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Molecular programming aims to systematically engineer molecular and chemical systems of autonomous function and ever-increasing complexity. A key goal is to develop embedded control circuitry within a chemical system to direct molecular events. Here we show that systems of DNA molecules can be constructed that closely approximate the dynamic behavior of(More)
A highly desired part of the synthetic biology toolbox is an embedded chemical microcontroller, capable of autonomously following a logic program specified by a set of instructions, and interacting with its cellular environment. Strategies for incorporating logic in aqueous chemistry have focused primarily on implementing components, such as logic gates,(More)
Fault-tolerance is a critical issue for biochemical computation. Recent theoretical work on algorithmic self-assembly has shown that error correcting tile sets are possible, and that they can achieve exponential decrease in error rates with a small increase in the number of tile types and the scale of the construction [24, 4]. Following [17], we consider(More)
Biological organisms perform complex information processing and control tasks using sophisticated biochemical circuits, yet the engineering of such circuits remains ineffective compared with that of electronic circuits. To systematically create complex yet reliable circuits, electrical engineers use digital logic, wherein gates and subcircuits are composed(More)
Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to(More)
Motivated by the intriguing complexity of biochemical circuitry within individual cells we study Stochastic Chemical Reaction Networks (SCRNs), a formal model that considers a set of chemical reactions acting on a finite number of molecules in a well-stirred solution according to standard chemical kinetics equations. SCRNs have been widely used for(More)
Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology, CRNs are a promising language for the design of artificial molecular control circuitry. Nonetheless, despite the(More)
Molecular self-assembly is a promising approach to bottom-up fabrication of complex structures. A major impediment to the practical use of self-assembly to create complex structures is the high rate of error under existing experimental conditions. Recent theoretical work on algorithmic self-assembly has shown that under a realistic model of tile addition(More)