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

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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Graph-theoretic formalization of hybridization in dna sticker complexes

Graph-theoretic formalization of hybridization in DNA sticke...

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17th international conference on dna computing and molecular programming

作者： Brijder, Robert Gillis, Joris J. M. Van den Bussche, Jan Hasselt Univ Diepenbeek Belgium Transnat Univ Limburg Diepenbeek Belgium

ISBN: (纸本)9783642236372

Sticker complexes are a formal graph-based data model for a restricted class of dna complexes, motivated by potential applications to databases. this data model allows for a purely declarative definition of hybridization. We introduce the notion of terminating hybridization, which intuitively means that only a finite number of different products can be generated. We characterize this notion in purely graph-theoretic terms. Under a finite alphabet, each product is shown to be of polynomial size. Yet, terminating hybridization can still produce results of exponential size, in that there may be exponentially many different (nonisomorphic) finished products. We indicate a class of complexes where hybridization is guaranteed to be polynomially bounded.

关键词： dna Hybridization Graph-theory Complexity

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Strand Algebras for dna computing

Strand Algebras for DNA Computing

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15th international conference on dna computing and molecular programming

作者： Cardelli, Luca Microsoft Res Cambridge CB3 0FB England

We present a process algebra for dna computing, discussing compilation of other formal systems into the algebra, and compilation of the algebra into dna structures.

ISBN: (纸本)9783642106033

We present a process algebra for dna computing, discussing compilation of other formal systems into the algebra, and compilation of the algebra into dna structures.

关键词： Algebra

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Synthesizing Small and Reliable Tile Sets for Patterned dna Self-assembly

Synthesizing Small and Reliable Tile Sets for Patterned DNA ...

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17th international conference on dna computing and molecular programming

作者： Lempiainen, Tuomo Czeizler, Eugen Orponen, Pekka Aalto Univ Sch Sci HIIT Dept Informat & Comp Sci FI-00076 Aalto Finland

ISBN: (纸本)9783642236372;9783642236389

We consider the problem of finding, for a given 2D pattern of colored tiles, a minimal set of tile types self-assembling to this pattern in the abstract Tile Assembly Model of Winfree (1998). this Patterned self-Assembly Tile set Synthesis (PATS) problem was first introduced by Ma and Lombardi (2008), and subsequently studied by Goos and Orponen (2011), who presented an exhaustive partition-search branch-and-bound algorithm (briefly PS-BB) for it. However, finding the true minimal tile sets is very time consuming, and PS-BB is not well-suited for finding small but not necessarily minimal solutions. In this paper, we modify the basic partition-search framework by using a heuristic to optimize the order in which the algorithm traverses its search space. We find that by running several parallel instances of the modified algorithm PS-H, the search time for small tile sets can be shortened considerably. We also introduce a method for computing the reliability of a tile set, i.e. the probability of its error-free self-assembly to the target tiling, based on Winfree's analysis of the kinetic Tile Assembly Model (1998). We present data on the reliability of tile sets found by the algorithms and find that also here PS-H constitutes a significant improvement over PS-BB.

关键词： Reliability analysis

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Improved dna-sticker arithmetic: tube-encoded-carry, Logarithmic Number System and Monte-Carlo methods

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NATURAL computing 2013年第2期12卷 235-246页

作者： Arnold, Mark G. POB 605 Laramie WY 82070 USA

the sticker model of computation, implemented using robotic processing of dna, manipulates in parallel many bitstrings, called strands, that are contained in a limited number of tubes. Prior sticker arithmetic algorithms, patterned on digital-electronics, generate carry bits in the strand, either wasting bits or using a clear operation (with problematic biochemical implementation). the novel addition algorithm here does not need to record the carry. Instead, which tube holds a particular strand implicitly encodes the carry. the speed and number of tubes are half that of prior approaches. Further encoding data in the Logarithmic Number System (LNS) allows such integer operations to perform cost-effective real multiplications, divisions and roots. An example LNS Euclidian norm is more efficient than prior methods, assuming perfect operations. Unfortunately, dna-stickers are unreliable. this paper uses sticker unreliability as a source of randomness to implement Monte-Carlo (MC) arithmetic (previously fabricated in silicon at the cost of pseudo-random generators). With stickers, the randomness is free. MC engineering mimics natural systems using unreliable but redundant components. Here, MC randomness is only useful in low-order bits. Multiple re-testing of the same bit ("refinement") trades improved reliability for slower operation using more tubes. Simulations (with different sizes, probabilities and refinement) show that increasing refinement as a function of bit position allows imperfect implementations to achieve suitable MC strand-error distributions, predicting 1000x speed-mass advantage of sticker-MCLNS over conventional supercomputers.

