摘要:
DNA计算机的可扩展性问题是近年来生物计算领域的重要研究重点之一.根据精确覆盖问题DNA计算求解过程中的并行计算需求,将Aldeman-Lipton模型的操作与粘贴模型的解空间结合,引入荧光标记和凝胶电泳技术,提出了一种求解精确覆盖问题的DNA计算模型和基于分治方法的DNA计算机算法.算法由初始解空间生成算法Init()、冗余解删除算法IllegalRemove()和并行搜索器ParallelSeacher()共3个子算法组成.与同类算法的性能比较分析表明:本算法在保持多项式生物操作复杂性的条件下,将求解n维精确覆盖问题的DNA链数从O(2\+n)减少至O(1.414\+n),从而将DNA计算机在试管内可求解的精确覆盖问题集合的基数从60提高到120,改进了相关文献的研究结果.
Abstract:
The scalability problem in DNA computer has been one of the important research areas in DNA computing. According to the requirement of the DNA parallel computing for exact cover problem, a DNA model for good scalability is proposed, which is based on the biological operations in the Adleman-Lipton model and the solution space of stickers in the sticker-based model by simultaneously taking the method of fluorescence labeling and the technique of gel electrophoresis into the model. Based on this model, a DNA-based algorithm for the exact cover problem, by making use of the strategem of divide-and-conquer, is also proposed which consists of three sub-algorithms: Init(), IllegalRemove(), and ParallelSeacher(). Compared with by far the best molecular algorithm for the exact cover problem with n variables and m sets in which O(2\+n) DNA strands are used, this algorithm can solve the same problem only using O(1.414\+n) DNA strands on the condition of not varying the time complexity. Therefore, the cardinal number of the exact cover problem that can be theoretically resolved in a test tube may be enlarged from 60 to 120, and thus the proposed algorithm is an improved result over the past researches.
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