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检索条件"任意字段=17th International Conference on DNA Computing and Molecular Programming"

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SIMD||dna: Single Instruction, Multiple Data Computation with dna Strand Displacement Cascades 1

引用

25th international conference on dna computing and molecular programming, dna 2019

作者： Wang, Boya Chalk, Cameron Soloveichik, David The University of Texas at Austin Austin United States

ISBN: (数字)9783030268077

ISBN: (纸本)9783030268060

Typical dna storage schemes do not allow in-memory computation, and instead transformation of the stored data requires dna sequencing, electronic computation of the transformation, followed by synthesizing new dna. In contrast we propose a model of in-memory computation that avoids the time consuming and expensive sequencing and synthesis steps, with computation carried out by dna strand displacement. We demonstrate the flexibility of our approach by developing schemes for massively parallel binary counting and elementary cellular automaton Rule 110 computation. © 2019, Springer Nature Switzerland AG.

关键词： dna

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A type system for dnaQL

A type system for DNAQL

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18th international conference on dna computing and molecular programming, dna 18

作者： Brijder, Robert Gillis, Joris J. M. Van Den Bussche, Jan Hasselt University Belgium University of Limburg Belgium

ISBN: (纸本)9783642322075

Recently we have introduced a formal graph-based data model for dna complexes geared towards database applications. the model is accompanied by the programming language dnaQL for querying databases in dna. Due to natural restrictions on the implementability and termination of operations on dna, programs in dnaQL are not always well defined on all possible inputs. Indeed, a problem left open by our previous work has been to devise a type system for dnaQL, with a soundness property to the effect that well-typed programs are well defined on all inputs adhering to given input types. the contribution of the present paper is to propose such a type system and to establish soundness. Moreover, we show that the type system is flexible enough so that any database manipulation expressible in the relational algebra is also expressible in dnaQL in a well-typed manner. © 2012 Springer-Verlag.

关键词： dna

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12th international conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018

12th International Conference on Practical Applications of C...

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12th international conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018

ISBN: (纸本)9783319987019

the proceedings contain 26 papers. the special focus in this conference is on Practical Applications of Computational Biology and Bioinformatics. the topics include: A bioinformatics protocol for quickly creating large-scale phylogenetic trees;Deep learning analysis of binding behavior of virus displayed peptides to AuNPs;compression of amino acid sequences;NET-ASAR: A tool for dna sequence search based on data compression;Can an integrative SNP approach substitute standard identification in comprehensive case/control analyses?;simple pattern-only heuristics lead to fast subgraph matching strategies on very large networks;in silico predictions for fucoxanthin production by the diatom phaeodactylum tricornutum;EvoPPI: A web application to compare protein-protein interactions (PPIs) from different databases and species;a review on metabolomics data analysis for cancer applications;parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search;a framework for the automatic combination and evaluation of gene selection methods;parallel cellular automaton tumor growth model;MOSCA: An automated pipeline for integrated metagenomics and metatranscriptomics data analysis;metabolite integration pipeline for the improvement of human metabolic models;a genetic programming approach applied to feature selection from medical data;A dna sequence corpus for compression benchmark;17α-ethinylestradiol analysis of endo- and exometabolome of ulva lactuca (chlorophyta) by 1H-NMR spectroscopy and bioinformatics tools;in silico modeling and simulation approach for apoptosis caspase pathways;molecular dynamic simulations suggest that P152R mutation within MeCP2 can lead to higher dna binding affinity and loss of selective binding to methylated dna.

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Grammar-based immune programming

Grammar-based immune programming

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15th international conference on dna computing and molecular programming

作者： Bernardino, Heder S. Barbosa, Helio J. C. Lab Nacl Computacao Cient BR-25651075 Petropolis RJ Brazil

this paper describes Grammar-based Immune programming (GIP) for evolving programs in an arbitrary language by immunological inspiration. GIP is based on Grammatical Evolution (GE) in which a grammar is used to define a language and decode candidate solutions to a valid representation (program). However, by default, GE uses a Genetic Algorithm in the search process while GIP uses an artificial immune system. Some modifications are needed of an immune algorithm to use a grammar in order to efficiently decode antibodies into programs. Experiments are performed to analyze algorithm behavior over different aspects and compare it with GEVA, a well known GE implementation. the methods are applied to identify a causal model (an ordinary differential equation) from an observed data set, to symbolically regress an iterated function f(f(x)) = g(x), and to find a symbolic representation of a discontinuous function.

关键词： Artificial immune system Grammatical evolution Immune programming Symbolic regression Model inference

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Prediction Nucleic Acid Secondary Structure with Planar Pseudoknots and Genetic Algorithm 9

Prediction Nucleic Acid Secondary Structure with Planar Pseu...

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9th international conference on Bio-Inspired computing - theories and Applications (BIC-TA)

作者： Zhang, Kai Huang, Xinquan Hu, Wei Liu, Jun Wuhan Univ Sci & Technol Sch Comp Sci Wuhan 430081 Peoples R China

ISBN: (纸本)9783662450482

In recent years, dna and RNA molecules have shown great potential as a design medium for the construction of nanostructures and the programmed assembly of molecular computing. In this paper, we propose a novel genetic algorithm to predict nucleic acid secondary structure with planar pseudoknots. In our algorithm, the free energy and the number of continues base pairs stacking are used as fitness function to evaluate the individuals. We have compared the results obtained by our algorithm with RNAStructure. As will be discussed, our algorithm can efficiently predict the planar pseudoknots with lower free energy and more continues base pairs stacking.

