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Parallel pairwise operations on data stored in dna: Sorting, shifting, and searching 27

Parallel pairwise operations on data stored in dna: Sorting,...

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27th international conference on dna computing and molecular programming, dna 2021

作者： Chen, Tonglin Solanki, Arnav Riedel, Marc Department of Electrical and Computer Engineering University of Minnesota MinneapolisMN United States

ISBN: (纸本)9783959772051

Prior research has introduced the Single-Instruction-Multiple-Data paradigm for dna computing (SIMD dna). It offers the potential for storing information and performing in-memory computations on dna, with massive parallelism. this paper introduces three new SIMD dna operations: Sorting, shifting, and searching. Each is a fundamental operation in computer science. Our implementations demonstrate the effectiveness of parallel pairwise operations with this new paradigm. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： Sorting

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computing Real Numbers with Large-Population Protocols Having a Continuum of Equilibria 28

Computing Real Numbers with Large-Population Protocols Havin...

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28th international conference on dna computing and molecular programming, dna 2022

作者： Huang, Xiang Huls, Rachel N. Department of Computer Science University of Illinois Springfield United States Department of Mathematics University of Illinois Springfield United States

ISBN: (纸本)9783959772532

Bournez, Fraigniaud, and Koegler [6] defined a number in [0,1] as computable by their Large-Population Protocol (LPP) model, if the proportion of agents in a set of marked states converges to said number over time as the population grows to infinity. the notion, however, restricts the ordinary differential equations (ODEs) associated with an LPP to have only finitely many equilibria. this restriction places an intrinsic limitation on the model. As a result, a number is computable by an LPP if and only if it is algebraic, namely, not a single transcendental number can be computed under this notion. In this paper, we lift the finitary requirement on equilibria. that is, we consider systems with a continuum of equilibria. We show that essentially all numbers in [0,1] that are computable by bounded general-purpose analog computers (GPACs) or chemical reaction networks (CRNs) can also be computed by LPPs under this new definition. this implies a rich series of numbers (e.g., the reciprocal of Euler’s constant, π/4, Euler’s γ, Catalan’s constant, and Dottie number) are all computable by LPPs. Our proof is constructive: We develop an algorithm that transfers bounded GPACs/CRNs into LPPs. Our algorithm also fixes a gap in Bournez et al.’s construction of LPPs designed to compute any arbitrary algebraic number in [0,1]. © Xiang Huang and Rachel N. Huls.

关键词： Analog computers

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computing properties of thermodynamic binding networks: An integer programming approach 27

Computing properties of thermodynamic binding networks: An i...

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27th international conference on dna computing and molecular programming, dna 2021

作者： Haley, David Doty, David University of California DavisCA United States

ISBN: (纸本)9783959772051

the thermodynamic binding networks (TBN) model [9] is a tool for studying engineered molecular systems. the TBN model allows one to reason about their behavior through a simplified abstraction that ignores details about molecular composition, focusing on two key determinants of a system's energetics common to any chemical substrate: How many molecular bonds are formed, and how many separate complexes exist in the system. We formulate as an integer program the NP-hard problem of computing stable (a.k.a., minimum energy) configurations of a TBN: those configurations that maximize the number of bonds and complexes. We provide open-source software [13] solving this integer program. We give empirical evidence that this approach enables dramatically faster computation of TBN stable configurations than previous approaches based on SAT solvers [3]. Furthermore, unlike SAT-based approaches, our integer programming formulation can reason about TBNs in which some molecules have unbounded counts. these improvements in turn allow us to efficiently automate verification of desired properties of practical TBNs. Finally, we show that the TBN has a natural representation with a unique Hilbert basis describing the "fundamental components" out of which locally minimal energy configurations are composed. this characterization helps verify correctness of not only stable configurations, but entire "kinetic pathways" in a TBN. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： thermodynamics

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molecular machines from topological linkages 27

Molecular machines from topological linkages

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27th international conference on dna computing and molecular programming, dna 2021

作者： Breik, Keenan Luchsinger, Austin Soloveichik, David The University of Texas AustinTX United States

ISBN: (纸本)9783959772051

Life is built upon amazingly sophisticated molecular machines whose behavior combines mechanical and chemical action. Engineering of similarly complex nanoscale devices from first principles remains an as yet unrealized goal of bioengineering. In this paper we formalize a simple model of mechanical motion (mechanical linkages) combined with chemical bonding. the model has a natural implementation using dna with double-stranded rigid links, and single-stranded flexible joints and binding sites. Surprisingly, we show that much of the complex behavior is preserved in an idealized topological model which considers solely the graph connectivity of the linkages. We show a number of artifacts including Boolean logic, catalysts, a fueled motor, and chemo-mechanical coupling, all of which can be understood and reasoned about in the topological model. the variety of achieved behaviors supports the use of topological chemical linkages in understanding and engineering complex molecular behaviors. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： Binding sites

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Reactamole: Functional reactive molecular programming 27

Reactamole: Functional reactive molecular programming

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27th international conference on dna computing and molecular programming, dna 2021

