The protein memory

EE 428 Class Presentation

A Revolutionizing Idea in Memory Storage Industry : The Protein Memory

24/04/2016 Advanced Memory Technology

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


Storage

Primary

Registers Cache Main

Secondary

Magnetic Disk

Optical Disk

Tertiary

Primary Memory


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

Registers • These are located inside the processor. Each register typically holds a word of data (often 32 or 64 bits• Registers are the fastest of all forms of computer data storage.

Cache • It is an intermediate stage between ultra-fast registers and much slower main memory.•Most actively used information in the main memory is just duplicated in the cache memory, which is faster, but of much lesser capacity.

Main •Main memory is directly or indirectly connected to the central processing unit via a memory bus•It consists of RAM & ROM

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.

Magnetic•It is usually used as secondary storage. The time taken to access a given byte of information stored on a hard disk is typically a few thousandths of a second, or milliseconds.•It includes tape, Hard disk, floppy Disk etc.

Optical •An optical disk is a high-capacity storage medium. An optical drive uses reflected light to read data.•It includes CD-R, CD-RW, DVD, Blue ray etc.

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 conversionPurple

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

Thank You

The protein memory

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