[DIYbio] Re: Computer Memory Based on the Protein Bacteriorhodopsin Utilizing the Two-Photon Method for Read/Write Procedures

I woke up this morning and remembered this old piece of work. Who else
remembers it?

Computer Memory Based on the Protein Bacteriorhodopsin Utilizing the
Two-Photon Method for Read/Write Procedures
http://web.archive.org/web/20071029220616/http://www.cem.msu.edu/~cem181h/projects/96/memory/index.html

"While magnetic and semi-conductor based information storage devices
have been in use since the middle 1950's, today's computers and
volumes of information require increasingly more efficient and faster
methods of storing data. Whilethe speed of integrated circuit random
access memory (RAM) has increased steadily over the past ten to
fifteen years, the limits of these systems are rapidly approaching. In
response to the rapidly changing face of computing and demand for
physically smaller, greater capaticy, bandwidth, a number of
alternative methods to integrated circuit information storage have
surfaced recently. Among the most promising of the new alternatives
are photopolymer-based devices, holographic optical memory storage
devices, and protein-based optical memory storage using rhodopsin ,
photosynthetic reaction centers, cytochrome c, photosystems I and II,
phycobiliproteins, and phytochrome. This website focuses mainly on
protein-based  optical memory storage using the photosensitive protein
bacteriorhodopsin with the two-photon method of exciting the
molecules, but briefly describes what is involved in the other two.
Bacteriorhodopsin is a light-harvesting protein from bacteria that
live in salt marshes that has shown some promise as a feasible optical
data storage. The current work is to hybridize this biological
molecule with the solid state components of a typical computer."

"There have been many methods and proteins researched for use in
computer applications in recent years. However, among the most
promising approaches, and the focus of this particular webpage, is
3-Dimensional Optical RAM storage using the light sensitive protein
bacteriorhodopsin. Bacteriorhodopsin is a protein found in the purple
membranes of several species of bacteria, most notably Halobacterium
halobium. This particular bacteria lives in salt marshes. Salt marshes
have very high salinity and temperatures can reach 140 degrees
Fahrenheit. Unlike most proteins, bacteriorhodopsin does not break
down at these high temperatures. Early research in the field of
protein-based memories yielded some serious problems with using
proteins for practical computer applications. Among the most serious
of the problems was the instability and unreliable nature of proteins,
which are subject to thermal and photochemical degradation, making
room-temperature or higher-temperature use impossible. Largely through
trial and error, and thanks in part to nature's own natural selection
process, scientists stumbled upon bacteriorhodopsin, a
light-harvesting protein that has certain properties which make it a
prime candidate for computer applications. While bacteriorhodopsin can
be used in any number of schemes to store memory, we will focus our
attention on the use of bacteriorhodopsin in 3-Dimensional Optical
Memories."

"Three-dimensional optical memory storage offers significant promise
for the development of a new generation of ultra-high density RAMs
(Birge, Computer, 63). One of the keys to this process lies in the
ability of the protein to occupy different three-dimensional shapes
and form cubic matrices in a polymer gel, allowing for truly
three-dimensional memory storage. The other major component in the
process lies in the use of a two-photon laser process to read and
write data. As discussed earlier, storage capacity in two-dimensional
optical memories is is limited to approximately 1/lambda2 (lambda =
wavelength of light), which comes out to approximately 108 bits per
square centimeter. Three-dimensional memories, however, can store data
at approximately 1/lambda3, which yields densities of 1011 to 1013
bits per cubic centimeter. The memory storage scheme which we will
focus on, proposed by Robert Birge in Computer (Nov. 1992), is
designed to store up to 18 gigabytes within a data storage system with
dimensions of 1.6 cm * 1.6 cm * 2 cm. Bear in mind, this memory
capacity is well below the theoretical maximum limit of 512 gigabytes
for the the same volume (5-cm3)."

(For the moment, that's about 18 TB in the volume of what one of my
(non-flash-based) 1 TB drives takes up.)

"Bacteriorhodopsin, after being initially exposed to light (in our
case a laser beam), will change to between photoisomers during the
main photochemical event when it absorbs energy from a second laser
beam. This process is known as sequential one-photon architecture, or
two-photon absorption. While early efforts to make use of this
property were carried out at cryogenic temperatures (liquid nitrogen
temperatures), modern research has made use of the different states of
bacteriorhodopsin to carry out these operations at room-temperature.
The process breaks down like this: Upon initially being struck with
light (a laser beam), the bacteriorhodopsin alters its structure from
the bR native state to a form we will call the O state. After a second
pulse of light, the O state then changes to a P form, which quickly
reverts to a very stable Q state, which is stable for long periods of
time (even up to several years). The data writing technique proposed
by Dr. Birge involves the use of a three-dimensional data storage
system. In this case, a cube of bacteriorhodopsin in a polymer gel is
surrounded by two arrays of laser beams placed at 90 degree angles
from each other. One array of lasers, all set to green (called
"paging" beams), activates the photocycle of the protein in any
selected square plane, or page, within the cube. After a few
milliseconds, the number of intermediate O stages of bacteriorhodopsin
reaches near maximum. Now the other set, or array, of lasers - this
time of red beams - is fired. The second array is programmed to strike
only the region of the activated square where the data bits are to be
written, switching molecules there to the P structure. The P
intermediate then quickly relaxes to the highly stable Q state. We
then assign the initially-excited state, the O state, to a binary
value of 0, and the P and Q states are assigned a binary value of 1.
This process is now analogous to the binary switching system which is
used in existing semiconductor and magnetic memories. However, because
the laser array can activate molecules in various places throughout
the selected page or plane, multiple data locations (known as
"addresses") can be written simultaneously - or in other words, in
parallel. "

"The system for reading stored memory, either during processing or
extraction of a result, relies on the selective absorption of red
light by the O intermediate state of bacteriorhodopsin. To read
multiple bits of data in parallel, we start just as we do in the
writing process. First, the green paging beam is fired at the square
of protein to be read. After two milliseconds (enough time for the
maximum amount of O intermediates to appear), the entire red laser
array is turned on at a very low intensity of red light. The molecules
that are in the binary state 1 (P or Q intermediate states) do not
absorb the red light, or change their states, as they have already
been excited by the intense red light during the data writing stage.
However, the molecules which started out in the binary state 0 (the O
intermediate state), do absorb the low-intensity red beams. A detector
then images (reads) the light passing through the cube of memory and
records the location of the O and P or Q structures; or in terms of
binary code, the detector reads 0's and 1's. The process is complete
in approximately 10 milliseconds, a rate of 10 megabytes per second
for each page of memory. Clearly, there are many advantages to
protein-based memory, among the most significant being cost, size, and
memory density. However, there are still several barriers standing in
the way of mass-produced protein-based memories."

(Ewww, 10 MB/sec! For reference, SATA2 drives can do up to 3 GB/sec of
transfer, and USB2 has a theoretical max of 60 MB/sec.)

Also, here's what I've been reading on the subject.. rhodopsin geeks
might find it useful for other reasons:

http://designfiles.org/papers/bacteriorhodopsin_memory/

- Bryan
http://heybryan.org/
1 512 203 0507