作者： Klinge, Titus H. Lathrop, James I. Osera, Peter-Michael Rogers, Allison Drake University Des MoinesIA United States Iowa State University AmesIA United States Grinnell College GrinnellIA United States

ISBN: (纸本)9783959772051

Chemical reaction networks (CRNs) are an important tool for molecular programming, a field that is rapidly expanding our ability to deploy computer programs into biological systems for a variety of applications. However, CRNs are also difficult to work with due to their massively parallel nature, leading to the need for higher-level languages that allow for easier computation with CRNs. Recently, research has been conducted into a variety of higher-level languages for deterministic CRNs but modeling CRN parallelism, managing error accumulation, and finding natural CRN representations are ongoing challenges. We introduce Reactamole, a higher-level language for deterministic CRNs that utilizes the functional reactive programming (FRP) paradigm to represent CRNs as a reactive dataflow network. Reactamole equates a CRN with a functional reactive program, implementing the key primitives of the FRP paradigm directly as CRNs. the functional nature of Reactamole makes reasoning about molecular programs easier, and its strong static typing allows us to ensure that a CRN is well-formed by virtue of being well-typed. In this paper, we describe the design of Reactamole and how we use CRNs to represent the common datatypes and operations found in FRP. We also demonstrate the potential of this functional reactive approach to molecular programming by giving an extended example where a CRN is constructed using FRP to modulate and demodulate an amplitude modulated signal. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： Application programs

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Robust digital molecular design of binarized neural networks 27

Robust digital molecular design of binarized neural networks

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27th international conference on dna computing and molecular programming, dna 2021

作者： Linder, Johannes Chen, Yuan-Jyue Wong, David Seelig, Georg Ceze, Luis Strauss, Karin University of Washington Paul G. Allen School of Computer Science and Engineering SeattleWA United States Microsoft Research RedmondWA United States University of Washington Department of Bioengineering SeattleWA United States University of Washington Department of Electrical and Computer Engineering SeattleWA United States

ISBN: (纸本)9783959772051

molecular programming - a paradigm wherein molecules are engineered to perform computation - shows great potential for applications in nanotechnology, disease diagnostics and smart therapeutics. A key challenge is to identify systematic approaches for compiling abstract models of computation to molecules. Due to their wide applicability, one of the most useful abstractions to realize is neural networks. In prior work, real-valued weights were achieved by individually controlling the concentrations of the corresponding "weight" molecules. However, large-scale preparation of reactants with precise concentrations quickly becomes intractable. Here, we propose to bypass this fundamental problem using Binarized Neural Networks (BNNs), a model that is highly scalable in a molecular setting due to the small number of distinct weight values. We devise a noise-tolerant digital molecular circuit that compactly implements a majority voting operation on binary-valued inputs to compute the neuron output. the network is also rate-independent, meaning the speed at which individual reactions occur does not affect the computation, further increasing robustness to noise. We first demonstrate our design on the MNIST classification task by simulating the system as idealized chemical reactions. Next, we map the reactions to dna strand displacement cascades, providing simulation results that demonstrate the practical feasibility of our approach. We perform extensive noise tolerance simulations, showing that digital molecular neurons are notably more robust to noise in the concentrations of chemical reactants compared to their analog counterparts. Finally, we provide initial experimental results of a single binarized neuron. Our work suggests a solid framework for building even more complex neural network computation. © 2021 Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. All rights reserved.

关键词： Neural networks

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A Novel Autonomous molecular Mechanism Based on Spatially Localized dna Computation 15th

A Novel Autonomous Molecular Mechanism Based on Spatially Lo...

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15th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2020

作者： Wang, Yue Qian, Mengyao Hu, Wenxiao Wang, Luhui Dong, Yafei School of Computer Science Shaanxi Normal University Xi’an Shaanxi710119 China College of Life Science Shaanxi Normal University Xi’an Shaanxi710119 China

ISBN: (纸本)9789811613531

Contemporary dna synthesis technology matures, and the development provides intriguing possibilities for dynamic manipulation of dna self-assembly, which plays a pivotal role in the behavior of designing versatile nanodevices and generating controllable networks. Similarly, in synthetic molecular circuits, the spatially localized architecture furnishes a different strategy, allowing for immobilized dna molecules in close vicinity to each other. Herein, the formal modeling language was utilized to mark the address with a specific sequence of location tags, thus a set of routes were precisely arranged at the nanoscale. Beyond building a collection of separate modules, computer simulations were used to explore further complex assemblies of the building blocks. By orchestrating a series of dna strand displacement operations locally, autonomous movement and addressing operations were realized, completing the group transport and partition storage of dissimilar molecules. the nanodevice gives the dna molecule its mechanical properties and follows an embedded "molecular program". the simulation results of the Visual DSD tool provided qualitative and quantitative proof for the operation of the system. © 2021, Springer Nature Singapore Pte Ltd.

