Name
Abstract | ||
|---|---|---|
Modularity plays a fundamental role in the pre- diction of the behavior of a system from the behavior of its components, guaranteeing that the properties of individ- ual components do not change upon interconnection. Just as electrical, hydraulic, and other physical systems often do not display modularity, nor do many biochemical systems, and specifically, genetic and signaling networks. Here, we stud y the effect of interconnections on the input/output dynamic characteristics of transcriptional components, focusing on a concept, which we call "retroactivity" that plays a role similar to impedance in electrical circuits. In order to attenuate the effect of retroactivity on a system dynamics, we propose to design insulation devices based on a feedback mechanism inspired by the design of amplifiers in electronics. In particular, we introduce a bio-molecular realization of an insulation device based on phosphorylation.1 example the oscillator of (4) as a source generator to be employed to synchronize a number of downstream tran- scriptional processes. The oscillator is "interconnected " with these downstream processes by having one of the proteins of the oscillator be a transcription factor for the downstre am transcriptional processes. These downstream processes in turn act as a load on the oscillator by using up its output protein and by thus affecting its dynamics. We broadly call retroactivity the phenomenon by which the behavior of an upstream component changes upon interconnection. The above considerations strongly motivate the need for a novel theoretical framework to formally define and quantify retroactivity effects. In this paper, we review a recently pro- posed framework for studying, characterizing, and designing systems with retroactivity (5-7). We illustrate this frame work with engineering and biological examples, and study general approaches to the reduction of retroactivity by setting a |
Year | DOI | Venue |
|---|---|---|
2009 | 10.3166/ejc.15.389-397 | Control Conference |
Keywords | DocType | Volume |
association,biochemistry,biomimetics,biomolecular electronics,feedback,genetics,insulators,interconnected systems,interconnections,molecular biophysics,molecular configurations,reaction kinetics theory,amplifier design,biochemical system,biomolecular system,component behavior,component interconnection effect,component property change,electrical circuit impedance,electrical system,electronics,engineering principle,feedback mechanism,genetic network,hydraulic system,input-output dynamic characteristics,insulation device design,modularity,phosphorylation,physical system,retroactivity effect attenuation,signaling network,system behavior prediction,system dynamics,transcriptional component,oscillations,input output,singular perturbation,transcription factor,electrical circuit | Journal | 15 |
Issue | ISSN | ISBN |
3-4 | 0947-3580 | 978-3-9524173-9-3 |
Citations | PageRank | References |
5 | 0.56 | 1 |
Authors | ||
2 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Domitilla Del Vecchio | 1 | 515 | 57.22 |
| Eduardo D. Sontag | 2 | 3134 | 781.88 |