Asphaltenes are known as the “cholesterol” of crude oil. They form nanoaggregates, precipitate, adhere to surfaces, block rock pores, and may alter the wetting characteristics of mineral surfaces within the reservoir, hindering oil recovery efficiency. Despite a significant research effort, the structure, aggregation, and deposition of asphaltenes under flowing conditions remain poorly understood. For this reason, we have investigated asphaltenes, their aggregation, and their deposition in capillary flow using multi-scale simulations and experiments. At the colloid scale, we use a hybrid simulation approach. For the solvent, we used the stochastic rotation dynamics (also known as multi-particle collision dynamics) simulation method, which provides both hydrodynamics and Brownian motion. This is coupled to a coarse-grained molecular dynamics (MD) approach for the asphaltene colloids. The colloids interact through a screened Coulomb potential with varying well depth ε. Here, we present results for deposition of asphaltenes in their whole oil in comparison to our previous results on extracted asphaltenes. Imposing a constant pressure drop over the capillary length, we observe that the transient solvent flow rate decreases with an increasing well depth ε. We find that the dimensionless conductivity measured in the experiment can be well-matched by simulation results using an interaction potential well depth of 8kBT. This means that extracted asphaltenes are more sticky than asphaltenes in whole oil. The interactions between the mesoscopic asphaltene colloids can be related to atomistic MD simulations. Molecular structures for the atomistic calculations were obtained using the quantitative molecular representation approach. Using these structures, we calculate the potential of mean force (PMF) between pairs of asphaltene molecules in an explicit solvent. We obtain a reasonable fit using a −1/r2 attraction for the attractive tail of the PMF at intermediate distances. We speculate that this is due to the two-dimensional nature of the asphaltene molecules. Finally, we discuss how we can relate this interaction to the mesoscopic colloid aggregate interaction. We assume that the colloidal aggregates consist of nanoaggregates. Taking into account observed solvent entrainment effects, we deduct the presence of lubrication layers between the nanoaggregates, which leads to a significant screening of the direct asphaltene−asphaltene interactions.