Browsing Selected Publications by Title
Now showing items 1-20 of 21
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Automatic Quantifications of Dynamics of Genetic Circuits in a Single Cell in Chemostat
(2015-08-31)Modular design of genetic circuits requires iterations of experimental and theoretical efforts to make the design process reliable and the resulting behaviors predictable. This technical report demonstrates a fully automatic ... -
Competition for binding targets results in paradoxical effects for simultaneous activator and repressor action - Extended Version
(2024-03-21)In the context of epigenetic transformations in cancer metastasis, a puzzling effect was recently discovered, in which the elimination (knock-out) of an activating regulatory element leads to increased (rather than decreased) ... -
Controller design under safety specifications for a class of bounded hybrid automata
(IEEE, 2016-12)Motivated by driver-assist systems that warn the driver before taking control action, we study the safety problem for a class of bounded hybrid automata. We show that for this class there exists a least restrictive safe ... -
Design of a lane departure driver-assist system under safety specifications
(2016-03-04)We use a controlled invariance approach to design a semi-autonomous lane departure assist system that is guaranteed to keep the vehicle in the lane. The controlled invariant safe set is the set of system states from which ... -
A Dynamical Model for the Low Efficiency of Induced Pluripotent Stem Cell Reprogramming (Extended Version)
(2016-03-22)In the past decade, researchers have been able to obtain pluripotent stem cells directly from an organism’s differentiated cells through a process called cell reprogramming. This opens the way to potentially groundbreaking ... -
Error Bound for Hill-Function Approximations in a Class of Stochastic Transcriptional Network Models
(2023-04-01)Hill functions are often used in stochastic models of gene regulation to approximate the dependence of gene activity on the concentration of the transcription factor which regulates the gene. It is incompletely known, ... -
Genetic Circuit-Host Ribosome Transactions: Diffusion-Reaction Model
(2018-09-18)Deterministic models of bacterial genetic circuits commonly assume a well-mixed ensemble of species. This assumption results in ordinary differential equations (ODEs) describing the rate of change of the mean species ... -
Mitigation of ribosome competition through distributed sRNA feedback (extended version)
(2016-09-23)A current challenge in the robust engineering of synthetic gene networks is context dependence, the unintended interactions among genes and host factors. Ribosome competition is a specific form of context dependence, where ... -
An N-stage Cascade of Phosphorylation Cycles as an Insulation Device for Synthetic Biological Circuits
(2016-03-27)Single phosphorylation cycles have been found to have insulation device abilities, that is, they attenuate the effect of retroactivity applied by downstream systems and hence facilitate modular design in synthetic ... -
The Number of Equilibrium Points of Perturbed Nonlinear Positive Dynamical Systems (Extended Version)
(2019-07-26)The number of equilibrium points of a dynamical system dictates important qualitative properties such as the ability of the system to store different memory states, and may be significantly affected by state-dependent ... -
Robust model invalidation for chemical reaction networks using generalized moments (extended version)
(2023-03-31)Many biomolecular systems can be described by chemical reaction networks. Determining which chemical reaction network models are inconsistent with observed data can be done via model invalidation. In this work, we formulate ... -
Robust model invalidation for chemical reaction networks using generalized moments (extended version)
(2023-03-31)Many biomolecular systems can be described by chemical reaction networks. Determining which chemical reaction network models are inconsistent with observed data can be done via model invalidation. In this work, we formulate ... -
Signaling architectures that transmit unidirectional information
(2016-12-24)A signaling pathway transmits information from an upstream system to downstream systems, ideally unidirectionally. A key bottleneck to unidirectional transmission is retroactivity, which is the additional reaction flux ...