, Volume 3, Issue 4, pp 461-477

Virtual test tubes

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Abstract

By their structure and operation, biomolecules have resolved fundamental problems as a distributed computational system that we are just beginning to unveil. One advantageous approach to gain a good understanding of the processes and algorithms involved is simulation on conventional computers. Simulations allow better understanding of the capabilities of molecules because they can occur at the level of reliability, efficiency, and programmability that are standard in conventional computation and are desirable for experiments in vitro. Here, we describe in some detail the architecture of a general-purpose simulation environment in silico, EdnaCo, establish its soundness and reliability, and benchmark its performance. The system can be described as an emulation of the events in a real test tube. We describe the major pieces of its architecture, namely, a distributed memory (file) system, a kinetic engine, and input/output mechanisms. Finally, the ability of this environment in preserving major features of the wet counterpart in vitro is evaluated via an implementation on a cluster of PCs. The results of several simulations are summarized that establish the soundness, utility, applicability, and cost efficiency of the software to facilitate experimentation in vitro.