arXiv:2610.29567v1 Announce Type: new Abstract: In particle communication, particles released for different symbols can reach the receiver at overlapping times, making reliable detection difficult. This paper develops a digital communication framework that connects particle transport, pulse shaping, and receiver processing for three-dimensional free-space diffusion-advection channels. We derive the continuous-time and discrete-time frequency responses and explain how flow speed affects channel delay and bandwidth. Under advection-dominated conditions, the group delay approaches $R/V$, and the one-sided $3$-dB bandwidth scales as $V^{3/2}$. We design nonnegative, unit-energy transmit pulses using a packet-level SINR criterion that includes interference from both preceding and subsequent symbols under additive white Gaussian receiver noise. Simulations validate the analytical approximations and show that optimized pulses spread across more of the symbol interval when noise is substantial and become narrower as noise decreases. BER evaluations across SNR and symbol duration compare optimized, rectangular, and single-impulse pulses with several detection methods, identifying the operating conditions in which transmit-pulse design improves reliability.