# Thermodynamic Binding Networks

@inproceedings{Doty2017ThermodynamicBN, title={Thermodynamic Binding Networks}, author={David Doty and Trent A. Rogers and David Soloveichik and Chris Thachuk and Damien Woods}, booktitle={DNA}, year={2017} }

Strand displacement and tile assembly systems are designed to follow prescribed kinetic rules (i.e., exhibit a specific time-evolution). However, the expected behavior in the limit of infinite time—known as thermodynamic equilibrium—is often incompatible with the desired computation. Basic physical chemistry implicates this inconsistency as a source of unavoidable error. Can the thermodynamic equilibrium be made consistent with the desired computational pathway? In order to formally study this… Expand

#### 10 Citations

Thermodynamically Favorable Computation via Tile Self-assembly

- Computer Science
- UCNC
- 2018

A definition of what it means for a TBN to perform a computation is developed, and a set of constructions which are capable of performing computations by simulating the behaviors of space-bounded Turing machines and boolean circuits are presented. Expand

Computing properties of stable configurations of thermodynamic binding networks

- Computer Science
- Theor. Comput. Sci.
- 2019

The computational hardness of natural questions about TBNs are proved and a practical algorithm for verifying the correctness of constructions is developed by translating the problem into propositional logic and solving the resulting formula. Expand

Programming Substrate-Independent Kinetic Barriers With Thermodynamic Binding Networks

- Medicine, Computer Science
- IEEE/ACM Transactions on Computational Biology and Bioinformatics
- 2021

This work extends the recently-developed model known as thermodynamic binding networks, demonstrating programmable kinetic barriers that arise solely from the thermodynamic driving forces of bond formation and the configurational entropy of forming separate complexes. Expand

Programming Substrate-Independent Kinetic Barriers with Thermodynamic Binding Networks

- Computer Science, Materials Science
- CMSB
- 2018

This work extends the recently-developed model known as thermodynamic binding networks, demonstrating programmable kinetic barriers that arise solely from the thermodynamic driving forces of bond formation and the configurational entropy of forming separate complexes. Expand

Computing Properties of Thermodynamic Binding Networks: An Integer Programming Approach

- Computer Science
- DNA
- 2021

This work forms as an integer program the NP-hard problem of computing stable configurations of a TBN (a.k.a., minimum energy: those that maximize the number of bonds and complexes), and shows that the TBN's Graver basis has a natural interpretation as the "fundamental components" out of which locally minimal energy configurations are composed. Expand

Contrasting Geometric Variations of Mathematical Models of Self-assembling Systems

- Computer Science
- 2019

This thesis explores multiple augmentations of well known models of self-assembly to gain a better understanding of the roles that geometry and space play in their dynamics. Expand

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly

- Computer Science, Medicine
- Nature
- 2019

A set of 355 self-assembling DNA ‘tiles’ can be reprogrammed to implement many different computer algorithms—including sorting, palindrome testing and divisibility by three—suggesting that molecular self-assembly could be a reliable algorithmic component in programmable chemical systems. Expand

Limitations on counting in Boolean circuits and self-assembly

- Computer Science
- ArXiv
- 2020

This work defines a Boolean circuit model, called $n$-wire local railway circuits, where parallel wires are straddled by Boolean gates, each with matching fanin/fanout strictly less than $n, and shows that such a model can not count to $2^n$ nor implement any so-called odd bijective nor quasi-bijective function. Expand

A Loser-Take-All DNA Circuit.

- Medicine
- ACS synthetic biology
- 2021

A DNA strand-displacement implementation of loser-take-all circuits that is cascadable without dual-rail representation, maintaining the simplicity desired for scalability and could be more generally applied in other DNA circuit implementations including k-winner- take-all. Expand

Tenure Research Statement

- 2020

The history of technology is that of honing our ability to manipulate matter using top-down principles: chopping wood, welding metal, etc. Yet many of the traditional forms of top-down manual control… Expand

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