the proceedings contain 5 papers. the topics discussed include: geometric enumeration of localized dna strand displacement reaction networks;domain-based nucleic-acid minimum free energy: algorithmic hardness and para...
ISBN:
(纸本)9783959773447
the proceedings contain 5 papers. the topics discussed include: geometric enumeration of localized dna strand displacement reaction networks;domain-based nucleic-acid minimum free energy: algorithmic hardness and parameterized bounds;simulation of the abstract tile assembly model using crisscross slats;designing 3D RNA Origami nanostructures with a minimum number of kissing loops;and learning and inference in a lattice model of multicomponent condensates.
the proceedings contain 10 papers. the topics discussed include: minimum free energy, partition function and kinetics simulation algorithms for a multistranded scaffolded dna computer;dna tile self-assembly for 3d-sur...
ISBN:
(纸本)9783959772976
the proceedings contain 10 papers. the topics discussed include: minimum free energy, partition function and kinetics simulation algorithms for a multistranded scaffolded dna computer;dna tile self-assembly for 3d-surfaces: towards genus identification;on the runtime of chemical reaction networks beyond idealized conditions;rational design of dna sequences with non-orthogonal binding interactions;revisiting hybridization kinetics with improved elementary step simulation;reversible bond logic;accelerating self-assembly of crisscross slat systems;thermodynamically driven signal amplification;optimal information encoding in chemical reaction networks;and complexity of reconfiguration in surface chemical reaction networks.
the proceedings contain 9 papers. the topics discussed include: fast and robust strand displacement cascades via systematic design strategies;universal shape replication via self-assembly with signal-passing tiles;a c...
ISBN:
(纸本)9783959772532
the proceedings contain 9 papers. the topics discussed include: fast and robust strand displacement cascades via systematic design strategies;universal shape replication via self-assembly with signal-passing tiles;a coupled reconfiguration mechanism for single-stranded dna strand displacement systems;exploring material design space with a deep-learning guided genetic algorithm;modelling and optimization of a dna stack nano-device using probabilistic model checking;on Turedo hierarchies and intrinsic universality;computing real numbers with large-population protocols having a continuum of equilibria;the structural power of reconfigurable circuits in the Amoebot model;and fault-tolerant shape formation in the Amoebot model.
the proceedings contain 11 papers. the topics discussed include: robust digital molecular design of binarized neural networks;computing properties of thermodynamic binding networks: an integer programming approach;sel...
ISBN:
(纸本)9783959772051
the proceedings contain 11 papers. the topics discussed include: robust digital molecular design of binarized neural networks;computing properties of thermodynamic binding networks: an integer programming approach;self-replication via tile self-assembly;improved lower and upper bounds on the tile complexity of uniquely self-assembling a thin rectangle non-cooperatively in 3D;directed non-cooperative tile assembly is decidable;molecular machines from topological linkages;small tile sets that compute while solving mazes;reactamole: functional reactive molecularprogramming;parallel pairwise operations on data stored in dna: sorting, shifting, and searching;and predicting minimum free energy structures of multi-stranded nucleic acid complexes is APX-Hard.
A surface chemical reaction network (sCRN, Qian and Winfree in dnacomputing and molecularprogramming: 20thinternationalconference, dna 20, Kyoto, Japan, September 22-26, 2014. Proceedings 20. Springer, 2014) is an...
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A surface chemical reaction network (sCRN, Qian and Winfree in dnacomputing and molecularprogramming: 20thinternationalconference, dna 20, Kyoto, Japan, September 22-26, 2014. Proceedings 20. Springer, 2014) is an emergent paradigm for molecularprogramming, 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.
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 b...
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.
In recent years, a novel molecular computation model known as surface chemical reaction network (Qian, In: dnacomputing and molecularprogramming: 20thinternationalconference, dna 20, Proceedings, 2014) has garnere...
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In recent years, a novel molecular computation model known as surface chemical reaction network (Qian, In: dnacomputing and molecularprogramming: 20thinternationalconference, 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 molecularprogramming. 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.
the rate of development in today's IT industry is unprecedented. Information is being stored and transformed at a faster and faster rate. therefore, the importance of protecting sensitive data is growing. Everyone...
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this paper aims to extract common dna consecutive sequences appearing in both of the complete genomes of viruses and that of mammals. Withthese common dna sequences as genomic fossils, biologists or virologists can t...
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ISBN:
(纸本)9783031702471;9783031702488
this paper aims to extract common dna consecutive sequences appearing in both of the complete genomes of viruses and that of mammals. Withthese common dna sequences as genomic fossils, biologists or virologists can trace possible pathway of genomic evolution across species. To meet the requirement of huge computation to extract common dna sequences from complete genomes of all viruses and mammals selected, this study adopts one previously developed approach that was based on MapReduce programming model. this study has experiments for extracting common dna sequences run on a Hadoop cluster containing ten computing nodes. Experimental resources includes the whole genomic sequences of 7,538 viruses and five selected mammals, including Homo sapiens (Human), Pan troglodytes (Chimpanzee), Mus musculus (House Mouse), Rattus norvegicus (Brown Rat) and Sus scrofa (Wild Boar). there are a huge amount of common dna consecutive sequences extracted and, for simplicity, there are only 26 ones whose lengths are longer than 50 base-pair (bp) selected for illustration. Among above 26, there are 13 reverified as no repetitive sequences that could be seemed as the clues to reinspect the relationship of viruses and mammals. Via cloud computingthat can provide with more computing nodes then ten used in this study, it is believed that this approach can handle with more complete genomes of species, and then provide more common genomic fossils to biologists or virologist to verify the potential connections among diverse species in the future.
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