Not having read the article or not knowing anything about how an event is detected... It rather sounds if CPUs are not the best tool for the job. FPGAs should be able to run data acquisition and filtering in real time, doing most of the heavy lifting. A single FPGA (rather large FPGA like the Virtex range from Xilinx) can do thousands of multiply accumulates in parallel. GPUs like the Tesla or similar may also be a better fit.