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Recent advances in measurement technology provide us with rich source of data for estimating parameters in biomolecular circuit models, particularly in simplified in vitro transcription-translation systems, so-called molecular “bread-boards”. In this paper, we elaborate on a mass action type dynamic model for such an in vitro system and detail a parameter estimation procedure that may be used with...
Kinetic systems form a wide nonlinear system class with good descriptive power that can efficiently be used for the dynamical modeling of non-negative models emerging not only in (bio)chemistry but in other important scientific and engineering fields as well. The directed graph structure assigned to kinetic models give us important information about the qualitative dynamical properties of the system...
In this paper, we develop an experimentally validated MATLAB software toolbox as an accompaniment to an in vitro cell-free biomolecular “breadboard” system. The toolbox gives insight into the dynamics of unmeasured states in the cell-free system, accounting especially for resource usage. Parameter lumping and the reduced order modeling are used to maintain computational tractability and to avoid ill-conditioning...
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