关键词： dna

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Ensnano: A 3d modeling software for dna nanostructures 27

Ensnano: A 3d modeling software for dna nanostructures

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27th international conference on dna computing and molecular programming, dna 2021

作者： Levy, Nicolas Schabanel, Nicolas France and Ixxi France

ISBN: (纸本)9783959772051

Since the 1990s, increasingly complex nanostructures have been reliably obtained out of self-assembled dna strands: From "simple" 2D shapes to 3D gears and articulated nano-objects, and even computing structures. the success of the assembly of these structures relies on a fine tuning of their structure to match the peculiar geometry of dna helices. Various softwares have been developed to help the designer. these softwares provide essentially four kind of tools: An abstract representation of dna helices (e.g. cadnano, scadnano, dnapen, 3dna, Hex-tiles);a 3D view of the design (e.g., vHelix, Adenita, oxdnaviewer);fully automated design (e.g., BScOR, Daedalus, Perdix, Talos, Athena), generally dedicated to a specific kind of design, such as wireframe origami;and coarse grain or thermodynamical physics simulations (e.g., oxdna, Mrdna, SNUPI, Nupack, ViennaRNA,.). Magicdna combines some of these approaches to ease the design of configurable dna origamis. We present our first step in the direction of conciliating all these different approaches and purposes into one single reliable GUI solution: the first fully usable version (design from scratch to export) of our general purpose 3D dna nanostructure design software ENSnano. We believe that its intuitive, swift and yet powerful graphical interface, combining 2D and 3D editable views, allows fast and precise editing of dna nanostructures. It also handles editing of large 2D/3D structures smoothly, and imports from the most common solutions. Our software extends the concept of grids introduced in cadnano. Grids allow to abstract and articulated the different parts of a design. ENSnano also provides new design tools which speeds up considerably the design of complex large 3D structures, most notably: A 2D split view, which allows to edit intricate 3D structures which cannot easily be mapped in a 2D view, and a copy, paste & repeat functionality, which takes advantage of the grids to design swiftly large repetitive chunks of

关键词： dna

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Simplifying chemical reaction network implementations with two-stranded dna building blocks 26

Simplifying chemical reaction network implementations with t...

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26th international conference on dna computing and molecular programming, dna 2020

作者： Johnson, Robert F. Qian, Lulu California Institute of Technology PasadenaCA United States

ISBN: (纸本)9783959771634

In molecular programming, the Chemical Reaction Network model is often used to describe real or hypothetical systems. Often, an interesting computational task can be done with a known hypothetical Chemical Reaction Network, but often such networks have no known physical implementation. One of the important breakthroughs in the field was that any Chemical Reaction Network can be physically implemented, approximately, using dna strand displacement mechanisms. this allows us to treat the Chemical Reaction Network model as a programming language and the implementation schemes as its compiler. this also suggests that it would be useful to optimize the result of such a compilation, and in general to find effective ways to design better dna strand displacement systems. We discuss dna strand displacement systems in terms of "motifs", short sequences of elementary dna strand displacement reactions. We argue that describing such motifs in terms of their inputs and outputs, then building larger systems out of the abstracted motifs, can be an efficient way of designing dna strand displacement systems. We discuss four previously studied motifs in this abstracted way, and present a new motif based on cooperative 4-way strand exchange. We then show how Chemical Reaction Network implementations can be built out of abstracted motifs, discussing existing implementations as well as presenting two new implementations based on 4-way strand exchange, one of which uses the new cooperative motif. the new implementations both have two desirable properties not found in existing implementations, namely both use only at most 2-stranded dna complexes for signal and fuel complexes and both are physically reversible. there are reasons to believe that those properties may make them more robust and energy-efficient, but at the expense of using more fuel complexes than existing implementation schemes. © Robert F. Johnson and Lulu Qian;licensed under Creative Commons License CC-BY.

关键词： dna

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the topology of scaffold routings on non-spherical mesh wireframes 26

The topology of scaffold routings on non-spherical mesh wire...

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26th international conference on dna computing and molecular programming, dna 2020

作者： Mohammed, Abdulmelik Jonoska, Nataa Saito, Masahico Department of Mathematics and Statistics University of South Florida TampaFL United States

ISBN: (纸本)9783959771634

the routing of a dna-origami scaffold strand is often modelled as an Eulerian circuit of an Eulerian graph in combinatorial models of dna origami design. the knot type of the scaffold strand dictates the feasibility of an Eulerian circuit to be used as the scaffold route in the design. Motivated by the topology of scaffold routings in 3D dna origami, we investigate the knottedness of Eulerian circuits on surface-embedded graphs. We show that certain graph embeddings, checkerboard colorable, always admit unknotted Eulerian circuits. On the other hand, we prove that if a graph admits an embedding in a torus that is not checkerboard colorable, then it can be re-embedded so that all its non-intersecting Eulerian circuits are knotted. For surfaces of genus greater than one, we present an infinite family of checkerboard-colorable graph embeddings where there exist knotted Eulerian circuits. © Abdulmelik Mohammed, Nataa Jonoska, and Masahico Saito;licensed under Creative Commons License CC-BY.

关键词： dna

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