Protein-based optical memory storage
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Computer Science Clay
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01-03-2009, 02:10 PM


Protein-based optical memory storage

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. While the 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 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.
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seminar surveyer
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20-10-2010, 05:19 PM


PRESENTED BY :
NJOKU CHIKWADO


.doc   PROTEIN MEMORY.doc (Size: 81 KB / Downloads: 148)


Abstract
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. While the 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 capacity, 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 article 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 feasible optical data storage. The current work is to hybridize this biological molecule with the solid state components of a typical computer.

INTRODUCTION
Since the dawn of time, man has tried to record important events and techniques for everyday life. At first, it was sufficient to paint on the family cave wall how one hunted. Then come the people who invented spoken languages and the need arose to record what one was saying without hearing it firsthand. Therefore, years later, earlier scholars invented writing to convey what was being said. Pictures gave way to letters which represented spoken sounds. Eventually clay tablets gave way to parchment, which gave way to paper. Paper was, and still is, the main way people convey information. However, in the mid twentieth century computers began to come into general use.

Computers have gone through their own evolution in storage media. In the forties, fifties, and sixties, everyone who took a computer course used punched cards to give the computer information and store data. In 1956, researchers at IBM developed the first disk storage system. This was called RAMAC (Random Access Method of Accounting and Control)

Since the days of punch cards, computer manufacturers have strived to squeeze more data into smaller spaces. That mission has produced both competing and complementary data storage technology including electronic circuits, magnetic media like hard disks and tape, and optical media such as compact disks.

Today, companies constantly push the limits of these technologies to improve their speed, reliability, and throughput -- all while reducing cost. The fastest and most expensive storage technology today is based on electronic storage in a circuit such as a solid state "disk drive" or flash RAM. This technology is getting faster and is able to store more information thanks to improved circuit manufacturing techniques that shrink the sizes of the chip features. Plans are underway for putting up to a gigabyte of data onto a single chip.

Magnetic storage technologies used for most computer hard disks are the most common and provide the best value for fast access to a large storage space. At the low end, disk drives cost as little as 25 cents per megabyte and provide access time to data in ten milliseconds. Drives can be ganged to improve reliability or throughput in a Redundant Array of Inexpensive Disks (RAID). Magnetic tape is somewhat slower than disk, but it is significantly cheaper per megabyte. At the high end, manufacturers are starting to ship tapes that hold 40 gigabytes of data. These can be arrayed together into a Redundant Array of Inexpensive Tapes (RAIT), if the throughput needs to be increased beyond the capability of one drive.

For randomly accessible removable storage, manufacturers are beginning to ship low-cost cartridges that combine the speed and random access of a hard drive with the low cost of tape. These drives can store from 100 megabytes to more than one gigabyte per cartridge.

Standard compact disks are also gaining a reputation as an incredibly cheap way of delivering data to desktops. They are the cheapest distribution medium around when purchased in large quantities ($1 per 650 megabyte disk). This explains why so much software is sold on CD-ROM today. With desktop CD-ROM recorders, individuals are able to publish their own CD-ROMs.

With existing methods fast approaching their limits, it is no wonder that a number of new storage technologies are developing. Currently, researches are looking at protein-based memory to compete with the speed of electronic memory, the reliability of magnetic hard-disks, and the capacities of optical/magnetic storage. We contend that three-dimensional optical memory devices made from bacteriorhodopsin utilizing the two photon read and write-method is such a technology with which the future of memory lies.


