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检索条件"任意字段=16th International Conference on DNA Computing and Molecular Programming"

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

25th International Conference on DNA Computing and Molecular...

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

ISBN: (纸本)9783030268060

the proceedings contain 12 papers. the special focus in this conference is on dna computing and molecular programming. the topics include: Error-Free Stable Computation with Polymer-Supplemented Chemical Reaction Networks;SIMD||dna: Single Instruction, Multiple Data Computation with dna Strand Displacement Cascades;Implementing Arbitrary CRNs Using Strand Displacing Polymerase;real-Time Equivalence of Chemical Reaction Networks and Analog Computers;a Reaction Network Scheme Which Implements Inference and Learning for Hidden Markov Models;Efficient Parameter Estimation for dna Kinetics Modeled as Continuous-Time Markov Chains;new Bounds on the Tile Complexity of thin Rectangles at Temperature-1;non-cooperatively Assembling Large Structures;simulation of Programmable Matter Systems Using Active Tile-Based Self-Assembly;combined Amplification and molecular Classification for Gene Expression Diagnostics.

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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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DROM: Read Only Memory Storage in dna computing 4

DROM: Read Only Memory Storage in DNA Computing

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4th international conference on Sustainable Technologies for Industry 4.0, STI 2022

作者： Tabassum, Tamanna Akter, Fatema Uddin, Mohammed Nasir Jagannath University Dept of Computer Science and Engineering Bangladesh Green University Bangladesh Dept of Computer Science and Engineering Bangladesh

ISBN: (纸本)9781665490450

Biomolecular programming performs computing utilizing many sorts of reactions and stores the information in biological macromolecules (proteins and nucleic acids). dna (Deoxyribose Nucleic Acid) exhibits highly predictable molecular behavior, which assists in the construction of logical versions of operating systems and molecular computers. Read Only Memory (ROM), is a form of electronic storage that is built into a device during the manufacturing process. It might be a programmable general-purpose logic device, and a client can customize the storage device as a basic logic gate operation to complex mechanisms on a chip. In this proposed work, a ROM is designed using dna-based gates. the attributes of dna-based computing enable dna-based ROM to execute billions of operations consecutively as well as provide immense storage in a compact space. © 2022 IEEE.

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...

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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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Construction of Complex Logic Circuit Based on dna Logic Gate AND and OR 16th

Construction of Complex Logic Circuit Based on DNA Logic Gat...

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

作者： Hu, Mengyang Wang, Luhui Xi, Sunfan Liu, Rong Dong, Yafei Department of Computer Science Shaanxi Normal University Xi’ an710119 China Department of Life Science Shaanxi Normal University Xi’ an710119 China

ISBN: (纸本)9789811912559

dna, as one of the most promising research objects for molecular computing, is often used to construct the basic modules of computing. A simple and multiplexable dna logic computing platform comprising a basic two input logic gate AND and OR, is designed by using G-quadruplex combined with NMM to generate fluorescence mechanism as output signal and dna strand as input signal. Designed dna strand displacement and catalytic hairpin self-assembly, achieving enzyme-free and label-free, simplified the design and reduced the cost. Strand displacement reactions not only enable signal amplification, but also provide methods to implement multi-layer cascading and solve complex computational problems by utilizing the basic logic gate AND and OR. In summary, this logic platform can realize the design of complex logic circuit by the constructed simple underlying logic gate AND and OR, which provides the potential to solve complex computational problems. © 2022, Springer Nature Singapore Pte Ltd.

关键词： Logic gates

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A Review of dna Cryptography: From a Data Protection Perspective

A Review of DNA Cryptography: From a Data Protection Perspec...

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Security of Information and Networks (SIN), international conference on

作者： Parth Parmar Jekil Gadhiya Satvik Vats Deepak Kumar Verma Krunal Vaghela Computer Engineering Marwadi University Rajkot India Computer Science and Engineering Graphic Era Hill University Dehradun India

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 is concerned about preventing hackers from gaining access to their personal data. Several algorithms from the fields of classical cryptography and steganography can be used to conceal data. dna cryptography is an emerging field that aims to protect information kept in dna. dna cryptography takes use of dna's innate computing power at the molecular level. In this paper, we are exploring diverse cryptographic algorithms and methods that are used to secure the stored data in dna. the paper represents the critical review that includes merits and demerits of the diverse cryptographic algorithms for securing the data in dna.

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Synchronization of Chaos with a Single Driving Variable Feedback Control Based on dna Strand Displacement 16th

Synchronization of Chaos with a Single Driving Variable Feed...

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

作者： Meng, Zijie An, Xiaoyu Sun, Junwei Zhengzhou University of Light Industry Zhengzhou450002 China

ISBN: (纸本)9789811912559

dna molecular reaction is one of methods to build next generation operational circuit. It has demonstrated the capacity to design control systems. In this paper, a PID controll based on dna strand displacement (DSD) is presented to realize synchronization of chaotic system. Based on the theory of synchronization and design principle of control, the proportion terms, integration terms, and differentiation terms are added to chaotic oscillatory systems for implementing synchronization by DSD. the two four-variable chaotic oscillatory systems are tended to be synchronization by PID control. there are four chemical reaction modules which are proposed to realize the systems. the modeling and simulation results demonstrate the validity of chemical reaction terms and control systems by visual DSD and matelab. Achieved the ideal results when it is applied to the chaotic system synchronization. © 2022, Springer Nature Singapore Pte Ltd.

