With recent development of microfluidic devices in which cells are deformed in tight constrictions, modeling the capsules to understand their dynamics has gained importance. The capsule deformation in microfluidic devices takes place at the microscopic level. Modeling the fluid behavior at such microscopic length scales is important in order to describe the physics of the fluid flow. At smaller length scales, the discreteness of the fluid manifests itself, and atomistic forces such as the Brownian effects and Van der Waals forces play an important role in the hydrodynamics. Dissipative particle dynamics (DPD) is a coarse-grained model widely believed to capture the correct hydrodynamics at the mesoscale. In the present study, DPD is used to study the deformation of a capsule in microfluidic channels. In particular, the transport of a capsule in a fluid flowing in a converging-diverging channel with a constriction in the middle is studied in detail. An important effect of the deformation of the capsule in the flow is the appearance of pores on the capsule membrane. The pore density in the capsule membrane due to the developed strain is analyzed. The intracellular delivery of drugs is dependent on the pore density. In the current study, the effectiveness of the delivery is calculated based on the strain developed during deformation in the microchannels.