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Digital flow cytometry offers the flexibility to explore novel feature extraction and classification schemes for efficient sorting of biological cells. A prototype of a second-generation digital data acquisition system (DDAPS-2) - a mixed-signal design operating at 40 MHz - was built to interface to a commercial flow cytometer. The DDAPS-2 intercepts the analog signal from the photomultiplier tube and preamp, performs analog-to-digital conversion, extracts various features and then feeds these extracted features into one of the several pattern classification algorithms. This paper describes the design and operation of the various sub-systems that constitute the DDAPS-2. The novelty of the DDAPS-2 is the use of dual-buffering FIFO memories to acquire digital samples of the pulse voltage signal. Experimental results demonstrate the improvement in the pulse capture performance of DDAPS-2 over DDAPS-1, which used a single-buffering FIFO memory.