Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> An investigation was made of the two-photon photochromism of spiropyran solutions subjected to ruby laser radiation. The two-photon absorption cross section of spiropyran was calculated. At high laser radiation intensities the dependence of the optical density of the photoinduced form of spiropyran on the incident radiation intensity deviated from the square law. The cause of this deviation was considered. <s> BIB001 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> We report the effective nonlinearity for photochromic conversion in a blue-membrane bacteriorhodopsin film hosted in a dry polyvinyl alcohol matrix. The shift in absorption maximum on photoconversion in this film is larger than that of the same material in hydrated form, thus offering a larger modulation of the refractive index. The photoexcited index modulation is stable for several months, which provides for holographic data recording and long-term photochromic data storage. The effective index modulation is experimentally measured and is in good agreement with the theoretical predictions based on the Kramers–Kronig transformation. <s> BIB002 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> In just three years, the green fluorescent protein (GFP) from the jellyfish Aequorea victoria has vaulted from obscurity to become one of the most widely studied and exploited proteins in biochemistry and cell biology. Its amazing ability to generate a highly visible, efficiently emitting internal fluorophore is both intrinsically fascinating and tremendously valuable. High-resolution crystal structures of GFP offer unprecedented opportunities to understand and manipulate the relation between protein structure and spectroscopic function. GFP has become well established as a marker of gene expression and protein targeting in intact cells and organisms. Mutagenesis and engineering of GFP into chimeric proteins are opening new vistas in physiological indicators, biosensors, and photochemical memories. <s> BIB003 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> It is generally accepted that the colors displayed by living organisms are determined by low molecular weight pigments or chromoproteins that require a prosthetic group. The exception to this rule is green fluorescent protein (GFP) from Aequorea victoria that forms a fluorophore by self-catalyzed protein backbone modification. Here we found a naturally nonfluorescent homolog of GFP to determine strong purple coloration of tentacles in the sea anemone Anemonia sulcata. Under certain conditions, this novel chromoprotein produces a trace amount of red fluorescence (emission lambda(max) = 595 nm). The fluorescence demonstrates unique behavior: its intensity increases in the presence of green light but is inhibited by blue light. The quantum yield of fluorescence can be enhanced dramatically by single amino acid replacement, which probably restores the ancestral fluorescent state of the protein. Other fluorescent variants of the novel protein have emission peaks that are red-shifted up to 610 nm. They demonstrate that long wavelength fluorescence is attainable in GFP-like fluorescent proteins. <s> BIB004 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> We have cloned a gene encoding a fluorescent protein from a stony coral, Trachyphyllia geoffroyi, which emits green, yellow, and red light. The protein, named Kaede, includes a tripeptide, His-Tyr-Gly, that acts as a green chromophore that can be converted to red. The red fluorescence is comparable in intensity to the green and is stable under usual aerobic conditions. We found that the green-red conversion is highly sensitive to irradiation with UV or violet light (350–400 nm), which excites the protonated form of the chromophore. The excitation lights used to elicit red and green fluorescence do not induce photoconversion. Under a conventional epifluorescence microscope, Kaede protein expressed in HeLa cells turned red in a graded fashion in response to UV illumination; maximal illumination resulted in a 2,000-fold increase in the ratio of red-to-green signal. These color-changing properties provide a simple and powerful technique for regional optical marking. A focused UV pulse creates an instantaneous plane source of red Kaede within the cytosol. The red spot spreads rapidly throughout the cytosol, indicating its free diffusibility in the compartment. The extensive diffusion allows us to delineate a single neuron in a dense culture, where processes originating from many different somata are present. Illumination of a focused UV pulse onto the soma of a Kaede-expressing neuron resulted in filling of all processes with red fluorescence, allowing visualization of contact sites between the red and green neurons of interest. <s> BIB005 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> Proteins are naturally occurring nanosystems endowed with diverse properties and functions. Biotechnology affords means of modifying proteins to alter their properties and hence their function. Bionanotechnology is a rapidly emerging area of research with challenging opportunities and formidable challenges. Light-activated proteins, e.g., bacteriorhodopsin, manifest state changes when subjected to light, which can be exploited to store information in the range of terabytes. We describe the retroengineering of bacteriorhodopsin by rational site-specific mutagenesis to enhance its thermal and photochemical properties. Bacteriorhodopsin-based memory systems are amenable to writing and reading information at comparable speeds. With silicon-based technologies reaching their technological limits, protein-based memory systems are one viable alternate technology for the future. