High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits
It is found that simple insulating motifs can suppress retroactivity at a low fuel cost by coupling only weakly to the upstream system, but this design approach reduces the signalling network's robustness to perturbations from leak reactions, and potentially compromises its ability to respond to rapidly-varying signals.
Optimizing enzymatic catalysts for rapid turnover of substrates with low enzyme sequestration
- BiologyBiol. Cybern.
This article analyses the mechanism of enzyme-substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, while maintaining at least a minimum reaction flux and finds that the optimal design will saturate the bound on the minimal flux and reflects a basic trade-off in catalytic operation.
A control theoretic framework for modular analysis and design of biomolecular networks
- Computer ScienceAnnu. Rev. Control.
Synthetic biology by controller design
The progression of control systems design in synthetic biology is discussed, from the purpose of understanding the function of naturally occurring regulatory motifs to that of creating genetic circuits whose function is sufficiently robust for biotechnology applications.
NSF Workshop: Systems and Control Theory for Synthetic Biology
The engineering of biological systems, whether within the cell (bacterial or mammalian) or in cell-free extracts, can be applied to a number of areas, ranging from diagnostic, biosafety (i.e.…
Zebrafish airinemes optimize their shape between ballistic and diffusive search
The shape of airinemes in zebrafish are demonstrated to be consistent with a finite persistent random walk model, and the ability of the target cell to infer direction of the airineme’s source is explored, finding that there is a theoretical trade-off between search optimality and directional information.
26th International Conference on DNA Computing and Molecular Programming, DNA 26, September 14-17, 2020, Oxford, UK (Virtual Conference)
It is proved that if a graph admits an embedding in a torus that is not checkerboard colorable, then it can be re-embedded so that all its non-intersecting Eulerian circuits are knotted.
Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts
This work proposes a new framework for constructing catalytic DSD networks: Active Circuits of Duplex Catalysts (ACDC), and analyzes the capability of the framework to implement catalytic circuits analogous to phosphorylation networks in living cells.
In pursuit of mathematical principles in systems biology
• A submitted manuscript is the author's version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published…
Precision and Sensitivity in Detailed-Balance Reaction Networks
- Computer ScienceSIAM J. Appl. Math.
This work gives various upper and lower bounds on the optimal values of Sensitivity and Precision, characterized in terms of the stoichiometry, by using a combination of ideas from matroid theory and differential-equation theory.
SHOWING 1-10 OF 65 REFERENCES
Modular cell biology: retroactivity and insulation
- BiologyMolecular systems biology
Here, the effect of interconnections on the input–output dynamic characteristics of transcriptional components are studied, focusing on a property, which is called ‘retroactivity’, that plays a role analogous to non‐zero output impedance in electrical systems.
Dissecting the puzzle of life: modularization of signal transduction networks
- BiologyComput. Chem. Eng.
Selected Papers On Mathematical Trends In Control Theory
Stability and error bounds in the numerical integration of ordinary differential equations
Modularity, Retroactivity, and Structural Identification
This paper first reviews one popular reverse-engineering technique, introduced by the author and collaborators, and discusses why conclusions drawn from its (mis-)use may be misleading due to ‘retroactivity’ (impedance or load) effects.
GTPase activating proteins: critical regulators of intracellular signaling.
- BiologyBiochimica et biophysica acta
Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis.
- BiologyAnnual review of genetics
This work has shown that activation of the Spo0A transcription factor by phosphorylation serves as a developmental checkpoint and to integrate several physiological signals that control entry into the sporulation pathway.