Jellium (J) and Quarkonium (Q)

In addition to real chemical elements, garlic accepts two imaginary elements: "jellium" (J) and "quarkonium" (Q). Jellium is inert and it never binds to neighboring atoms, no matter how close they are. Quarkonium binds to other quarkonium atoms which have adjacent atomic serial numbers. For example, if some quarkonium atom has serial number i, it may form bonds with quarkonium atoms i-1 and i+1. The interatomic distance is not important! Quarkonium is capable to form at most two bonds. To break the polygonal line, skip one serial index. For example, if three consecutive Q atoms in PDB file have serial numbers i-1, i and i+2, the atoms i-1 and i will be bound, but there will be no bond between atoms i and i+2. The same trick may be used to force Q atom to form no bonds: use indices i-2, i and i+2.

Both elements were introduced to enable drawing of special objects. Quarkonium may be used to draw polygonal lines in three dimensions. The original idea was to adapt garlic for visualization of some medical data. For example, quarkonium may be used to represent blood vessels and jellium to represent retraction balls characteristic for broken axons in human brain. Click here for an example.

By the way, quarkonium is a serious thing in high energy physics, but there it looks quite different. The term jellium is used is solid state physics (jellium model for electrons in solid). Note that symbols J and Q are not used in the periodic table of elements. For that reason these two terms were abused in garlic. If I should be thrown through the window at the next meeting of Croatian Physical Society, please note that my colleague Dario Faj deserves the same treatment, he was also involved in this dirty job.