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Membrane filtration fouling is a very complex process and is determined by many properties such as the membrane internal morphology, membrane pore structure, flow rate and contaminant properties. In a very slow filtration process or during the late stage of filtration, when the flow rate is naturally low and Péclet number is small, particle diffusion is essential and cannot be neglected, while in typical filtration models, especially in moderate and fast filtration process, the main contribution stems from the particle advection. The objectives of this study is to formulate mathematical models that can (i) investigate how filtration process varies under possible effects of particles diffusion; and (ii) describe how membrane morphology evolves and investigate the filtration performance during the filtration process. We also compare the results with the case that diffusion is less important and make a prediction about what kind of membrane filter pore structure should be employed to achieve a particular optimum filtration performance. According to our results, the filtrate and efficiency of particle separation are found to be under the trade-off relationship, and the selection of the membrane properties depends on the requirement of the filtration.