This thesis attempts to bridge science with technology applications by developing two lines of research, one theoretical and one practical. On the practical side, we describe the microscopic behaviour of a fuel cell, specifically a catalyst layer where the oxygen reduction reaction (ORR) takes place. The processes taking place in the catalyst layer are inefficient at ambient conditions and so this fuel cell component is, together with high price of platinum as the catalyst, the main bottleneck inhibiting large- scale deployment of fuel cell electric vehicles and competition with internal combustion engines. There has been an ongoing debate in the literature about the resistance in the catalyst layer the origin of which is unknown and exact microscopic mechanism not properly understood. The candidate causes include not only the catalysis of the ORR on the surface of platinum nanoparticles, but also the thin ionomer film inhibiting mass transport of protons, oxygen or water. The aim of this thesis is to understand the structure of thin ionomer films in the catalyst layer. To this end, we employ mesoscale dissipative particle dynamics (DPD), a well-established coarse-grained molecular dynamics method, to model such thin film confined from both sides. Our results summarised in Chapter 2 reveal a confinement-induced water clustering as well as a diffusivity anisotropy increasing with decreasing film thickness, confirming that the behaviour of a thin film is significantly different from the bulk membrane. The percolation network of water clusters and channels in the ionomer film is strongly dependent on the hydrophobicity of the confining material. In Chapter 3, we return to the bulk membrane and explore using DPD its structure and behaviour under different preparation paths. These results enable us to address the experiments by Gebel [1] and update this author’s proposed microscopic models. On the theory side, having realised that currently available computational methods such as DPD were inadequate for simulating truly realistic settings in the catalyst layer on the scale of tens of nanometres, in Chapter 6 we present our work on many-body dissipative particle dynamics (MDPD), a method suitable for simulating porous environments but so far poorly understood and impossible to apply to real systems. By varying a wide range of input parameters we uncover a rich phase diagram and devise a top-down parametrisation method based on compressibility and surface tension that enables to capture the correct behaviour of real liquids v as well as mixtures. We thoroughly discuss the role of coarse-graining degree as a simulation input and present a way to adjust simulation parameters in order to consistently predict material properties across scales. Testing on a few simple mixtures yields reasonable agreement with experiment. Besides our work on MDPD, we revisit some of the older theory behind standard DPD. In Chapter 4, we restate the role of reduced units in a clearer manner and rederive the temperature dependence of the interaction parameter. We also explain in general terms how simulation inputs need to be adjusted with respect to coarse-graining degree in order to make the outputs, which are compared with experiment, invariant across scales. In Chapter 5 we present an attempt to develop a bottom-up parametrisation for standard DPD based on clustering molecules and matching radial distribution functions. In the present form, this work should be viewed as a playground for ideas rather than a proven simulation tool. Finally, to demonstrate the power of MDPD, in Chapter 7 we apply the newly developed parametrisation method to an unconfined thin Nafion film with free space on one side, a setting inaccessible by standard DPD. These simulations should provide a more reliable view on the structure of the thin ionomer film in the catalyst layer. We find out that films of thickness of 5 nm or less cannot accommodate water inside and, as a result, have hydrophilic outer surfaces. Surface hydrophobicity increases with film thickness and decreases with water content, with important consequences for fuel cell operation.