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.

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.

Relative Size of Proteins, Nanoparticles, Antibodies, Peptides, and Drugs

Needing to know the relative size of these elements in biochemical systems often comes up in my research, so I've decided to write them.

Component	Size [nm]	Reference
Gold Nanoparticle	~20	Can vary, most common is 20. Frens (1973)
Iron Oxide Nanoparticle	5-15	Can be much larger with emulsion methods. This size is most common when magentic properties are desired. Called partial reduction coprecipitation method.
Antibody	15.5 x 11	PDB: 1igt measured in VMD
Human Serum Albumin	7.6 x 7	PDB: 1e7i measured in VMD
10 Amino Acid Peptide	~1.5 (coiled globule sphere)	Paper I wrote on Peptide Conformations
Salicylic Acid (drug)	0.6 x 0.5	PubChem structure measured in VMD

Approximate Restricted Integer Partition With Exact Part Number

I'm interested in a certain type of mathematical structure this week: integer partitions. An integer partition, p(n), is the set of sets of integers that add up to n. For example,

• p(3) = 1 + 1 + 1, 1 + 2, 3
• p(4) = 1 + 1 + 1 + 1, 1 + 1 + 2, 2 + 2, ...