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
Thermodynamically Favorable Computation via Tile Self-assembly
TLDR
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
TLDR
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
TLDR
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
TLDR
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
TLDR
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
TLDR
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
TLDR
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
TLDR
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.
TLDR
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
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 controlExpand

References

SHOWING 1-10 OF 17 REFERENCES
Computing properties of stable configurations of thermodynamic binding networks
TLDR
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
Thermodynamic Analysis of Interacting Nucleic Acid Strands
TLDR
This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures. Expand
Programmable Control of Nucleation for Algorithmic Self-Assembly
TLDR
This work demonstrates that growth of objects via algorithmic self-assembly can proceed both efficiently and with an arbitrarily low error rate, even in a model where local growth rules are probabilistic. Expand
Algorithmic Self-Assembly of DNA
Summary form only given. Nucleic acids have proven to be remarkably versatile as an engineering material for chemical tasks including the storage of information, catalyzing reactions creating andExpand
An information-bearing seed for nucleating algorithmic self-assembly
TLDR
This work demonstrates how DNA origami seeds enable the easy, high-yield, low-error-rate growth of algorithmic crystals as a route toward programmable bottom-up fabrication. 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
The thermodynamics of DNA structural motifs.
TLDR
This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement. Expand
The thermodynamics of computation—a review
Computers may be thought of as engines for transforming free energy into waste heat and mathematical work. Existing electronic computers dissipate energy vastly in excess of the mean thermalExpand
Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components
TLDR
It is demonstrated that discrete three-dimensional DNA components can specifically self-assemble in solution on the basis of shape-complementarity and without base pairing, and may be finely controlled by global parameters such as cation concentration or temperature and by an allosteric mechanism based on strand-displacement reactions. 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
...
1
2
...