In nature, viruses are self-replicating entities that differ from one another in their genomic makeup (RNA or DNA), their genome sizes (spanning two orders of magnitude), and their host-ranges (spanning all kingdoms of life), yet all viruses share the need to express their own genome-encoded functions as mRNA, direct the synthesis of their proteins using the translation machinery of their host, copy their genomes, and assemble their resulting progeny genomes in protective coatings prior to their release to the extracellular environment. However, beyond these and perhaps a few other generic attributes, common features among viruses are not so readily apparent. The most compelling conserved traits of viruses will be revealed at the integrated process level, by seeking common patterns in the dynamic networks that direct intracellular resources toward virus growth. Such patterns will be sought in three ways: by formulating and refining in-silico models for the intracellular development of three viruses that represent diverse information-processing strategies: phage T7, human immunodeficiency virus (HIV-1) and vesicular stomatitis virus (VSV); by identifying common characteristics in the intracellular development of these viruses, focusing on the dynamics and efficiencies of information, material and energy flows, and by assessing the feasibility of applying in-silico mutagenesis to generate and characterize the functional diversity within population distributions of viruses, so-called quasi-species. At the level of broader impacts, this is a highly interdisciplinary project that will employ computer simulations to characterize the dynamics and control of cellular resource processing during the development of viruses. The cross-disciplinary experience gained by students and co-workers who pursue this research, as well as the refereed publications, technical presentations and supplements to course lectures that result from this work, will contribute toward the advancement of research and education in biological information processing.
