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21st international conference on dna computing and molecular programming, 2015

ISBN: (纸本)9783319219981

The proceedings contain 13 papers. The special focus in this conference is on dna computing and molecular programming. The topics include: Dominance and T-invariants for petri nets and chemical reaction networks;synthesizing and tuning chemical reaction networks with specified behaviours;universal computation and optimal construction in the chemical reaction network-controlled tile assembly model;optimal program-size complexity for self-assembly at temperature 1 in 3D;concentration independent coin flips in tile self-assembly;new geometric algorithms for fully connected staged self-assembly;leader election and shape formation with self-organizing programmable matter;leakless dna strand displacement systems;supervised learning in an adaptive dna strand displacement circuit;automated design and verification of localized dna computation circuits;on low energy barrier folding pathways for nucleic acid sequences and stochastic simulation of the kinetics of multiple interacting nucleic acid strands.

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dna computing and molecular programming: 21st international conference, dna 21 Boston and Cambridge, MA, USA, August 17-21, 2015 Proceedings 21st

DNA Computing and Molecular Programming: 21st International ...

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21st international conference on dna computing and molecular programming, 2015

作者： Phillips, Andrew Yin, Peng Microsoft Research Cambridge United Kingdom Wyss Institute BostonMA United States

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Reflections on tiles (in self-assembly)

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NATURAL computing 2017年第2期16卷 295-316页

作者： Hendricks, Jacob Patitz, Matthew J. Rogers, Trent A. Univ Wisconsin Dept Comp Sci & Informat Syst River Falls WI 54022 USA Univ Arkansas Dept Comp Sci & Comp Engn Fayetteville AR 72701 USA

We define the Reflexive Tile Assembly Model (RTAM), which is obtained from the abstract Tile Assembly Model (aTAM) by allowing tiles to reflect across their horizontal and/or vertical axes. We show that the class of directed temperature-1 RTAM systems is not computationally universal, which is conjectured but unproven for the aTAM, and like the aTAM, the RTAM is computationally universal at temperature 2. We then show that at temperature 1, when starting from a single tile seed, the RTAM is capable of assembling squares for n odd using only n tile types, but incapable of assembling squares for n even. Moreover, we show that n is a lower bound on the number of tile types needed to assemble squares for n odd in the temperature-1 RTAM. The conjectured lower bound for temperature-1 aTAM systems is . Finally, we give preliminary results toward the classification of which finite connected shapes in can be assembled (strictly or weakly) by a singly seeded (i.e. seed of size 1) RTAM system, including a complete classification of which finite connected shapes can be strictly assembled by mismatch-free singly seeded RTAM systems.

关键词： Self-assembly Tile assembly model molecular computing

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Using RNA as molecular Code for programming Cellular Function

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ACS SYNTHETIC BIOLOGY 2016年第8期5卷 795-809页

作者： Kushwaha, Manish Rostain, William Prakash, Satya Duncan, John N. Jaramillo, Alfonso Univ Warwick Warwick Integrat Synthet Biol Ctr WISB Coventry CV4 7AL W Midlands England Univ Warwick Sch Life Sci Coventry CV4 7AL W Midlands England Univ Paris Saclay UEVE CNRS GenopoleISSB Evry France

RNA is involved in a wide-range of important molecular processes in the cell, serving diverse functions: regulatory, enzymatic, and structural. Together with its ease and predictability of design, these properties can lead RNA to become a useful handle for biological engineers with which to control the cellular machinery. By modifying the many RNA links in cellular processes, it is possible to reprogram cells toward specific design goals. We propose that RNA can be viewed as a molecular programming language that, together with protein-based execution platforms, can be used to rewrite wide ranging aspects of cellular function. In this review, we catalogue developments in the use of RNA parts, methods, and associated computational models that have contributed to the programmability of biology. We discuss how RNA part repertoires have been combined to build complex genetic circuits, and review recent applications of RNA-based parts and circuitry. We explore the future potential of RNA engineering and posit that RNA programmability is an important resource for firmly establishing an era of rationally designed synthetic biology.

关键词： Peptides and proteins Genetics Circuits Protein dynamics Molecules

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A dna-Based Archival storage System 16

A DNA-Based Archival Storage System

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21st international conference on Architectural Support for programming Languages and Operating Systems

作者： Bornhol, James Lopez, Randolph Carmean, Douglas M. Ceze, Luis Seelig, Georg strauss, Karin Univ Washington Seattle WA 98195 USA Microsoft Res Redmond WA USA

ISBN: (纸本)9781450340915

Demand for data storage is growing exponentially, but the capacity of existing storage media is not keeping up. Using dna to archive data is an attractive possibility because it is extremely dense, with a raw limit of 1 exabyte/mm(3) (10(9) GB/mm(3)), and long-lasting, with observed half-life of over 500 years. This paper presents an architecture for a dna-based archival storage system. It is structured as a key-value store, and leverages common biochemical techniques to provide random access. We also propose a new encoding scheme that offers controllable redundancy, trading off reliability for density. We demonstrate feasibility, random access, and robustness of the proposed encoding with wet lab experiments involving 151 kB of synthesized dna and a 42 kB random-access subset, and simulation experiments of larger sets calibrated to the wet lab experiments. Finally, we highlight trends in biotechnology that indicate the impending practicality of dna storage for much larger datasets.