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003 <s> BIB006 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> The observation of the regulation of fast protein dynamics in a cellular context requires the development of reliable technologies. Here, a signal regulation cascade reliant on the stimulus-dependent acceleration of the bidirectional flow of mitogen-activated protein kinase (extracellular signal-regulated kinase) across the nuclear envelope was visualized by reversible protein highlighting. Light-induced conversion between the bright and dark states of a monomeric fluorescent protein engineered from a novel coral protein was employed. Because of its photochromic properties, the protein could be highlighted, erased, and highlighted again in a nondestructive manner, allowing direct observation of regulated fast nucleocytoplasmic shuttling of key signaling molecules. <s> BIB007 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> In recent years, molecular switches have attracted considerable interest because they hold great promises as molecular electronic and photonic devices. In contrast to commonplace switches that turn electric appliances on and off, molecular switches enable the storage of information on a molecular level, and their application in nanotechnology, biomedicine, and computer chip design opens up whole new horizons. Usually, molecular switches are addressed by an electrical field, a scanning tunneling microscope tip, or a chemical or electrochemical reaction to specifically switch the <s> BIB008 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> We have been pursuing protein-based memory using genetically altered bacteriorhodopsin (bR) and exploring limits of high density optical recording using far-field and near-field approach. bR was immobilized on very thin LB films <s> BIB009 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> The recent discovery of photoconvertible and photoswitchable fluorescent proteins (PCFPs and RSFPs, respectively) that can undergo photoinduced changes of their absorption/emission spectra opened new research possibilities in subdiffraction microscopy and optical data storage. Here we demonstrate the proof-of-principle for read only and rewritable data storage both in 2D and 3D, using PCFPs and RSFPs. The irreversible burning of information was achieved by photoconverting from green to red defined areas in a layer of the PCFP Kaede. Data were also written and erased several times in layers of the photochromic fluorescent protein Dronpa. Using IrisFP, which combines the properties of PCFPs and RSFPs, we performed the first encoding of data in four colours using only one type of fluorescent protein. Finally, three-dimensional optical data storage was demonstrated using three mutants of EosFP (d1EosFP, mEosFP and IrisFP) in their crystalline form. Two-photon excitation allowed the precise addressing of regions of interest (ROIs) within the three-dimensional crystalline matrix without excitation of out-of-focus optical planes. Hence, this contribution highlights several data storage schemes based on the remarkable properties of PCFPs/RSFPs. <s> BIB010 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> Peptide nanotubes (PNT) are emerging alternates frontier to carbon nanotubes (CNT). PNT's can be engineered by solid phase synthesis with desired properties. Chemically PNT's are reactive in sharp contrast to CNT's and hence require less site specific functionalization for nanotechnology applications. In this paper we are reporting the electronic coupling between the Phe-Phe dipeptide which is calculated using the density functional theory method. The calculations are performed for linear and cyclic structures of diphenylalanine peptide. The calculated electronic coupling is sensitive to the peptide electronic structure and shows a significant dependence for conformations. The band gaps obtained for PNT are compared with Boron Nitride and CNT. Peptide nanotubes (PNT) exhibit no cytotoxicity and hence offer tantalizing prospects in biomedical applications for example in drug delivery. Copyright © 2011 VBRI press. <s> BIB011 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> In recent years we are witnessing an intensive integration of bio-organic nanomaterials in electronic devices. Here we show that the diphenylalanine bio-molecule can self-assemble into tiny peptide nanodots (PNDs) of ∼2 nm size, and can be embedded into metal-oxide-semiconductor devices as charge storage nanounits in non-volatile memory. For that purpose, we first directly observe the crystallinity of a single PND by electron microscopy. We use these nanocrystalline PNDs units for the formation of a dense monolayer on SiO2 surface, and study the electron/hole trapping mechanisms and charge retention ability of the monolayer, followed by fabrication of PND-based memory cell device. <s> BIB012 </s> Natural Data Storage: A Review on sending Information from now to then via Nature <s> PROTEIN HARD DRIVE <s> Self-assembling peptides represent a growing class of inexpensive, environmentally benign, nanostructured materials. In particular, diphenylalanine (FF) self-assembles into nanotubes with remarkable strength and thermal stability that have found use in a wide variety of applications, including as sacrificial templates and scaffolds for structuring inorganic materials and as interfacial "nanoforests" for superhydrophobic surfaces and high-performance supercapacitors and biosensors. However, little is known about the assembly mechanisms of FF nanotubes or the forces underlying their stability. Here, we perform a variety of molecular dynamics simulations on both zwitterionic and capped (uncharged) versions of the FF peptide to understand the early stages of self-assembly. We compare these results to simulations of the proposed nanotube X-ray crystal structure. When comparing the zwitterionic and uncharged FF peptides, we find that, while electrostatic interactions steer the former into more ordered dimers and trimers, the hydrophobic side chain interactions play a strong role in determining the structures of larger oligomers. Simulations of the crystal structure fragment also suggest that the strongest interactions occur between side chains, not between the charged termini that form salt bridges. We conclude that the amphiphilic nature of FF is key to understanding its self-assembly, and that the early precursors to nanotube structures are likely to involve substantial hydrophobic clustering, rather than hexamer ring motifs as has been previously suggested. <s> BIB013
