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Towards computational nanotechnology based on protein automata

Claudio Nicolini a, b, c,*, Alessandro Vinciarellic, Victor Sivozhelezova

aFondazione El.B.A., Corso Europa 30, Genova, 16132, Italy
bInstitute of Biophysics, University of Genova, Corso Europa 30, Genova 16132, Italy
cPolo Nazionale Bioelettronica, Via Roma 28, Marciana (Li), 57030, Italy

This is an abstract for a presentation given at the
Sixth Foresight Conference on Molecular Nanotechnology.
There will be a link from here to the full article when it is available on the web.


Considering that the dimensions of the current smallest electronic device (ca 100 nm, 108 atoms) would lead, at the current rate of progress, to the atomic scale in twenty years, computational nanotechnology at least for what concerns dimensions. While such kind of progress is just quantitative the utilization of biopolymers might add a difference in behaviuor with respect to inorganic semiconductors also in qualitative terms, giving to the word computers a new and broader sense. The performance of computers would then be not only increased but also changed. To understand how the performance will change, we need first to model as better as possible the physical properties of the new materials we have using, then try to give the physical phenomena a semantic that could allow the device to perform a given computational task. To outline our progress towards this end is indeed the goal of our comunication.

Cholesterol side chain cleavage cytochrome P450scc is the biopolymer utilized in this study because on the one hand, stable monolayers of cytochrome P450scc and its complex with adrenodoxin are found to be easily formed by Langmuir techniques and covalently immobilized on the solid substrates, and, on the other hand, it is unusual among member of this class of enzymes in showing a high degree of substrate specificity.

Cellular Automation is implemented to model and to understand the nanocomputational properties emerging (if any) from the interactions among the P450scc molecules which are here described in terms of their electrostatic potential distribution pattern of P450scc monolayers. In this pattern, the molecules should be oriented in such a way as to avoid exposure of their charged areas to the air-water interface. A simulation with cellular automata has been performed where each protein is initially treated as an electric dipole and interacts only with the neighboring molecules changing its orientation in order to achieve the energy minimum.

This model needs a rotational mobility of the proteins that is actually present in the LB films formed at the air/water interface. The dipoles now present only two directions (vertical and horizontal) and for each direction the two charges can be positioned in two alternative ways. The next step of the model will be the extension from a Von-Neumann neighbourhood to a Moore neighbourhood and an increase of the possible configurations of the dipoles and the quadrupoles.

The interesting features emerging from the time evolution of the trexture and their relevance to computational nanotechnology will be discussed.

*Corresponding Address:
Prof. Claudio Nicolini
Institute of Biophysics, University of Genoa
Corso Europa 30, 16132 Genova Italia
Tel. ++39-10-3538381; Fax ++39-10-3538346


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