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 ...
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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.
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 ...
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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.
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 ...
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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 biomolecularcomputing, including demonstrations of biomolecularcomputing, theoretical models of biomolecularcomputing, biomolecular algorithms, computational processes in vitro and in vivo, analysis and theoretical models of laboratory techniques, biotechnological and other applications of dnacomputing, 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.
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 leng...
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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 dnathat help overcome kinetic energy traps, similar to dna walkers.
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 syst...
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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.
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...
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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, we prove that unique shape verification problem in the 2HAM is coNP(NP)-complete.
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 polyelectr...
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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.
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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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...
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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.
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 mainl...
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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.
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