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In vitro compartmentalization of biochemical reaction networks is a crucial step towards engineering artificial cell-scale devices and systems. At this scale the dynamics of molecular systems becomes stochastic, which introduces several engineering challenges and opportunities. Here we study a programmable transcriptional oscillator system that is(More)
The realization of artificial biochemical reaction networks with unique functionality is one of the main challenges for the development of synthetic biology. Due to the reduced number of components, biochemical circuits constructed in vitro promise to be more amenable to systematic design and quantitative assessment than circuits embedded within living(More)
—This paper addresses the problem of cooperative control of a team of distributed agents with decoupled nonlinear discrete-time dynamics, which operate in a common environment and exchange-delayed information between them. Each agent is assumed to evolve in discrete-time, based on locally computed control laws, which are computed by exchanging delayed state(More)
— This paper proposes a synthetic in vitro circuit that aims at regulating the rate of RNA transcription through positive feedback interactions. This design is dual to a previously synthesized transcriptional rate regulator based on self-repression. Two DNA templates are designed to interact through their transcripts, creating cross activating feedback(More)
— This paper describes a synthetic in vitro genetic circuit programmed to work as an insulating device. This circuit is composed of nucleic acids, which can be designed to interact according to user defined rules, and of few proteins that perform catalytic functions. A model of the circuit is derived from first principle biochemical laws. This model is(More)
— The objective of the paper is the design of a stabilizing switching control scheme for a class of nonlinear systems. Such systems are relevant to nonlinear plants represented by means of a finite set of nonlinear discrete–time models. A finite set of receding–horizon control laws is defined for each of the nonlinear discrete–time models representing the(More)
— In this paper we consider a set of dynamically decoupled systems interconnected by control agents. We can visualize this architecture as a graph where subsystems are associated to nodes and control agents are associated to arcs. The interconnection between subsystems is determined by their input matrix. The decisions of each control agent can directly(More)
— We design a new negative feedback molecular oscillator and study its properties analytically and numerically. This oscillator is composed of two synthetic genes interconnected through their RNA outputs. Regulation of the genes activity is achieved by controlling the activity of the enzymes rather than the activity of the promoters. We show that a simple(More)
— We design a new biomolecular circuit with the potential for bistable behavior. We study this candidate toggle switch and find sufficient conditions on key parameters that guarantee bistability. The circuit structure is based on a positive feedback loop created by the mutual repression of two synthetic genes. Repression is generated not by direct(More)