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Weak chirality in ordered dna phases

molecular CRYSTALS AND LIQUID CRYSTALS SCIENCE AND TECHNOLOGY SECTION A-molecular CRYSTALS AND LIQUID CRYSTALS 1997年第1期299卷 265-275页

作者： Kamien, RD [a] Department of Physics and Astronomy University of Pennsylvania Philadelphia PA 19104 USA

Recent experiments(1) on aligned dna show hexatic order with no sign of macroscopic chirality. I make the analogy between smectic liquid crystals and chiral hexatics and show how the absence of chirality cannot occur in a thermodynamic phase of chiral molecules. In addition, I discuss the microscopic origin of chiral mesophases in liquid crystals and show that, within the context of central forces between ''atoms'' on ''molecules'', chiral interactions can occur only if there are biaxial correlations between the mesogens. Weak biaxial correlations can therefore lead to small cholesteric pitches.

关键词： dna

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Synthesizing Minimal Tile Sets for Patterned dna Self-assembly

Synthesizing Minimal Tile Sets for Patterned DNA Self-assemb...

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16th international conference on dna computing and molecular programming

作者： Goos, Mika Orponen, Pekka Aalto Univ Sch Sci & Technol TKK Dept Informat & Comp Sci FI-00076 Aalto Finland

ISBN: (纸本)9783642183041

the Pattern self-Assembly Tile set Synthesis (PATS) problem is to determine a set of coloured tiles that self-assemble to implement a given rectangular colour pattern. We give an exhaustive branch-and-bound algorithm to find tile sets of minimum cardinality for the PATS problem. Our algorithm makes use of a search tree in the lattice of partitions of the ambient rectangular grid, and an efficient bounding function to prune this search tree. Empirical data on the performance of the algorithm shows that it compares favourably to previously presented heuristic solutions to the problem.

关键词： Self assembly

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dna computing and molecular programming 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Yasubumi Sakakibara Yongli Mi

ISBN: (数字)9783642183058

ISBN: (纸本)9783642183041

this book constitutes the thoroughly refereed post-conference proceedings of the 16th international conference on dna computing and molecular programming, dna16, held in Hong Kong, China, in June 2010. the 16 revised full papers presented were carefully selected during two rounds of reviewing and improvement from 59 submissions. the papers are well balanced between theoretical and experimental work and address all areas that relate to biomolecular computing, including demonstrations of biomolecular computing, theoretical models of biomolecular computing, biomolecular algorithms, computational processes in vitro and in vivo, analysis and theoretical models of laboratory techniques, biotechnological and other applications of dna computing, dna nanostructures, dna devices such as dna motors, dna error evaluation and correction, in vitro evolution, molecular design, self-assembled systems, nucleic acid chemistry, and simulation tools.

关键词： Computation by Abstract Devices Algorithm Analysis and Problem Complexity Computational Biology/Bioinformatics Artificial Intelligence Data Structures

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High-Fidelity dna Hybridization Using Programmable molecular dna Devices

High-Fidelity DNA Hybridization Using Programmable Molecular...

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16th international conference on dna computing and molecular programming

作者： Gopalkrishnan, Nikhil Chandran, Harish Reif, John Duke Univ Dept Comp Sci Durham NC 27708 USA

ISBN: (纸本)9783642183041

the hybridization of complementary nucleic acid strands is the most basic of all reactions involving nucleic acids, but has a major limitation: the specificity of hybridization reactions depends critically on the lengths of the complementary pairs of strands and can drop to very low values for sufficiently long strands. this reduction in specificity occurs especially in the presence of noise in the form of other competing strands that have sequence segments identical to the target. this limits the scale and accuracy of biotechnology and nanotechnology applications which depend on hybridization reactions. Our paper develops techniques for ensuring specific high-fidelity dna hybridization reactions for target strands of arbitrary length. Our protocol is executed autonomously, without external mediation and driven by a series of conversions of single stranded dna into duplex dna that help overcome kinetic energy traps, similar to dna walkers.

关键词： dna hybridization strand displacement

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Search and Validation of Short Genome-Wide Biomarkers for Bacterial Biological Phylogenies

Search and Validation of Short Genome-Wide Biomarkers for Ba...

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16th international conference on dna computing and molecular programming

作者： Garzon, Max H. Wong, Tit-Yee Univ Memphis Memphis TN 38152 USA

ISBN: (纸本)9783642183041

We continue the exploration of dna-based indexing as a universal coordinate system in dna spaces to characterize very large groups (families, genera, and even phylla) of organisms on a uniform biomarker reference system, a comprehensive "Atlas of Life", as it is or as it could be on earth. We provide a second confirmation that dna noncrosshybridizing (nxh) sets can be successfully applied to infer ab-alitio phylogenetic trees by providing a method to measure distances among entire genomes indexed by sets of short oligonucleotides selected so as to minimize crosshybridization. these phylogenies are solidly established and well accepted in bacterial biology, albeit done by analyses of relatively small segments of highly conserved rybozomic dna. Second, it is further demonstrated that dna indexing does provide novel and principled genome-wide predictions into the phylogenesis of organisms hitherto inaccessible by current methods, such as a prediction of the origin of the Salmonella plasmid 50 as being acquired horizontally, likely from some bacteria somewhat related to Yesinia. We conclude with some discussion about the scalability and potential of this method to develop a comprehensive tree of life based on genome-wide methods.

