Protein-based memory

The fact that bacteriorhodopsin is photochromic implies that laser light can conveniently be used to write and read information to and from materials where the protein is the information carrier. The most commonly used transition between intermediates in the photocycle is the one from the resting state (bR) to the M-state, which is stable at room temperature (Fig. 2.8). 

To read the memory, the same combination of green and red laser can be used, only that the red laser is reduced in intensity such that it does not induce structural changes. However, the red light will be absorbed by the O intermediates, which the green light will only produce in the 0 sites, and it will not be absorbed by the molecules in the P and Q states. 

Thus simultaneous writing of ca. 100 kbytes in one cube can be achieved in less than 

10 milliseconds. While this corresponds to a rather slow semiconductor memory, the speed can be further increased by addressing several cubes simultaneously. 

Of course the sheer presence of a third dimension which can be used gives the rhodopsin memory (and holographic memories made from inorganic crystals such as lithium niobate) a major advantage over two-dimensional media such as the CD-ROM. As Robert Birge wrote in Scientific American in March 1995, we should anticipate that the major near-term impact of bioelectronics on computer hardware will be in the area of volumetric memory.  

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Kim SU, Yagati AK, Min JH, Choi JW (2010) Nanoscale protein-based memory device composed of recombinant azurin. Biomateiials 31 1293-1298... 

Bitge R R 1990 Nature of the primary photochemical events in rhodopsin and bacteriorhodopsin Biochim. Biophys. Acta 1016 293-327 Birge R R 1992 Protein-based optical computing and memories IEEE Comput. 25 56-67... 

Birge, R.R. et al, Biomolecular electronics protein-based associative processors and volumetric memories. /. Phys. Chem. B., 1999,103 10746-10766. 

Dirge, R.R. (1994) Protein-based three-dimensional memory. American Scientist 82, 348-355. 

Several attempts were made to apply nanostructures made of DNA or proteins to the development of alternative computation or computer memory. The concept of DNA computing was developed as an alternative computation approach based on information and data stored as sequenced DNA nucleotides and DNA-specific hybridization and elongation as a means to reach the answer or solution to a problem. Available tools of molecular biology were employed to identify and analyze the results [66-68]. This multistage computation is based on the assumption that solutions can be sought in parallel, thus compensating for the relatively slow processing time. 

Density functional theory (DFT),32 also a semi-empirical method, is capable of handling medium-sized systems of biological interest, and it is not limited to the second row of the periodic table. DFT has been used in the study of some small protein and peptide surfaces. Nevertheless, it is still limited by computer speed and memory. DFT offers a quantum mechanically based approach from a fundamentally different perspective, using electron density with an accuracy equivalent to post Hartree-Fock theory. The ideas have been around for many years,33 34 but only in the last ten years have numerous studies been published. DFT, compared to ab initio... 

This difference between the two divisions of biologically important polymers is also reflected in the likelihood that there are two molecules with the exact same structure. For molecules such as polysaccharides and those based on terpene-like structures the precise structures of individual molecules vary, but for proteins and nucleic acids the structures are identical from molecule to molecule. This can be considered a consequence of the general function of the macromolecule. For polysaccharides the major, though not the sole, functions are energy and structure. For proteins and nucleic acids, the main functions include memory and replication, in addition to proteins sometimes also serving a structural function. 

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