关键词： Archival storage molecular computing dna

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Supervised learning in an adaptive dna strand displacement circuit 1

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21st international conference on dna computing and molecular programming, 2015

作者： Lakin, Matthew R. stefanovic, Darko Department of Computer Science University of New Mexico AlbuquerqueNM87131 United States Center for Biomedical Engineering University of New Mexico AlbuquerqueNM87131 United States

ISBN: (数字)9783319219998

ISBN: (纸本)9783319219981

The development of dna circuits capable of adaptive behavior is a key goal in dna computing, as such systems would have potential applications in long-term monitoring and control of biological and chemical systems. In this paper, we present a framework for adaptive dna circuits using buffered strand displacement gates, and demonstrate that this framework can implement supervised learning of linear functions. This work highlights the potential of buffered strand displacement as a powerful architecture for implementing adaptive molecular systems. © Springer international Publishing Switzerland 2015.

关键词： Supervised learning

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An application of grid computing to pharmacophore discovery using inductive logic programming

An application of grid computing to pharmacophore discovery ...

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21st international conference on Computers and Their Applications, CATA 2006

作者： Johnson, Nathan P. Graham, James H. Intelligent Systems Research Laboratory Dept. of Computer Engineering and Computer Science University of Louisville Louisville KY 40292 United States

ISBN: (纸本)9781604234961

In this paper we show that Inductive Logic programming (ILP) algorithms for pharmacophore discovery can run efficiently on a grid of inexpensive computers. Designing a new drug is a long, tedious, and very expensive process that can take many years to complete. Machine learning techniques and ILP algorithms have been shown to be valuable aids in speeding discovery of candidate molecular structures. This paper describes a case study utilizing structure activity relationships and ILP for pharmacophore discovery on an "Xgrid" of Apple G4 computers available at high schools in Kentucky. With this architecture, an algorithm that requires about 9 hours on a single processor, and a little less time on an older tightly-coupled cluster computer, executed in 32 minutes using the donated idle cycles of a large number of loosely-coupled processors in a computational grid.

关键词： Grid computing

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Automated design and verification of localized dna computation circuits 1

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21st international conference on dna computing and molecular programming, 2015

作者： Boemo, Michael A. Turberfield, Andrew J. Cardelli, Luca Department of Physics Clarendon Laboratory University of Oxford Parks Road OxfordOX1 3PU United Kingdom Department of Computer Scienc Wolfson Building University of Oxford Parks Road OxfordOX1 3QD United Kingdom Microsoft Research Cambridge Station Road CambridgeCB1 2FB United Kingdom

ISBN: (数字)9783319219998

ISBN: (纸本)9783319219981

Simple computations can be performed using the interactions between single-stranded molecules of dna. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a dna circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri net onto a continuous time Markov chain, which can also be used to find an optimal design for the circuit. This theoretical machinery can be applied to create software that automatically designs a dna circuit, linking an abstract propositional formula to a physical dna computation system that is capable of evaluating it. © Springer international Publishing Switzerland 2015.

关键词： Petri nets

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Reflections on tiles (in self-assembly) 1

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21st international conference on dna computing and molecular programming (dna)

作者： Hendricks, Jacob Patitz, Matthew J. Rogers, Trent A. Univ Wisconsin Dept Comp Sci & Informat Syst River Falls WI 54022 USA Univ Arkansas Dept Comp Sci & Comp Engn Fayetteville AR 72701 USA

ISBN: (数字)9783319219998

ISBN: (纸本)9783319219981

关键词： Self-assembly Tile assembly model molecular computing

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Speedy Colorful Subtrees 21st

Speedy Colorful Subtrees

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21st Annual international computing and Combinatorics conference (COCOON)

作者： White, W. Timothy J. Beyer, stephan Duehrkop, Kai Chimani, Markus Boecker, Sebastian Univ Jena Chair Bioinformat Jena Germany Univ Osnabruck Inst Comp Sci Osnabruck Germany

ISBN: (纸本)9783319213989;9783319213972

Fragmentation trees are a technique for identifying molecular formulas and deriving some chemical properties of metabolites-small organic molecules-solely from mass spectral data. computing these trees involves finding exact solutions to the NP-hard Maximum Colorful Subtree problem. Existing solvers struggle to solve the large instances involved fast enough to keep up with instrument throughput, and their performance remains a hindrance to adoption in practice. We attack this problem on two fronts: by combining fast and effective reduction algorithms with a strong integer linear program (ILP) formulation of the problem, we achieve overall speedups of 9.4 fold and 8.8 fold on two sets of real-world problems-without sacrificing optimality. Both approaches are, to our knowledge, the first of their kind for this problem. We also evaluate the strategy of solving global problem instances, instead of first subdividing them into many candidate instances as has been done in the past. Software (C++ source for our reduction program and our CPLEX/Gurobi driver program) available under LGPL at https://***/wtwhite/speedycolorfulsubtrees/.

关键词： Integer programming

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