We have succeeded in extending the Brownian dynamics analyses to systems consisting of nonspherical nanoparticles interconnected by conservative forces or holonomic constraints. The formal theory takes fully into account both nanoparticle size and surface topography. Our theory also incorporates stretching, bending and torsional stiffness between nearest neighbor subunits, excluded volume effects, external force fields, fluid flow and fluid-dynamic interactions. The generalized conformation space diffusion equations are rigorously derived from kinetic theory. The equivalent stochastic differential equations are used as our basis for development of the associated Brownian dynamics algorithms. These algorithms may be employed to carry out equilibrium as well as non-equilibrium simulations of the conformational dynamics and transport properties for a wide class of nanoparticle systems embedded in viscous fluids. To test the validity of the theory and the numerical algorithms, we present the results from a simulation example. (C) 2004 Elsevier Ltd. All rights reserved.