Computation = Self-assembly + Conformational Change Toward New Computing Paradigms. to app.pdf

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Computation = Self-assembly + Conformational Change Toward New Computing Paradigms. to app.pdf

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Computation=Self-assemblyConformationalChangeTowardNewComputingParadigms.toapp

(Presented at DLT99, Aachen, July 6-9, 1999.) Computation = Self-assembly + Conformational Change : Toward New Computing Paradigms Takashi Yokomori Department of Mathematics, School of Education, Waseda University, 1-6-1 Nishi-waseda, Shinjuku-ku, Tokyo 169-8050, JAPAN: yokomori@mn.waseda.ac.jp Abstract. Molecular Computing is a novel computing paradigm recently emerged from and stimulated by a groundbreaking wet lab experimental work by Adleman in 1994. Since then, a great number of computation models have been proposed in the context of both biomolecular experiments and theoretical computer science (e.g., [2, 3, 7, 9, 10, 11, 13, 17, 19, 20]), trying to break through the so-called NP-completeness barrier or to establish new computation paradigms with universal capability. This paper proposes new computing paradigms based on self-assembly and conformational change. These two principles have already appeared in an extensive variety of literature in natural science, while relatively a few studies have discussed these two together in the context of computing. In order to demonstrate a new computing schema : computation = self- assembly + conformational change, we rst discuss a framework of computing model CCC (Computing by Conformational Change) by showing examples of solving several NP-complete problems within the framework. We then review that the proposed new computing paradigm is computationally universal. 1 conformational change fusion circle Natural Constraints (surface tension) rectangle Artificial Constraints + + conformational change fusion ? Figure 1: Examples of Uncoded Self-assembly([21]) 1 Self-Assembly Computations | Coded v.s. Un- coded The phenomena of so-called self-assembly can be seen at various places, time, and occasions. For example, \ raindrops on a leaf autonomously merge together into one bigger drop. This is known as a typical example of uncoded self-assembly, where self-assembly of each component is obeyed by a simple principle of po