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Due to the physical limitations on the speed of individual processors, we are currently experiencing a paradigm shift in computer architecture towards multi-processor, multi-core and multi-subcore systems. In order to take full advantage of these new architectures, some of the basic models, algorithms and data structures in Molecular Dynamics simulations need to be re-thought. In this paper, I present some simple, generic algorithmic considerations that can improve the performance of such simulations on the IBM Cell Broadband Engine Architecture, a multi-subcore processor. The accumulated effects of these improvements are on par with what can be achieved with hand-tuned architecture-specific optimizations in the innermost loops of the simulation. [ABSTRACT FROM AUTHOR]