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Information technologies enable programmers and engineers to design and synthesize systems of startling complexity that nonetheless behave as intended. This mastery of complexity is made possible by a hierarchy of formal abstractions that span from high-level programming languages down to low-level implementation specifications, with rigorous connections between the levels. DNA nanotechnology presents us with a new molecular information technology whose potential has not yet been fully unlocked in this way. Developing an effective hierarchy of abstractions may be critical for increasing the complexity of programmable DNA systems. Here, we build on prior practice to provide a new formalization of ‘domain-level’ representations of DNA strand displacement systems that has a natural connection to nucleic acid biophysics while still being suitable for formal analysis. Enumeration of unimolecular and bimolecular reactions provides a semantics for programmable molecular interactions, with kinetics given by an approximate biophysical model. Reaction condensation provides a tractable simplification of the detailed reactions that respects overall kinetic properties. The applicability and accuracy of the model is evaluated across a wide range of engineered DNA strand displacement systems. Thus, our work can serve as an interface between lower-level DNA models that operate at the nucleotide sequence level, and high-level chemical reaction network models that operate at the level of interactions between abstract species.
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SwitchLog: A Logic Programming Language for Network Switches
The development of programmable switches such as the Intel Tofino has allowed network designers to implement a wide range of new in-network applications and network control logic. However, current switch programming languages, like P4, operate at a very low level of abstraction. This paper introduces SwitchLog, a new experimental logic programming language designed to lift the level of abstraction at which network programmers operate, while remaining amenable to efficient implementation on programmable switches. SwitchLog is inspired by previous distributed logic programming languages such as NDLog, in which programmers declare a series of facts, each located at a particular switch in the network. Logic programming rules that operate on facts at different locations implicitly generate network communication, and are updated incrementally, as packets pass through a switch. In order to ensure these updates can be implemented efficiently on switch hardware, SwitchLog imposes several restrictions on the way programmers can craft their rules. We demonstrate that SwitchLog can be used to express a variety of networking applications in a mere handful of lines of code.
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- Award ID(s):
- 2223515
- PAR ID:
- 10430321
- Editor(s):
- Hanus, Michael; Inclezan, Daniela
- Date Published:
- Journal Name:
- Practical Aspects of Declarative Languages
- Page Range / eLocation ID:
- 180-196
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1007/978-3-031-24841-2_12
