if you are interested, check my website:

  2. I have a question. How many atoms of gold are in the gold nanoparticle?

  3. The lattice structure is probably not correct, but in the image there are 10,242 gold atoms.