关键词： Secondary structure prediction Genetic algorithm Minimum free energy Dynamic programming Pseudoknots

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5th international conference on theory and Practice of Natural computing, TPNC 2016

5th International Conference on Theory and Practice of Natur...

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5th international conference on theory and Practice of Natural computing, TPNC 2016

ISBN: (纸本)9783319490007

the proceedings contain 17 papers. the special focus in this conference is on Invited Talk, Applications of Natural computing, Evolutionary Computation, Formal Models and Machine Learning. the topics include: Managing natural noise in recommender systems;realization of periodic functions by self-stabilizing population protocols with synchronous handshakes;localized load balancing in RFID systems;how to implement a random bisection cut;a discrete artificial bee colony algorithm based on similarity for graph coloring problems;a multi-objective evolutionary approach to Pareto optimal model trees. a preliminary study;real time traffic intersection management using multi-objective evolutionary algorithm;simulating stochastic dynamic interactions with spatial information and flux;implementation of Turing machine using dna strand displacement;a quantum annealing approach to biclustering;determining player skill in the game of go with deep neural networks;flexible generalized fuzzy Petri nets for rule-based systems and learning grammar rules in probabilistic grammar-based genetic programming.

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

Simplifying chemical reaction network implementations with t...

引用

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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Rational Design of dna Sequences with Non-Orthogonal Binding Interactions 29

Rational Design of DNA Sequences with Non-Orthogonal Binding...

引用

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

作者： Berleant, Joseph Don Department of Biological Engineering Massachusetts Institute of Technology CambridgeMA United States

ISBN: (纸本)9783959772976

molecular computation involving promiscuous, or non-orthogonal, binding interactions between system components is found commonly in natural biological systems, as well as some proposed human-made molecular computers. Such systems are characterized by the fact that each computational unit, such as a domain within a dna strand, may bind to several different partners with distinct, prescribed binding strengths. Unfortunately, implementing systems of molecular computation that incorporate non-orthogonal binding is difficult, because researchers lack a robust, general-purpose method for designing molecules with this type of behavior. In this work, we describe and demonstrate a process for the rational design of dna sequences with prescribed non-orthogonal binding behavior. this process makes use of a model that represents large sets of non-orthogonal dna sequences using fixed-length binary strings, and estimates the differential binding affinity between pairs of sequences through the Hamming distance between their corresponding binary strings. the real-world applicability of this model is supported by simulations and some experimental data. We then select two previously described systems of molecular computation involving non-orthogonal interactions, and apply our sequence design process to implement them using dna strand displacement. Our simulated results on these two systems demonstrate both digital and analog computation. We hope that this work motivates the development and implementation of new computational paradigms based on non-orthogonal binding. © Joseph Don Berleant;licensed under Creative Commons License CC-BY 4.0.

关键词： dna sequences

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Tuning Geometric Conformations of Curved dna Structures by Controlling Positions of Nicks 1

引用

17th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2022

作者： Xie, Chun Hu, Yingxin Chen, Kuiting Chen, Zhekun Pan, Linqiang Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China College of Information Science and Technology Shijiazhuang Tiedao University Shijiazhuang050043 China

ISBN: (数字)9789819915491

ISBN: (纸本)9789819915484

dna origami is one of the powerful techniques that utilize dna as building blocks to synthesize nanostructures. Traditionally, through introducing different numbers of insertions and deletions of base pairs in dna helices, the in-plane bending angle of curved dna structures could be roughly tuned. Here, we explored a strategy that used the position patterns of nicks in staple strands to tune the geometric conformation of curved dna origami structures, including in-plane bending, out-of-plane bending, and twisting angles. When the structure adopted different patterns of nicks positions, great difference appeared in the geometric properties. Further, by combining subunits of different nicks position patterns, the bending and twisting of the combined structure was effectively tuned. the strategy increases the design accuracy of curved dna origami structures and expands the toolbox for designing dna structures. © 2023, the Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： molecular dynamics

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Geometric Enumeration of Localized dna Strand Displacement Reaction Networks 30

Geometric Enumeration of Localized DNA Strand Displacement R...

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30th international conference on dna computing and molecular programming, dna 30 2024

作者： Lakin, Matthew R. Kumar, Sarika Department of Computer Science University of New Mexico United States Department of Chemical & Biological Engineering University of New Mexico United States Center for Biomedical Engineering University of New Mexico United States

ISBN: (纸本)9783959773447

Localized molecular devices are a powerful tool for engineering complex information-processing circuits and molecular robots. their practical advantages include speed and scalability of interactions between components tethered near to each other on an underlying nanostructure, and the ability to restrict interactions between more distant components. the latter is a critical feature that must be factored into computational tools for the design and simulation of localized molecular devices: unlike in solution-phase systems, the geometries of molecular interactions must be accounted for when attempting to determine the network of possible reactions in a tethered molecular system. this work aims to address that challenge by integrating, for the first time, automated approaches to analysis of molecular geometry with reaction enumeration algorithms for dna strand displacement reaction networks that can be applied to tethered molecular systems. By adapting a simple approach to solving the biophysical constraints inherent in molecular interactions to be applicable to tethered systems, we produce a localized reaction enumeration system that enhances previous approaches to reaction enumeration in tethered system by not requiring users to explicitly specify the subsets of components that are capable of interacting. this greatly simplifies the user’s task and could also be used as the basis of future systems for automated placement or routing of signal-transmission and logical processing in molecular devices. We apply this system to several published example systems from the literature, including both tethered molecular logic systems and molecular robots. © Matthew R. Lakin and Sarika Kumar

关键词： molecular docking

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