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

ISBN: (纸本)9783959771634

the proceedings contain 11 papers. the topics discussed include: the topology of scaffold routings on non-spherical mesh wireframe;simplifying chemical reaction network implementations with two-stranded dna building blocks;composable computation in leaderless, discrete chemical reaction networks;CRNs exposed: a method for the systematic exploration of chemical reaction networks;population-induced phase transitions and the verification of chemical reaction networks;ALCH: an imperative language for chemical reaction network-controlled tile assembly;implementing non-equilibrium networks with active circuits of duplex catalysts;design automation of polyomino set that self-assembles into a desired shape;verification and computation in restricted tile automata;and turning machines.

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26th international conference on dna computing and molecular programming

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Leibniz international Proceedings in Informatics, LIPIcs 2020年 174卷

作者： Geary, Cody Patitz, Matthew J. Interdisciplinary Nanoscience Centre University of Aarhus Denmark Department of Computer Science and Computer Engineering University of Arkansas FayettevilleAR United States

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A Cellular Automaton Approach for Efficient computing on Surface Chemical Reaction Networks

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NEW GENERATION computing 2024年第2期42卷 217-235页

作者： Yu, Sihai Xu, Wenli Lee, Jia Isokawa, Teijiro Chongqing Univ Coll Comp Sci 174 Shazhengjie Chongqing 400044 Shapingba Peoples R China Univ Hyogo Grad Sch Engn 2167 Shosha Himeji Hyogo 6712280 Japan

A surface chemical reaction network (sCRN, Qian and Winfree in dna computing and molecular programming: 20th international conference, dna 20, Kyoto, Japan, September 22-26, 2014. Proceedings 20. Springer, 2014) is an emergent paradigm for molecular programming, in which a chemical molecule is placed at each site of a lattice, and each molecule may undergo either bi-molecular reactions associated with one of the nearest molecules or uni-molecular reactions autonomously. the lattice structure as well as the localized reactions between molecules facilitate an effective formalization of sCRNs in the framework of cellular automata. this formalism not only allows a systematic evaluation of the complexity of a sCRN, but also enables a formal approach to reduce the model's complexity for the sake of improving its effectiveness. To this end, this paper proposes a new sCRN model that has less complexity measured in terms of the numbers of both cell states and transition rules. Especially, universality of computations will be shown by implementing all asynchronous circuits, including the well-known full-adder, into the sCRN. the decreased complexity may enhance the feasibility of the proposed sCRN model for physical implementation.

关键词： molecular programming Surface CRN Cellular automata Universal computation Asynchronous circuit

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Universality of a surface chemical reaction network using only bi-molecular reactions

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JOURNAL OF MEMBRANE computing 2024年第3期6卷 169-178页

作者： Yu, Sihai Lee, Jia Isokawa, Teijiro Chongqing Univ Coll Comp Sci 174 Shazhengjie Chongqing 400044 Peoples R China Univ Hyogo Grad Sch Engn 2167 Shosha Himeji Hyogo 6712280 Japan

In recent years, a novel molecular computation model known as surface chemical reaction network (Qian, In: dna computing and molecular programming: 20th international conference, dna 20, Proceedings, 2014) has garnered significant attention. In this approach, a chemical molecule is placed at each lattice site, and each molecule undergoes bi-molecular reactions with neighboring molecules or uni-molecular reactions autonomously. the advantages of surface chemical reaction networks have facilitated new opportunities and challenges in the field of molecular programming. To accomplish more intricate computational tasks, establishing a practical computational model with lower complexity on surface chemical reaction networks becomes imperative. To this end, this paper proposes a novel model of surface chemical reaction networks using only ten species and ten reactions, the numbers of which are less than the previous model (Clamons, J R Soc Interface 17(166):20190790, 2020). In particular, this model employs merely bi-molecular reactions, by excluding all uni-molecular reactions. We show that our new model can be used to implement a universal set of Brownian circuit elements, thereby giving rise to the universality for constructing all asynchronous circuits, like the well-known logic function, called D-latch, on the surface chemical reaction network.

关键词： Surface chemical reaction network Delay-insensitive circuits molecular computation

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COMPUTATIONAL dna DROPLETS BASED ON LIQUID-LIQUID PHASE SEPARATION FOR CANCER DIAGNOSIS 26

COMPUTATIONAL DNA DROPLETS BASED ON LIQUID-LIQUID PHASE SEPA...

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26th international conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2022

作者： Gong, Jing Tsumura, Nozomi Sato, Yusuke Takinoue, Masahiro Tokyo Institute of Technology Japan Kyushu Institute of Technology Japan

ISBN: (纸本)9781733419048

We demonstrate a computational dna droplet that can recognize specific combinations of tumor marker microRNAs (miRNAs) as molecular inputs and output the results of dna logic operations through physical dna droplet phase separation, which achieves the fusion of biosensing and molecular logic computation in dna droplets. Phase-separated biomolecular droplets are formed in cells to regulate various biological processes. Such droplet systems can be reproduced by programmable phase-separated droplets, called dna droplets, as artificial intracellular compartments. We integrated biosensing and logic computing into dna droplets to achieve information processing control. We demonstrated that upon reaction with miRNAs, the computational dna droplet was phase-separated into three dna droplets and can perform miRNA pattern recognition represented by the logical formula ((miRNA-1 ∧ miRNA-2) ∧ (miRNA-3 ∧ ¬miRNA-4)). © 2022 MicroTAS 2022 - 26th international conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： dna

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Minimum Free Energy, Partition Function and Kinetics Simulation Algorithms for a Multistranded Scaffolded dna Computer 29

Minimum Free Energy, Partition Function and Kinetics Simulat...

