Cyclone IV reconfiguration

I am new to the FPGA stuff, so i don't know it is possible to use FPGA for the task i am struggling with. The subject of the task is to model the neuroevolution remotly controlled by a desktop PC. The population consists of a set of wheeled robots. During the entire process of neuroevolution, the NIOS II soft processor has to be implemented on an FPGA.

My idea of the whole process consits of the following steps:

1. The new structure of the neural network is downloaded by the NIOS processor from the PC and implemented on the rest of the FPGA.

2. Weights of the neural network are modified by means of a Hebbian leraning rule during the whole life of the individual.

3. Then the fitness of the individual is calculated by the NIOS processor and sent back to the PC.