Process: Boiling, Whirlpool, Chilling, Aeration

After lautering (the separation of wort from the spent grain), the wort is heated to a rolling boil. 

Boiling the wort accomplishes several things:

1) High heat pasteurizes the wort, killing unwanted bacteria that may cause off flavors.

2) Boiling stops any enzyme activity.

3) Unwanted volatile compounds evaporate.

Dimethyl sulfide (DMS) is the most important one to know about. Having DMS in the finished product is considered a fault as it contributes flavors of cooked vegetables. Beer faults will be covered in depth in another post.

4) Proteins coagulate.

Proteins can cause a haze in beer, but under high heat, these proteins coagulate to form called what is called hot break. The coagulated protein can be easily removed from the wort.

5) Bittering and aroma compounds are extracted from the hops.

Hops are used in different phases of the boil in order to achieve different results.

The alpha acids found in hops contribute bitterness to beer. Alpha acids are extracted from hops by extended boiling, so hops used for bittering go in at the beginning of the boil. Boiling also causes some chemical changes in the alpha acids.

Boiling alters, or isomerizes, the alpha acids. Isomerization is the process which transforms a molecule is into another molecule made of the same atoms, but in a different arrangement.

The amount of Alpha Acid in Beer is measured in International Bitterness Units, or IBUs. One IBU is equal to 1 milligram of isomerized alpha acid in 1 liter of beer.

Hop's essential oils add aroma to beer. These oils will evaporate during extended boiling, so hops used for aroma are added at the end of the boil.

Whirlpool

After the boiling has finished (about one hour), hop cone remnants and coagulated proteins must be removed from the wort. This sticky mess is called trub (pronounced troob), and while a home brewer might filter it out with a sieve, a commercial brewery usually removes the trub by causing a whirlpool in the wort. The swirling liquid causes the solid trub to collect in the center of the vortex. When the wort is drained out, the trub remains behind in a pile in the center of the vessel.

Cooling

After boiling, the wort is hot enough to kill yeast, so the wort must be cooled before yeast is added, or pitched.

The cooling must be done rapidly, because a warm tub of sugar water is a fertile breeding ground for bacterial infection. The wort is usually cooled by running it through a heat exchanger. In the diagram below, the red line would be the hot wort and the blue line would be cold water or chilled glycol.

Rapid cooling also curbs the development of additional DMS. Hot wort is still generating DMS, but without boiling, much less of the DMS is evaporating.

Another benefit of rapid cooling is that additional proteins are forced out of suspension.
 
In the days before mechanical refrigeration, wort was placed in a large, shallow open top fermentor to cool. This tray was called a coolship (which is a bastardization of the Dutch word koelschip).

Most modern breweries use a heat exchanger and a closed fermentor, but some, such as Cantillon and Alagash, still use coolships to add unique properties to their beer.

Aeration

After the wort is cooled, it is aerated to dissolve oxygen into the wort. 

If the wort were aerated while hot, oxygen would bind to certain wort compounds, and would later give the beer a stale, cardboard-like flavor. More on beer faults in another post.
 
Cooler liquids can hold more oxygen than warm liquids, and oxygen is used by the yeast to develop their cell membranes. It is important for yeast to have well developed cell membranes as they use up all the oxygen in the wort and begin the process of fermentation, which will be the subject of the next post.

For additional research:

How to Brew 
by John Palmer
Ch. 7

Tasting Beer 
by Randy Mosher
p 47 - 53