Google brings plenty of sites on this subject. I just selected two:

www.me.iastate.edu/biodiesel/Technical%20Papers/Canakci_Paper3_as%20revised%20after%20review.pdf

www.en.wikipedia.org/wiki/Biodiesel

In first approximation any combustible liquid or solid
can  be used as fuel in an IC engine

1.) if it can be finelly dsitributed so it burns fast enough
2.) if the products of combustion can be easily removed
3.) if it doesn't cause too much corrosion or erosion

The rest is engineering and economics  

Plesae read FAQ240-1032
My WEB: <http://geocities.com/nbucska/>

25362, thanks for the links. But I had already checked Wiki earlier and they don't mention about how the biodiesel itself is being reacted/converted to produce the power. They focus more on the manufacture of biodiesel. And the other link you provided only talks about the experiments and emissions/performance etc.

I'm looking more at what happens at a molecular level when you put the biodiesel into a diesel car/engine (not during manufacture, I already know that part). Physically and chemically, what happens to the biodiesel methyl ester?

---engineering your life---

ddkm - biodiesel just burns in the diesel engine. Are you wondering why it is better than petroleum diesel. The answer lies in what happens to the carbon outside of the engine (the carbon cycle). I hope this helps the discussion.

HAZOP at www.curryhydrocarbons.ca

owg, in a way, I'm also wondering why the biodiesel can burn better. What are the similar chemical structures between biodiesel and its petroleum cousin?

Also, could you elaborate more what happens to the carbon outside of the engine? Thanks.

---engineering your life---

Apparently the oxygen in the ester molecule faciltates combustion.

Petroleum diesel ignites more slowly (see first link of 25362's above) and burns less completely due to the presence of polycyclic aromatic hydrocarbons (PAHs) [co-joined benzene rings].  These are complex structures requiring complex, stepwise bond breaking during combustion.

Many of the emissions in diesel smoke (aldehydes, benzene and VOCs) are the result of incomplete combustion of PAHs.  The lower molecular weight compounds initially present in the fuel actually burn rather cleanly.
"Technical Report No. 1: Toxic Emissions from Diesel Vehicles in Australia"
http://www.deh.gov.au/atmosphere/airquality/publications/report1/index.html

There are already EPA restrictions on aromatic content of diesel fuel in California & Texas (maybe nationwide, soon?) and overseas.  As sulfur content is mostly attached to the PAHs, the new EPA restriction on sulfur content in diesel (15 ppm) effective Oct. 15, 2006 (already in California), I believe will also lower the PAH content.  Although PAHs have a high energy content due to higher C-to-H ratio than say alkanes, energy is wasted if combustion is incomplete.

"Lower Sulphur Diesel - What Does This Mean?"
http://www.med.govt.nz/templates/Page____10375.aspx

"Effects of Fuels with a Low Aromatic Content on Diesel Engine Exhaust Emissions" [abstract only w/o subscription]
It mentions that "Oxygenated fuels showed lower smoke and NOx emissions."
http://www.ingentaconnect.com/content/pep/jae/2000/00000214/00000007/art00011;jsessionid=32goio9tm772.alice  

We are trying to epoxidize a biodiesel or methyl ester from soybean oil in order to get a sort of plasticizer to be ued for PVC compounding.Any experience and/or comments?

No reply as yet on my question on Epoxidized methyl esters(biodiesel)Am trying to contact someone who had done some work on this.Is it possible?

Suggest starting a new thread -- this one deals with combustion reactions of biodiesel.
Good luck.