You need to take into consideration if the program(s) can use more than 4 cores and if Hyper Threading (HT) is taken advantage of.
While the AMD's FX CPU do have up to 8 cores, each core is not as powerful as a CPU in an Intel Core i3/i5/i7 CPU. Therefore, if the scientific programs do not take advantage of more than 4 cores, then there is no real reason to choose an AMD FX CPU over a comparable Core i5/i7 CPU other than cost.
If the programs can take advantage of HT, then going with a Core i7 (which has HT) over a Core i5 of the same clock speed can result in a 20% - 40% improvement in performance depending on how well HT has been implemented. If HT is poorly implemented, then naturally the performance boost will be small.