Computer Memory Based on the Protein Bacteriorhodopsin Utilizing the Two-Photon Method for Read/Write Procedures


Brought to you by:
Gregory Brown
Patrick Chun
and
Faiz Ikramulla


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. 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.

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 came the people who invented spoken languages and the need arose to record what one was saying without hearing it firsthand. Therefore, years later, more early 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 protien-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.

For more information on the current state of technology:
Information about the current state of technology

Problem

The demands made upon computers and computing devices are increasing each year. Processor speeds are increasing at an extremely fast clip. However, the RAM used in most computers is the same type of memory used several years ago. The limits of making RAM more dense are being reached. Surprisingly, these limits may be economical rather than physical. A decrease by a factor of two in size will increase the cost of manufacturing of semiconductor pieces by a factor of 5.

Currently, RAM is available in modules called SIMMs or DIMMS. These modules can be bought in various capacities from a few hundred kilobytes of RAM to about 64 megabytes. Anything more is both expensive and rare. These modules are generally 70ns, however 60ns and 100ns modules are available. The lower the nanosecond rating, the more the module will cost. Currently, a 64MB DIMM costs over $400. All Dimms are 12cm by 3cm by 1cm or about 36 cubic centimeters. Whereas a 5 cubic centimeter block of bacteriorhodopsin studded polymer could theoretically store 512 gigabytes of information. When this comparision is made, the advantage becomes quite clear. Also, these bacteriorhodopsin modules could also theoretically run 1000 times faster.

In response to the demand for faster, more compact, and more affordable memory storage devices, several viable alternatives have appeared in recent years. Among the most promising approaches include memory storage using holography, polymer-based memory, and our focus, protein-based memory.

Protein-Based Memory

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.

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).

Data Writing Technique

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 write process
This image was scanned from the March 1995 issue of Scientific American

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.

Data Reading Technique

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.

The read process
This image was scanned from the March 1995 issue of Scientific American

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. Find out more about what needs to be done before protein-based RAMs appear on the market.


References:

Proptein Based Computers Birge, Robert R., Scientific American Mar ch 1995 pp 90 - 95

Organic Chemistry Baker, A. David, Robert Engel. West Publishing Co., New York
MacUser, December, 1996. Ziff-Davis Publishing Company, pp 220-227
Kingston Technical Support

Pertinent Links

Please, please, please email us.

Greg Brown

Patrick Chun

Faiz Ikramulla