Protein plays central role in the functioning of the body and stores the behaviour of human in form of folded chain of amino acids. The communication takes place between various organs at particular instance of the time in response to specific protein. In order to use protein as the storage medium, identification of proteins which can replicate the binary storage technique was inevitable. The study of photo-switching protein has revealed many applications in nanoscience technology one of which is data storage BIB008 ]. The foundations for the same was laid by Hirschberg and colleague by proposing first photochemical memory model based on the color transformation of molecule called spiropyrans which can flip to other form on absorption of single photon  ]. Furthermore, using photo-induced fluorescence proteins that can switch between two states for data storage is described in BIB003 ]. Switching mechanism can be between the state of two different colors like red and green, other can be dark or light state. Researchers in the area found solution to it by studying family of proteins called photochromic proteins like Photo convertible Florescence proteins (PCFPs) and Reversible switching florescence proteins (RSFPs) which are light driven switchable florescent proteins BIB010 . Not only reading and writing the data but they could erase the data and rewrite it again on the proteins. So this was first remarkable attempt of creating rewritable natural data storage. PCFPs protein called Kaede BIB005 and RSFPs protein known as Dronpa BIB007 ] was used to write and rewrite the data. Cis/trans isomerization of chromophore BIB004 ] along with photon induces protonation of chromophore is responsible for photo-switching in two different states. The information can be stored in the area designated green and red colors which are similar to 0 and 1. The state was determined by using EosFP, a fluorescent marker protein which is UV-inducible green-to-red fluorescence. Different material as described in BIB010 were used for surface coating of all proteins. To write data on the protein surface, an inverted laser-scanning microscope with particular specification was used. The reading, writing and erasing of data was done by using the laser beam at different intensity levels. The idea of using single crystals of PCFPs/RSFPs protein as 3D storage medium had been implemented where protein molecule in the crystal would represent a data bit  . In this instead of binary encoding, four color florescence switching proteins was used with mutant of RSFPS which can built the 4-base data storage system by using two photon excitation (TPE) technique BIB001 . Using the mutant of PCFP EosFP, IrisFP ] the 4 based data storage was implemented as it had combine property of both the proteins of irreversible switching from green to red and other reversible from dark to bright state. This technique is more efficient as it focus on the precise location for the storage. One other idea was implemented by group of Venkatesan Renugopalakrishnan at Harvard University using the Bacteriorhodopsin (bR) protein for data storage. The concept of using bR was spearheaded by Jack tallent BIB002 . The researchers used Bacteriorhodopsin (bR) light-activated protein found in the membrane of a salt marsh microbe Halobacterium salinarum (which use it for their photo synthesis) to coat storage device DVD which may increase the data storage capacity up to 50 TB BIB009 ]  [?]. It convert light energy into chemical energy. When lights comes in contact it produces some molecules of different state and remain in the state for few minutes or days  . Unlike today's storage device the bR molecule of 2 nm in diameter has demonstrated a longterm stability with a shelf life of at least 10 years at room temperature and is believed to be stable at temperatures up to 140 degree Celsius. The team modified bR protein to enhance its thermal and photochemical properties in a way that it can remain in this intermediate state for few years at high temperature BIB006 . In this the binary encoding is done by the concept that protein in brighter state is considered as 0 and in dark state can be considered as 1. They worked on how to use charge transporting proteins such as Bacteriorhodopsin in the building of data storage and transmission devices for applications in computer technology. When laser of one color incidents on the protein, it get arrange into one shape designated as zero in binary system and when laser of another wave length stimulates the protein to take another shape represented as one. Once the laser system is switched off, data can be stored for several year. To read the data from stored protein, a low power laser beam is delivered on this protein slowly so that the protein confirmation is not disturbed but only the light is absorbed by the pattern in the protein which can be detected by the machine and can generate a string of 0s and 1s. The property of bR to shifts between intermediated states made it potential for rewritable data storage. Using peptide as storage device was implemented by amalgamation of the nm scaled bio-organic nano dots into bio-electronic devices BIB012 . This bioorganic nano-dots called peptide nano dots (PNDs) of 2 nm size, were self-assembled from the Diphenylalanine (FF) peptides BIB013 and can be embedded into metal-oxide-semiconductor devices as charge storage nano-units in non-volatile memory. FF gets self assemble into nano tubes and the structure is stabilized by the noncovalent interactions BIB011 . Size limitation (micrometer) of the FF tubes jeopardized it's use for the bio-electronic devices. But researcher observed that in anhydrous condition, FF tubes get dissemble into stable building blocks of PNDs, paving the way for using it in bio-electronic devices. PNDs were successfully used as charged storage elements for the non volatile memory devices (NVM) by replacing the ONO(oxide-nitride-oxide) dielectric in the NVM. Many other nano-dots like Au and Pt and organic dyes were earlier employed for the same, but the beauty of PNDS to be nano-crystalline, uniform nm size, low temperature deposition makes them superior. Two crucial steps were followed to use FF PNDs in NVMS. First the property of each nano-dots was deciphered using electron microscopy. Using their electron diffraction pattern, nano crystalline structure was confirmed. Following it mono layer of PNDs which serves as memory stack was formed which retains the charge. For the detail procedure, reader is advised to refer BIB012 . Protein bases information storage systems are at infancy stage and opens many challenges like reading and writing the data, data rate, speed of data access and deciphering the mutants of the photo-chromic proteins for intense research.