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\section{Abstract}  The bacterial conjugation, despite of its importance, is poorly understood systemically. In this work we propose a new framework for the individual-based modeling which hinge on two main key points, namely the cell-cycle timing when conjugative is most likely to occur and the metabolic penalizations incurred by donor cells during the conjugative transfer and by the transconjugants cells once they have been infected and have to express the required gene products for the plasmid housekeeping. We have evaluated the model predictions using eight different plasmids on E. coli host.  \section{Introduction}  The Domain Bacteria encompass one of most diverse and abundant form of life on earth. Part of this diversity is certainly in part a direct consequence of a succinct genome complemented by the existence of a feature rich supra-individual gene pool which is readily available for individuals in a population through different mechanisms. One of these mechanisms is the bacterial conjugation which is basically a form of horizontal gene transfer where cluster of genes are transferred from cell to cell in some population. The plasmids, which are the fundamental unit of horizontal gene transfer, are circular double stranded DNA and they are also autonomous replicons replicating independently of bacterial chromosome and having their own life-cycle.