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20-06-2011, 03:04 PM


.ppt   Protein based data storage.ppt (Size: 1.97 MB / Downloads: 125)
Introduction
Topic : Disk storage & relevant technologies
Title : Protein based optical data storage
Why new technology
Protein feasibility
Types of protein
bR
Read-Write-Erase
Concerns
The Future
Why new technology?
Design and construction of smaller is becoming difficult
Magnetic & semiconductor based storage are nearing up their limits
The cost of producing smaller chips is skyrocketing
laws of physics will halt the progression of decreasing die
But Demand for higher capacity is increasing
More Problems
Semiconductors rely on electrons
Electrons although fast have mass and are limited in velocity
Photolithography is used in manufacturing semiconductor based devices
light source must be at least as small as the features we're trying to fashion
the wavelengths of the spectrum are fixed and will not change
Optical computing(using Protein) will over come these
Optical computing relies on photons
Photons based on light waves have no mass & travel at the speed of light
Types of Protein available
Using Bacterorhodopdisin(bR)
Using phycobiliproteins
Using phytochrome
Using Cytochrome C
Ferritin
Fluroscent Protein(FP595)
Protein based storage
bR protein is used as storage
20 times more storage than Blue-ray disc
Stores 50 TB of data
New protein coated DVDs –medical,entertainment,defence
Molecular switches-reduction in hardware size(1/20th) of present size
More reliable
More efficient
Unaffected by electromagnetic interference
Faster
Incorporation of much thinner materials
No high temperature manufacturing
Why Bacteriorhodopsin(bR)?
Can withstand very high temperature
Resist photochemical damages
Posses stable intermediates
Photoactive protein
Reduction in wear & tear
Can be prepared in mass quantities.
bR is protected against photo-induced breakdown
The cubes' resistance to electromagnetic effects
bR Properties
Bacteriorhodopsin (bR) is found in purple membranes of Halobacterium halobium.
In salt marshes-salinity 6times of sea water
Temperature exceeds 150F for long period
Switching time, 500 femtoseconds
10,000 molecules/bit
Bistable red green switch
Coupled with 3D Technology
Structure of Bacteriorhodopsin
3-D Optical Memory
Ability of the protein to occupy different 3D shapes in polymer gel
Form cubic matrices in polymer gel in cuvette
Use of two photon laser process
Ultra high density RAMs
Faster database transactions
Storage capacity in 2D optical memories is approx 1/lambda2 i.e. 108 bits per cm2
3D-memories, store s data at approx 1/lambda3 - yields densities of 1011 -1013 bits per cm3
18 GB within a data storage system - 1.6 cm * 1.6 cm * 2 cm.
Theoretical maximum limit of 512 GB for the same volume (5-cm3).
3-D Model
Two Photon Method
Red-Green-Blue laser source are used
A Read-Write-Erase Process
All of the molecules are reached without altering other molecules
The two photons would each have only part of the energy needed to change the
state of bR.
They would pass through the polymer until they coincided at a point and changed a molecule of bR
Photocycle
Chromophore : Light absorbing component in bR
The Method
Molecule changes states within microseconds
Combined steps to read or write operation take about 10 milliseconds
device obtains data pages in parallel
Speed currently limited by laser addressing
At present 10Mbps
Write Process
2 arrays of laser beams placed at 90 degree
Green array activates the Photocycle of the protein in any selected square plane, or page, within the cube.
O stages of bR reaches near maximum.
Now the red beams fired.
The second array(red) strikes 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.
Cntd..
O->0
P->1
Q->1
laser array activate molecules in various places throughout the selected page or plane
multiple data locations (known as "addresses") can be written in parallel
Read Process
Green paging beam is fired at the square of protein to be read
Red laser array is turned on
The molecules that are in the binary state 1 (P or Q intermediate states) do not absorb the red light
The molecules -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
records the location of the O and P or Q structures
In terms of binary code, the detector reads 0's and 1's.
Data Read
Data Erasing
Blue laser erases encoded data
Q state absorb blue light and return to original bR state
Individual data can be erased using blue laser
Global wipe possible with incoherent blue laser source
Data Reliability
Data is highly stable
Even the power is off, memory retains its information
Energy efficient computer that can be switched on/off instantly
No waste of booting time
Future Applications of bR
Ultra fast RAM

Erasable holographic memory\
Use in holographic interferometry camera
Electronic Ink(optical chameleon)
Pattern Recognition Systems-e.g.genetic library scanning,
Finger print processing
Neural Logic gates (genetic engineering)
High contrast displays
Image Processing
Limiting factors
Fear of pathogenic attacks
Low quantum efficiency of the data write process
Low yield of the O intermediate in the native protein at ambient temperatures
Must be extremely uniform in their composition
Unavailability for suitable polymer gel to put this protein in that will not break down faster than the protein
Mutations also could affect the photochemical properties of the protein
The native bR when in contact with a semiconductor, poisons the semiconductor when the metal cations migrate to it
Building a system around photonics isn't as easy
The Future is here..
Threshold of a new and exciting era in the wonderful world of computing
able to carry a small encyclopaedic cube containing all the information we need!
References
Protein Based Computers Birge, Robert R., Scientific American March 1995, pp 90 – 95
Gennis RB, Ebray TG. (1999). "Proton pump caught in the act". Science 286: 252-253.
U. Haupts, J. Tittor, E. Bamberg and D. Oesterhelt General Concept for Ion Translocation by Halobacterial Retinal Proteins: The Isomerization/Switch/Transfer Model. Biochemistry 36, 2-7 (1997)
U. Haupts, J. Tittor, D. Oesterhelt: Closing in on Bacteriorhodopsin: Progress in Understanding the Molecule. Ann. Rev. Biophys. Biomol. Struct. 28, 367-399 (1999)
H. Michel, D. Oesterhelt: Three-Dimensional Crystals of Membrane Proteins: Bacteriorhodopsin. Proc. Natl. Acad. Sci. USA 77, 1283-1285 (1980).
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