Rahul

Protein Optical BasedMemory

Rahul Kumar Sinha2006EEC17

Evolution of Storage Memory

Pictures

Carvings

Papers

Punch Cards (1725)

Punched Tapes (1846)

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

What is Protein Memory?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.

Source of BRArchaebacteria 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.

Source of H.salinarum

H. Salinarum Electronmicrograph

What is the Purple Membrane?The purple membrane patches are areas on

the membrane where BR is concentratedBR absorbs light @ 570 nm (visible green

light)Red and Blue light is reflected, giving

membrane its purple colour

Why Bacteriorhodopsin?The protein is extremely stable to

degradation, both thermally and photochemically.

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

Making of Protein CubeFirst 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.

Phototcycle of Bacteriorhodopsin

PHOTOCYCLE OF BACTERIORHODOPSIN 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. This 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

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.

Principle of Storage

Contd.

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 Implementation and Working

Data OperationData Writing TechniqueData Reading TechniqueData ErasingRefreshing the memory

Data Writing Technique• 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 ErasingTo 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 the memoryTo ensure data integrity during selective

page-erase operationsA 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.

Issues Left 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

Advantages of using protein memory: Because it is protein based it 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

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