Flow models for efficient simulation and engineering of transcription and translation elongation

Gene expression is a fundamental cellular process by which proteins are synthesized based on the information coded in the genes. Understanding, modeling and engineering this process have both important biotechnological applications and contributions to basic life science. In this paper I describe the flow models - a new approach for computationally modeling the biophysics of gene expression. The flow models can describe various stages of gene expression in a computationally efficient manner; in addition, they can be more readily analyzed mathematically than alternative models. Thus, these models provide a comprehensive framework for in-silico engineering of gene expression.