The protein memory

EE 428 Class Presentation
A Revolutionizing Idea in Memory Storage
Industry : The Protein Memory
24/04/2016 Advanced Memory Technol ogy

Evolution of Memory Storage
Pictures Papers Punched Tapes
Carvings
Punch Tapes

Selectron tubes
(1946) 4096 bits
Magnetic tape (1950)
Compact Cassette
(1963) 2 MB
The magnetic drum
(1932) 10 KB
World’s first hard
drive(1956) 4.6 MB

The floppy
disk(1969) 250 MB
The hard drive 500 GB
CD /DVD
700MB/8GB
Pen Drive 8GB
Protein Memory

Memory Hierarchy

Primary Memory
Primary
storage
often
referred to
simply as
memory, is
the only one
directly
accessible
to the CPU.
The CPU
continuousl
y reads
instructions
stored there
and
executes
them as
required.

Secondary Memory
Secondary
storage differs
from primary
storage in that
it is not directly
accessible by
the CPU. The
computer
usually uses its
input/ output
channels to
access
secondary
storage and
transfers the
desired data
using
intermediate
area in primary
storage.

Introduction
 So far now memory is stored either mechanically, electrically, magnetically,
optically or chemically but concept of protein memory storage is a complete path
changing technology
 Chemical memory storage is known since long in different forms i.e. RNA, DNA
and some other organic polymer
 Owing to limitations, production hurdle these chemical memory storage are no
in common use
 Protein memory showing promising features and scalability is ready to embark
its journey

History
 Protein memory was discovered by Walther
Stoeckenius and Dieter Oesterhelt at
Rockefeller University in New York
They discovered that a protein isolated from a
salt marsh bacterium exhibited photosensitive
properties. They called this protein
bacteriorhodopsin, because it was very similar
to the protein, rhodopsin that founds in the
eyes of humans and animals

Building Block and Functioning
Protein memory is experimental means to store data up until now
Protein memory is based on bacteriorhodopsin that is extracted from bacteria
Bacteriorhodopsin is an organic molecule that can exist in a variety of chemical
states. It is relatively easy to detect which state the molecules are in, because each
state has different absorptions to light
By choosing two of these states, one for binary zero and the other as binary one,
it is possible to use this as a memory device

Bacteriorhodopsin
Purple membranes of Halo bacterium halobium
Changes mode of operation upon light incident
Light energy to chemical energy conversion
Purple
Membrane
The purple membrane patches are areas on the membrane where BR is conc.
BR absorbs light @ 570 nm (visible green light)
Red and Blue light is reflected, giving membrane its purple color

Why Bacteriorhodopsin?
 The protein is extremely stable to degradation, both thermally and photo
chemically
 It uses light energy to transport charges thereby converting energy from light to
chemical forms
 It self assembles into thin films
 Additionally, current advances in molecular biology imply that these proteins
can be easily mass produced

Sources of br
• Archaebacteria Halobacteria Salinarium are the source of
bacteriorhodopsin
• They are halophilic bacteria (found in very salty water e.g.
Great Salt Lake)
• This particular bacteria live 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

Making of Protein Cube
 First the bacterial DNA is splice and mutated to make the protein more efficient
for use as a volumetric memory
 The bacteria must be grown in large batches and the protein extracted
 Bacteriorhodopsin is then combined with inert transparent gel and stored in a
cube

Photocycle of br

Elaboration of Photocycle
 Bacteriorhodopsin comprises a light absorbing component known as
CHROMOPHORE , that absorbs light energy and triggers a series of complex
internal structural changes to alter the protein’s optical and electrical
characteristics and involved phenomenon is known as photocycle
 Green light Changes the initial resting state known as Br to the intermediate K
 Next K relaxes, forming M and then O
 The O state is the red absorbing intermediate state
 O converts to the P state and quickly relaxes to the Q state-a form that remains
stable indefinitely. Blue light will however convert Q back to bR

Cont…

Molecular Structure of br
Quite similar to Rhodopsin, the light detecting pigment in retina of eyes

Principle of Storage
 Two lasers are positioned next to the cube, one looking vertically through the cube (red laser),
and the other looking horizontally down (green laser). Each laser has an LCD display between
the laser and the cube.
 The green laser (paging LCD) illuminates a vertical slice of matter called ‘page memory’
 The red laser (write laser) illuminates the pattern displayed on the LCD (which is a binary
representation of the data) onto the matter on the cube as in fig.

Cont…
 The matter that is illuminated by the green laser and also hit by the red laser
shifts state. It requires both lasers to shift state, so the rest of the matter that is
illuminated by the green laser or the red laser only is not affected
 The pattern that was displayed on the LCD in front of the red laser has thus been
transferred onto the illuminated page of memory
 On the opposite side of the cube, in front of the red laser there is a CCD (charge-
coupled device) detector that is used to read the data from the memory

Actual Implementaion and Working

Data Operation(Writing)
• The green or 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 red beams is fired which 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

Data Reading Technique
 First, the green paging beam is fired at the square of protein to be read
 After two milliseconds 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

Data Erasing
 To erase data, a brief pulse from a blue laser returns molecules in the Q state
back to the rest state
 The blue light doesn't necessarily have to be a laser
 We can bulk-erase the cuvette by exposing it to an incandescent light with
ultraviolet output

Refreshing Memory
 To ensure data integrity during selective page-erase operations
 A page of data can be read nondestructively about 5000 times
 Each page is monitored by a counter, and after 1024 reads, the page is refreshed
via a new write operation

Advantage of Using Protein Memory
• Because it is protein based and thus is inexpensive to produce in quantity
• Can operate over a wider range of temperatures much larger than semiconductor
memory
• Non-volatile, can be used for storage and memory

Issues Needing to be Resolved
• The polymer gel that the protein is put in breaks down faster than the protein
itself. The protein can withstand the laser light, but the gel breaks down after a
while. This is a major obstacle for protein memory
• Mutations could affect the photochemical properties of the protein

Some other promising uses of br
• Ultra fast RAM
• Finger Print Processing
• Optical Switches
• Neural Logic Gates(genetic Engineering)

Conclusion
• During the past decade, the speed of computer processors increased almost 1,000
times, where as data storage capacities increased only by a factor of 50. Also, the
transfer of data within the computer remains the principal bottleneck that limits
performance
• Protein memories use laser beam, which improve their life with reduction in wear
and tear

References
• Protein Based Computers Birge, Robert R., Scientific American March 1995
• Molecular and Biomolecular Electronics, Birge, Robert R. Ed., American
Chemical Society
• Organic Chemistry Baker, A. David, Robert Engel
• www.che.syr.edu (Department of Chemistry, Syracuse University

The protein memory

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The protein memory