ゲノム情報科学研究教育機構  アブストラクト
Date June 7, 2004
Speaker Dr. Jian-Qin LIU, Network Informatics Laboratories, ATR
Title Kinase computing: exploring computational mechanism by signaling pathways in cells
Abstract
  Using the living cell, which is one of the most promising functional materials for building nanobiomachines for massively parallel computation, a new biomolecular computing method - Kinase Computing - is initiated.   Kinase computing process is carried out based on the signaling pathways of phosphorylation and dephosphorylation switched by kinases and phosphatases that are regulated by upstream pathways of Rho family GTPases in living cells.  In the viewpoint of methodology, kinase computing differs from the Adleman-Lipton paradigm of DNA computers.  The two main merits of this type of biomolecular computing process are the low cost of pathway control for cells and the high efficiency of the related computing processes, when certain pathway controllers are designed for the engineered pathway units of biomolecular computers.

  In this talk, feasible protocols (algorithms), a computation model, benchmark testing (by 3-SAT problem solving) and interaction/cross-talk mechanism of kinase computing will be presented.  In order to obtain high programmability from molecular computation, the pathway regulation schemes for universal computation are designed and simulated.  The latest results on designing feasible operators and the related computer architecture by the engineered pathways in cells under the regulation of Rho family GTPases for large-scale biomolecular computers will be discussed as well.  Here, the crosstalking processes among the pathways, feedback between the downstream and upstream pathways, and interaction with the nuclear receptors of cells are employed.  This is prerequisite for experimental implementation of a computing nanobiomachine based on the signaling pathways of Rho family GTPases and in the form of MDCK epithelial cells.  Consequently, the costs can be cut in the number of controlled signaling molecules for engineered pathways when the interaction ratings of pathways are regulated on the scale of an entire cell.  In terms of designed controllable cross-talk mechanism of engineered GTPase-based signaling communications, stable kinase computing under dynamical environment of cell culture (i.e., assay) can be obtained in theory and in simulation.  This is significant to the applications of molecular computing in modeling and simulation for medical designing by bioinformatics and is also expected to be helpful to new nature-inspired unconventional computing paradigms.
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