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. |