关键词： dna codeword design noncrosshybridizing oligonucleotide bases phylogenetic analysis genomic signatures dna chips 16S rRNA tree of life

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Verification in staged tile self-assembly

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NATURAL computing 2019年第1期18卷 107-117页

作者： Schweller, Robert Winslow, Andrew Wylie, Tim Univ Texas Rio Grande Valley Dept Comp Sci Edinburg TX 78539 USA

We prove the unique assembly and unique shape verification problems, benchmark measures of self-assembly model power, are coNP(NP)-hard and contained in PSPACE (and in II2sP for staged systems with s stages). En route... 详细信息

关键词： dna computing Biocomputing 2HAM Hierarchical

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dna multilayer film for loading and release of dna oligomer 16

DNA multilayer film for loading and release of DNA oligomer

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16th international conference on Organized molecular Films (ICOMF-LB)

作者： Kamimura, Y. Kato, N. Meiji Univ Grad Sch Sci & Technol Kawasaki Kanagawa 2148571 Japan

the Layer-by-Layer (LbL) method using polyelectrolytes is a typical strategy for preparing functional polymeric multi-layered films. Besides the electrostatic force between positively and negatively charged polyelectrolytes, the hybridization force between complementary dna strands can be also used for building the dna LbL films. Herein, we report the thermal responsible dna LbL film that is designed to release specific dna oligomers (10 bases) at an elevated temperature. Because the temperature and the ionic strength (IS) of the medium affect the hydrogen bonds in the double stranded dna, the structural stability of the film against temperature and IS was investigated. the loading and release of the releasable oligomers were repeatedly performed on the dna LbL film.

关键词： Ionic strength

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A Review of dna Cryptography: From a Data Protection Perspective 16

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

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16th international conference on Security of Information and Networks, SIN 2023

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

ISBN: (纸本)9798350343212

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. © 2023 IEEE.

关键词： dna

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Optimizing Tile Concentrations to Minimize Errors and Time for dna Tile Self-assembly Systems

Optimizing Tile Concentrations to Minimize Errors and Time f...

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16th international conference on dna computing and molecular programming

作者： Chen, Ho-Lin Kao, Ming-Yang CALTECH Ctr Math Informat Pasadena CA 91101 USA Northwestern Univ Dept Elect Engn & Comp Sci Evanston IL USA

ISBN: (纸本)9783642183041

dna tile self-assembly has emerged as a rich and promising primitive for nano-technology. this paper studies the problems of minimizing assembly time and error rate by changing the tile concentrations because changing the tile concentrations is easy to implement in actual lab experiments. We prove that setting the concentration of tile T-i proportional to the square root of N-i where N-i is the number of times T-i appears outside the seed structure in the final assembled shape minimizes the rate of growth errors for rectilinear tile systems. We also show that the same concentrations minimize the expected assembly time for a feasible class of tile systems. Moreover, for general tile systems, given tile concentrations, we can approximate the expected assembly time with high accuracy and probability by running only a polynomial number of simulations in the size of the target shape.

关键词： Self assembly

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Using molecular computing for a data analysis prototype

Using molecular computing for a data analysis prototype

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16th international conference on Mechatronics Technology, ICMT 2012

作者： Wu, Kee-Rong Yeh, Chung-Wei Chu, Chih-Ping Department of Marine Engineering National Kaohsiung Marine University Kaohsiung Taiwan Department of Management Information System Kao Yuan University Kaohsiung Taiwan Department of Computer Science and Information Engineering National Cheng Kung University Tainan Taiwan

ISBN: (纸本)9787900769428

We present a promising development of a data analysis model, DAdna, with operational procedures by using deoxyribonucleic acid (dna) computing solution to exploit vast parallelism. the proposed solution is based mainly on the innovative bio-operations by Adleman and Amos to implement table design, simulate relational algebra, cluster and solve query problems. DAdna consists of three layers: (1) a Data definition layer, in which the records are represented by dna strands, (2) an Operational procedure layer, in which fundamental relational and extended operations are executed by dna-based procedures, and (3) a Query-analysis layer, in which the query is executed, involving the construction of relational tables and executing the operations in the Operational procedure layer. Hence, the dna based data cluster design proceeded with our well-organized scheme. Our proposed model can be used as an algorithmic basis for database operational procedures embedded in biomolecular computations for the further development and performing generalized data analysis with inherent molecular parallelism.

关键词： dna

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