关键词： dna arithmetic Sticker system Addition Logarithmic Number System (LNS) Monte-Carlo Arithmetic

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Empirical modeling using genetic programming: a survey of issues and approaches

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NATURAL computing 2015年第2期14卷 303-330页

作者： Dabhi, Vipul K. Chaudhary, Sanjay Dharmsinh Desai Univ Dept Informat Technol Nadiad 387001 India Ahmedabad Univ Inst Informat & Commun Technol Ahmadabad 380009 Gujarat India

Empirical modeling, which is a process of developing a mathematical model of a system from experimental data, has attracted many researchers due to its wide applicability. Finding both the structure and appropriate numeric coefficients of the model is a real challenge. Genetic programming (GP) has been applied by many practitioners to solve this problem. However, there are a number of issues which require careful attention while applying GP to empirical modeling problems. We begin with highlighting the importance of these issues including: computational efforts in evolving a model, premature convergence, generalization ability of an evolved model, building hierarchical models, and constant creation techniques. We survey and classify different approaches used by GP researchers to deal with the mentioned issues. We present different performance measures which are useful to report the results of analysis of GP runs. We hope this work would help the reader by facilitating to understand key concepts and practical issues of GP and steering in selection of an appropriate approach to solve a particular issue effectively.

关键词： Genetic programming Research issues Efficiency of genetic programming Convergence rate of genetic programming Generalization of genetic programming solutions

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17th Annual conference on Foundations of Nanoscience, FNANO 2020: Self-Assembled Architectures and Devices

17th Annual Conference on Foundations of Nanoscience, FNANO ...

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17th Annual conference on Foundations of Nanoscience: Self-Assembled Architectures and Devices, FNANO 2020

the proceedings contain 76 papers. the topics discussed include: self-replication, exponential growth, mutations, directed evolution, colloidal architecture, and dna micro-machines;diverse recipes of dna self-assembly;triangulated wireframe structures: polymerase-assisted gap filling, and assembly from single-stranded tiles;self-assembly of nanotubes from distinct gamma-modified peptide nucleic acid oligomers in organic solvent mixtures;synthetic cellular constructs based on silica cell replication;membraneless organelles by design;single-molecule sequencing with polymerase nanocircuits;dynamic self-assembled hydrogels crosslinked with tunable, orthogonal reversible covalent (TORC) bonds;building star-like nanostructures with protein-dsdna assemblies;microscopic perspective on programming function in biological and man-made dna systems;soft matter biophysics study of dna capsules and dna droplets toward micrometer-sized molecular robots;and transmembrane signal transducing dna nanosensors for intact membrane enclosed biomarker detections.

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Analog and Digital Memory in Living Cells 17

Analog and Digital Memory in Living Cells

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4th ACM international conference on Nanoscale computing and Communication (ACM NANOCOM)

作者： Farzadfard, Fahim Lu, Timothy K. Synthet Biol Grp Massachusetts Inst Technol Cambridge MA 02139 USA

ISBN: (纸本)9781450349314

the ability to dynamically manipulate information stored in a genome, in a targeted, controlled and recurring manner, confers the great potential to study and engineer living cells. Here, we review some of the recent advances in the development of dna writers, i.e., molecular devices that enable targeted editing of dna of living cells, and discuss some of the potential uses of these devices in studying and programming cellular phenotypes.

关键词： Synthetic biology analog memory digital memory dna writing dna memory

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An improved molecular computation model of integer power using self-assembly of dna tiles 20

An improved molecular computation model of integer power usi...

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20th IEEE international conference on High Performance computing and Communications (HPCC) / 16th IEEE international conference on Smart City (SmartCity) / 4th IEEE international conference on Data Science and Systems (DSS)

作者： Li, Yongnan Peoples Publ Secur Univ China Sch Criminal Invest & Counter Terrorism Beijing 100038 Peoples R China

ISBN: (纸本)9781538666142

this paper proposes how to use self-assembly of dna tiles to calculate integer power over finite field GF(2n) with less assembly processing time. Two key functional components accomplish the computing process. One of them computes modular-multiplication and modularsquare in parallel, and the other one calculates modularsquare and transmits intermediate result. It achieves better performance than previous work for its optimized assembly rules. this tile assembly model requires 5316 types of computation tiles and 12 types of boundary tiles.

关键词： Binary finite field Tile assembly model dna computing Integer power

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dna Reservoir computing: A Novel molecular computing Approach

DNA Reservoir Computing: A Novel Molecular Computing Approac...

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19th international conference on dna computing and molecular programming

作者： Goudarzi, Alireza Lakin, Matthew R. Stefanovic, Darko Univ New Mexico Dept Comp Sci Albuquerque NM 87131 USA

ISBN: (纸本)9783319019284;9783319019277

We propose a novel molecular computing approach based on reservoir computing. In reservoir computing, a dynamical core, called a reservoir, is perturbed with an external input signal while a readout layer maps the reservoir dynamics to a target output. Computation takes place as a transformation from the input space to a high-dimensional spatiotemporal feature space created by the transient dynamics of the reservoir. the readout layer then combines these features to produce the target output. We show that coupled deoxyribozyme oscillators can act as the reservoir. We show that despite using only three coupled oscillators, a molecular reservoir computer could achieve 90% accuracy on a benchmark temporal problem.

关键词： Calculations

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