关键词： three term control systems

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Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic Hardness and Parameterized Bounds 30

Domain-Based Nucleic-Acid Minimum Free Energy: Algorithmic H...

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

作者： Demaine, Erik D. Gomez, Timothy Grizzell, Elise Hecher, Markus Lynch, Jayson Schweller, Robert Shalaby, Ahmed Woods, Damien Massachusetts Institute of Technology United States University of Texas Rio Grande Valley United States Hamilton Institute Department of Computer Science Maynooth University Ireland

ISBN: (纸本)9783959773447

molecular programmers and nanostructure engineers use domain-level design to abstract away messy dna/RNA sequence, chemical and geometric details. Such domain-level abstractions are enforced by sequence design principles and provide a key principle that allows scaling up of complex multistranded dna/RNA programs and structures. Determining the most favoured secondary structure, or Minimum Free Energy (MFE), of a set of strands, is typically studied at the sequence level but has seen limited domain-level work. We analyse the computational complexity of MFE for multistranded systems in a simple setting were we allow only 1 or 2 domains per strand. On the one hand, with 2-domain strands, we find that the MFE decision problem is NP-complete, even without pseudoknots, and requires exponential time algorithms assuming SAT does. On the other hand, in the simplest case of 1-domain strands there are efficient MFE algorithms for various binding modes. However, even in this single-domain case, MFE is P-hard for promiscuous binding, where one domain may bind to multiple as experimentally used by Nikitin [Nat Chem., 2023], which in turn implies that strands consisting of a single domain efficiently implement arbitrary Boolean circuits. © Erik D. Demaine, Timothy Gomez, Elise Grizzell, Markus Hecher, Jayson Lynch, Robert Schweller, Ahmed Shalaby, and Damien Woods

关键词： Domain-based dna designs efficient algorithms fixed-parameter tractable minimum free energy NC NP-hard P-hard

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Solution to Satisfiability Problem Based on molecular Beacon Microfluidic Chip computing Model 16th

Solution to Satisfiability Problem Based on Molecular Beacon...

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

作者： Yang, Jing Yin, Zhixiang Tang, Zhen Cui, Jianzhong Liu, Congcong School of Mathematics and Big Data Anhui University of Science and Technology Huainan232001 China School of Mathematics Physics and Statistics Shanghai University of Engineering Science Shanghai201620 China

ISBN: (纸本)9789811912559

the satisfiability problem is a well-known NPC problem in mathematics. In this paper, we report construction of a computational model based on molecular beacon microfluidic chip, to solve the satisfiability problem by using advantages such as;rapid, simple and economical measurement of molecular beacon probe. Taking 3-satisfiability problem as an example, we encode the variable and construct molecular beacon probe by combining the complement of corresponding dna strands with variable whose clause is 1. they are then fixed on the chip and placed in the microfluidic chip. It takes dna strands corresponding to all combinations of values as the initial data pool, and utilize the microfluidic chip to detect. If there are dna strands in the final data pool, it will be sequenced, and we call that this problem can be satisfied. If there are no dna strands, the problem is not satisfied. the complexity of the model is O(m) + O(n), where m is the number of clauses in conjunctive normal form, and n is the number of variables contained in the conjunctive normal form. this model represents great parallelism, massive storage capacity and high throughput, integration and multi-function of microfluidic chips. © 2022, Springer Nature Singapore Pte Ltd.

关键词： Microfluidic chips

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computing Robust Optimal Factories in Metabolic Reaction Networks 28th

Computing Robust Optimal Factories in Metabolic Reaction Net...

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28th Annual international conference on Research in Computational molecular Biology (RECOMB)

作者： Krieger, Spencer Kececioglu, John Carnegie Mellon Univ Ray & Stephanie Lane Computat Biol Dept Pittsburgh PA 15213 USA Univ Arizona Dept Comp Sci Tucson AZ 85721 USA

ISBN: (纸本)9781071639887;9781071639894

Perhaps the most fundamental model in synthetic and systems biology for inferring pathways in metabolic reaction networks is a metabolic factory: a system of reactions that starts from a set of source compounds and produces a set of target molecules, while conserving or not depleting intermediate metabolites. Finding a shortest factory-that minimizes a sum of real-valued weights on its reactions to infer the most likely pathway-is NP-complete. the current state-of-the-art for shortest factories solves a mixed-integer linear program with a major drawback: it requires the user to set a critical parameter, where too large a value can make optimal solutions infeasible, while too small a value can yield degenerate solutions due to numerical error. We present the first robust algorithm for optimal factories that is both parameter-free (relieving the user from determining a parameter setting) and degeneracy-free (guaranteeing it finds an optimal nondegenerate solution). We also give for the first time a complete characterization of the graph-theoretic structure of shortest factories via cuts of hypergraphs that reveals two important classes of degenerate solutions which were overlooked and potentially output by the prior state-of-the-art. In addition we settle the relationship between the two established pathway models of hyperpaths and factories by proving that hyperpaths are actually a subclass of factories. Comprehensive experiments over all instances from the standard metabolic reaction databases in the literature demonstrate our algorithm is fast in practice, quickly finding optimal factories in large real-world networks containing thousands of reactions. A preliminary implementation of our algorithm for robust optimal factories in a new tool called Freeia is available free for research use at http://***.

关键词： Integer programming

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