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29th international conference on dna computing and molecular programming, dna 2023

作者： Shalaby, Ahmed thachuk, Chris Woods, Damien Hamilton Institute Department of Computer Science Maynooth University Ireland Paul G. Allen School of Computer Science & Engineering University of Washington SeattleWA United States

ISBN: (纸本)9783959772976

Polynomial time dynamic programming algorithms play a crucial role in the design, analysis and engineering of nucleic acid systems including dna computers and dna/RNA nanostructures. However, in complex multistranded or pseudoknotted systems, computing the minimum free energy (MFE), and partition function of nucleic acid systems is NP-hard. Despite this, multistranded and/or pseudoknotted systems represent some of the most utilised and successful systems in the field. this leaves open the tempting possibility that many of the kinds of multistranded and/or pseudoknotted systems we wish to engineer actually fall into restricted classes, that do in fact have polynomial time algorithms, but we've just not found them yet. Here, we give polynomial time algorithms for MFE and partition function calculation for a restricted kind of multistranded system called the 1D scaffolded dna computer. this model of computation thermodynamically favours correct outputs over erroneous states, simulates finite state machines in 1D and Boolean circuits in 2D, and is amenable to dna storage applications. In an effort to begin to ask the question of whether we can naturally compare the expressivity of nucleic acid systems based on the computational complexity of prediction of their preferred energetic states, we show our MFE problem is in logspace (the complexity class L), making it perhaps one of the simplest known, natural, nucleic acid MFE problems. Finally, we provide a stochastic kinetic simulator for the 1D scaffolded dna computer and evaluate strategies for efficiently speeding up this thermodynamically favourable system in a constant-temperature kinetic regime. © Ahmed Shalaby, Chris thachuk, and Damien Woods;licensed under Creative Commons License CC-BY 4.0.

关键词： dna

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Fast, Flexible, and Exact Minimum Flow Decompositions via ILP 26th

Fast, Flexible, and Exact Minimum Flow Decompositions via ...

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26th international conference on Research in Computational molecular Biology, RECOMB 2022

作者： Dias, Fernando H. C. Williams, Lucia Mumey, Brendan Tomescu, Alexandru I. Department of Computer Science University of Helsinki Helsinki Finland School of Computing Montana State University BozemanMT United States

ISBN: (纸本)9783031047480

Minimum flow decomposition (MFD)—the problem of finding a minimum set of paths that perfectly decomposes a flow—is a classical problem in Computer Science, and variants of it are powerful models in multiassembly problems in Bioinformatics (e.g. RNA assembly). However, because this problem and its variants are NP-hard, practical multiassembly tools either use heuristics or solve simpler, polynomial-time solvable versions of the problem, which may yield solutions that are not minimal or do not perfectly decompose the flow. Many RNA assemblers also use integer linear programming (ILP) formulations of such practical variants, having the major limitation they need to encode all the potentially exponentially many solution paths. Moreover, the only exact solver for MFD does not scale to large instances, and cannot be efficiently generalized to practical MFD variants. In this work, we provide the first practical ILP formulation for MFD (and thus the first fast and exact solver for MFD), based on encoding all of the exponentially many solution paths using only a quadratic number of variables. On both simulated and real flow graphs, our approach runs in under 13 s on average. We also show that our ILP formulation can be easily and efficiently adapted for many practical variants, such as incorporating longer or paired-end reads, or minimizing flow errors. We hope that our results can remove the current tradeoff between the complexity of a multiassembly model and its tractability, and can lie at the core of future practical RNA assembly tools. Our implementations are freely available at ***/algbio/MFD-ILP. © 2022, the Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： RNA

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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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scadnano: A browser-based, scriptable tool for designing dna nanostructures 26

scadnano: A browser-based, scriptable tool for designing DNA...

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

作者： Doty, David Lee, Benjamin L. Stérin, Tristan University of California DavisCA United States Maynooth University Ireland

ISBN: (纸本)9783959771634

We introduce scadnano (short for "scriptable cadnano"), a computational tool for designing synthetic dna structures. Its design is based heavily on cadnano [24], the most widely-used software for designing dna origami [33], with three main differences: 1. scadnano runs entirely in the browser, with no software installation required. 2. scadnano designs, while they can be edited manually, can also be created and edited by a well-documented Python scripting library, to help automate tedious tasks. 3. the scadnano file format is easily human-readable. this goal is closely aligned with the scripting library, intended to be helpful when debugging scripts or interfacing with other software. the format is also somewhat more expressive than that of cadnano, able to describe a broader range of dna structures than just dna origami. © David Doty, Benjamin L Lee, and Tristan Stérin;licensed under Creative Commons License CC-BY.

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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