Programming Chemical Kinetics: Engineering Dynamic Reaction Networks with DNA Strand Displacement

@inproceedings{Srinivas2015ProgrammingCK,
  title={Programming Chemical Kinetics: Engineering Dynamic Reaction Networks with DNA Strand Displacement},
  author={Niranjan Srinivas},
  year={2015}
}
Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the… Expand
Noise Control for DNA Computing
TLDR
The noise-control algorithm for designing biochemical networks is developed, which structurally modifies any given reaction network under mass-action kinetics, in such a way that controllable state-dependent noise is introduced into the stochastic dynamics, while (ii) the deterministic dynamics are preserved. Expand
Analog Computation by DNA Strand Displacement Circuits.
TLDR
This work proposes an architecture for the systematic construction of DNA circuits for analog computation based on DNA strand displacement, and describes how DNA circuits to compute polynomial functions of inputs can be built. Expand
The Design Space of Strand Displacement Cascades with Toehold-Size Clamps
TLDR
This paper systematize the properties of the simplest of strand displacement cascades (a translator) with toehold-size clamps and finds a rich and diverse landscape for desired and undesired properties and trade-offs between them. Expand
Design and Analysis of Compact DNA Strand Displacement Circuits for Analog Computation Using Autocatalytic Amplifiers.
TLDR
A novel architecture to build compact DNA strand displacement circuits to compute a broad scope of functions in an analog fashion is proposed, inspired by Napier's use of logarithm transforms to compute square roots on a slide rule. Expand
DNA Strand-Displacement Timer Circuits.
TLDR
It is demonstrated that a simple synthetic DNA strand-displacement circuit can release target sequences of DNA into solution at a constant rate after a tunable delay that can range from hours to days. Expand
DNA Computing and Molecular Programming: 25th International Conference, DNA 25, Seattle, WA, USA, August 5–9, 2019, Proceedings
TLDR
Stochastic local search could be an important aspect of biological computation and should be exploited when engineering future artificial intelligence systems, as well as for search and thus for finding solutions to problems. Expand
A Formal Combinational Logic Synthesis With Chemical Reaction Networks
TLDR
Five systematic approaches of synthesizing combinational logic with chemical reactions are proposed, and a Karnaugh map, which well depicts the logic function of a certain CRN system, is required. Expand
Verifying Chemical Reaction Network Implementations: A Bisimulation Approach
TLDR
It is shown that by interpreting each implementation species as a set of formal species, the concept of weak bisimulation can be adapted to CRNs in a way that agrees with an intuitive notion of a correct implementation. Expand
Computational complexity of atomic chemical reaction networks
TLDR
The computational complexity of deciding whether a given network is atomic according to each of these definitions is investigated and equivalence relationships between these definitions and some cases of an existing definition of atomicity due to Gnacadja are demonstrated. Expand
A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities
TLDR
A CRN-to-DSD compiler, Nuskell, that makes a first step in this direction and to support the wide range of translation schemes that have already been proposed in the literature, as well as potential new ones that are yet to be proposed. Expand
...
1
2
...

References

SHOWING 1-10 OF 231 REFERENCES
Programmable chemical controllers made from DNA.
TLDR
This work implements several building-block reaction types and combines them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents. Expand
Programming an in vitro DNA oscillator using a molecular networking strategy
TLDR
The results show that the rational cascading of standard elements opens the possibility to implement complex behaviours in vitro, and these synthetic systems may thus accelerate the understanding of the underlying principles of biological dynamic modules. Expand
Abstractions for DNA circuit design
TLDR
A programming language for designing DNA strand displacement devices is presented, which allows device designs to be programmed using a common syntax and then analysed at varying levels of detail, with or without interference, without needing to modify the program. Expand
Computer-assisted design for scaling up systems based on DNA reaction networks
TLDR
DACCAD, a computer-assisted design software that supports the construction of systems for the DNA toolbox, illustrates its effectiveness by designing various systems, and highlights a variety of behaviours, such as enzymatic saturation and load effect, which would be hard to handle or even predict with a simpler model. Expand
Dynamic DNA-toolbox reaction circuits: a walkthrough.
TLDR
This paper defines a set of in vitro, DNA-based molecular transformations that can be linked to each other in such a way that the product of one transformation can activate or inhibit the production of one or several other DNA compounds, and shows how these reactions can be wired in arbitrary networks. Expand
Automated design of programmable enzyme-driven DNA circuits.
TLDR
This work presents an automated design procedure for generating optimal DNA sequences, exhibiting key characteristics deduced from the in silico analysis, and experimentally characterize unproductive sequestration of the exonuclease to phosphorothioate protected ssDNA strands. Expand
Programmability of Chemical Reaction Networks
TLDR
This work surveys known connections and gives new connections between SCRNs and Boolean Logic Circuits, Vector Addition Systems, Petri Nets, Gate Implementability, Primitive Recursive Functions, Register Machines, Fractran, and Turing Machines. Expand
Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA
TLDR
A design strategy is introduced that allows a specified input oligonucleotide to catalyze the release of a specified output oligon nucleotide, which in turn can serve as a catalyst for other reactions, which provides an amplifying circuit element that is simple, fast, modular, composable, and robust. Expand
A programming language for composable DNA circuits
TLDR
A programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism and includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure is presented. Expand
Efficient Turing-Universal Computation with DNA Polymers
TLDR
This work proposes a chemical implementation of stack machines -- a Turing-universal model of computation similar to Turing machines -- using DNA strand displacement cascades as the underlying chemical primitive, controlled by strand displacement logic. Expand
...
1
2
3
4
5
...