Trying to decide which to go on this one - this is built on budget and would like applicable bang per buck discussion. Perfectibility from people who've done this sorta thing as career/research.
Exactly what I plan to do (at the same time):
-parallel computations (cores doing different things/unsynced but they need to be able to interject information to each other, similar to thermo dynamical calculations), I also suspect I'll need to be able to hyper-tread each core in the future.
My current setup with a Athlon x2 has me running 2 week computations, I would like a cpu that'll bring it down to a day or two, while remaining useable for other processes.
More about :intel amd physics simulations modeling
Does this task benefit from GPU acceleration? If it does, that will vastly outperform any CPU. When selecting a GPU, unless the software is very specific on which ones it supports, you will want an AMD card for compute tasks, or an older Fermi card; the Kepler generation has crippled compute performance.
There is no direct answer to this as this will depend on many factors. Having worked with thermo some things you should consider would be:
1.) What OS are you using? I assume some form of Unix (in my case debian).
2.) Assuming you are doing this for work/thesis I assume you have access to some kind of mainframe/cluster/supercomputer (lets face it 2 weeks worth of calculations are small), you will want to use a CPU with similar architecture. In my case this was CSC, in Finnland.
Going off a tangent here but assuming you have access to 2.) you might also look into GPU compute with CUDA. The gtx480 offers some tremendous power for a fairly low price and offers a great entry way of getting into this field.
You never mentioned a budget but I would go with the other recommendations. Both the i7-3770 and i3-3240 offer hyper threading which should be of benefit for you and offer aggressive turbos when single threaded.
If ECC memory is a must, you might have to step up to a workstation CPU.