Towards molecular computers that operate in a biological environment
Towards molecular computers that operate in a biological environment
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DOI：
10.1016/j.physd.2008.01.027
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发表时间：
2008-07-01
影响因子：
4
通讯作者：
Shapiro, Ehud
中科院分区：
文献类型：
--
作者：
Kahan, Maya;Gil, Binyamin;Shapiro, Ehud
尽管电子计算机是我们唯一熟悉的计算机种类，但可编程计算机的数学概念与电子学无关。事实上，艾伦·图灵的概念计算机[L.M.图灵，可计算的数字，与应用程序的entcheidungsproblem，Proc。Math.Soc.42（1936）230-265]，它在1936年标志着现代计算机科学的诞生，并且仍然是它的核心，它与自然生物分子机器如核糖体和聚合酶比电子计算机具有更大的相似性。这种相似性导致了对基于DNA的计算机的研究[C.H.班尼特，计算热力学-综述，国际理论物理杂志21（1982）905-940; A. M. Adleman，组合问题解的分子计算，科学266（1994）1021-1024]。尽管DNA和RNA分子固有的并行性、序列特异性杂交和存储能力可以在分子计算机中被利用来解决复杂的数学问题[Q。Ouyang等人，最大团问题的DNA解决方案，科学278（1997）446-449; R. J. Lipton，硬计算问题的DNA解决方案，科学268（1995）542-545; R.S. Braich等人，DNA计算机上的20变量3-SAT问题的解决方案，Science 296（2002）499-502; Liu Q.，等，表面上的DNA计算，自然403（2000）175-179; D. Faulhammer等人，分子计算：RNA解决国际象棋问题，美国国家科学院院刊。Acad. Sci. USA 97（2000）1385-1389; C. Mao等人，使用DNA三重交叉分子的算法自组装进行逻辑计算，Nature 407（2000）493-496; AJRuben等人，分子计算的过去，现在和未来，Nat. Rev. Mol. Cell. 1（2000）69-72]，我们相信分子计算机更重要的潜力在于它们能够直接与诸如血流和活细胞的生物化学环境相互作用。从这个角度来看，即使是简单的分子计算，在适当的情况下执行时也可能产生重要的后果。我们设想，在生物环境中运行的分子计算机可以成为“智能药物”的基础，智能药物是只有在特定环境条件下才能激活的强效药物。这些病症可能包括指示特定疾病的生物环境的分子组成的异常。在这里，我们回顾的研究方向，设置这一愿景，并试图实现它。（c）2008年爱思唯尔B. V.保留所有权利。
Even though electronic computers are the only computer species we are accustomed to, the mathematical notion of a programmable computer has nothing to do with electronics. In fact, Alan Turing's notional computer [L.M. Turing, On computable numbers, with an application to the entcheidungsproblem, Proc. Lond. Math. Soc. 42 (1936) 230-265], which marked in 1936 the birth of modem computer science and still stands at its heart, has greater similarity to natural biomolecular machines such as the ribosome and polymerases than to electronic computers. This similarity led to the investigation of DNA-based computers [C.H. Bennett, The thermodynamics of computation - Review, Int. J. Theoret. Phys. 21 (1982) 905-940; A.M. Adleman, Molecular computation of solutions to combinatorial problems, Science 266 (1994) 1021-1024]. Although parallelism, sequence specific hybridization and storage capacity, inherent to DNA and RNA molecules, can be exploited in molecular computers to solve complex mathematical problems [Q. Ouyang, et a]., DNA solution of the maximal clique problem, Science 278 (1997) 446-449; R.J. Lipton, DNA solution of hard computational problems, Science 268 (1995) 542-545; R.S. Braich, et al., Solution of a 20-variable 3-SAT problem on a DNA computer, Science 296 (2002) 499-502; Liu Q., et al., DNA computing on surfaces, Nature 403 (2000) 175-179; D. Faulhammer, et al., Molecular computation: RNA solutions to chess problems, Proc. Natl. Acad. Sci. USA 97 (2000) 1385-1389; C. Mao, et al., Logical computation using algorithmic self-assembly of DNA triple-crossover molecules, Nature 407 (2000) 493-496; A.J. Ruben, et al., The past, present and future of molecular computing, Nat. Rev. Mol. Cell. Biol. 1 (2000) 69-72], we believe that the more significant potential of molecular computers lies in their ability to interact directly with a biochemical environment such as the bloodstream and living cells. From this perspective, even simple molecular computations may have important consequences when performed in a proper context. We envision that molecular computers that operate in a biological environment can be the basis of "smart drugs", which are potent drugs that activate only if certain environmental conditions hold. These conditions could include abnormalities in the molecular composition of the biological environment that are indicative of a particular disease. Here we review the research direction that set this vision and attempts to realize it. (c) 2008 Elsevier B.V. All rights reserved.