Numerical simulations and algorithms are developed to analyze the dynamics of the ellipsoidal-like particles in a three-dimensional spatial frame. In particular we study in this case of an open channel pore for which we calculate the PDF distributions in the bulk and in the depletion layer next to a solid boundary. We develop a theoretical model based in this case on the equations of Jeffrey for the dynamics of solid particles in fluids and the molecular dynamics by mechanical restitution for the diffusive collisions of the particles at the solid boundaries. Simulations are carried out to calculate the equilibrium PDF distributions for ellipsoidal molecular particles in suspension in a fluid under hydrodynamic flow. The simulation results for the PDF distributions for the spatial positions and the orientations of ellipsoidal particles are calculated for the bulk liquid and in the depletion layers next to an atomically flat solid surface boundary. They are calculated over several orders of magnitude of the rotational Peclet number, and for variable aspect ratios characteristic of the ellipsoidal particles under study. They demonstrate the importance and significance of modeling in a three-dimensional spatial frame as compared to the simulation results based in the Boeder approach over a two-dimensional spatial frame. In particular we are able to produce a complete topography for the PDF distributions segmented as a hierarchy in the depletion layer, covering a complete range of orientations in 3D space. The simulations permit to calculate, for the colloidal suspension, the nematic order parameter over its tensorial representation, for a variety of forms of ellipsoidal particles selected to correspond to real polymer particles. Our results for the nematic order parameter which may be calculated locally inside the space of the depletion layer are innovating and represent a new input as regards these systems. (C) 2013 Elsevier Ltd. All rights reserved.