Albert F. Lawrence

Optical Random Access Memory Based on Bacteriorhodopsin

During the past five years, investigators have shown considerable interest in the potential use of light transducing proteins to perform optical switching functions.1,2 There are significant advantages inherent in the use of biological molecules, either in their native form, or modified via organic synthesis or protein engineering, as active components in molecular electronic devices. These advantages derive in large part from the natural selection process, and the fact that nature has solved through trial and error problems of a similar nature to those encountered in harnessing organic molecules to carry out logic, switching and energy transducing functions. One example of this type of serendipity to be explored in the present paper is the use of the light harvesting protein, bacteriorhodopsin, as the photoactive element in an optically coupled random access memory.

Nonlinear Optical Properties of Bacteriorhodopsin: Assignment of Second Order Hyperpolarizabilities of Randomly Oriented Systems Using Two-Photon Spectroscopy

Abstract We demonstrate that the second order hyperpolarizability of a randomly oriented molecule can be determined directly from two-photon spectroscopic measurements on the low-lying excited state manifold. Equations are derived which allow not only a determination of β, but also a determination of the error associated with the numerical method. We apply our two-photon technique to an analysis of the second order hyperpolarizability of light adapted bacteriorhodopsin. Our analysis of this protein in D2O at ambient temperature yields a value of β (= βxxx + (1/3)[βxyy + 2βyyx + βxzz + 2βzzx]) of (2250 ± 240) × 10−30 cm5/esu for a laser wavelength of 1.06μ (Nd:YAG fundamental). The large second-order nonlinear properties of bacteriorhodopsin are due primarily to the large change in dipole moment associated with excitation into the lowest-lying strongly allowed “1Bu +” π, π* state (Δμ = 13.5 ± 0.8 D). We derive an equation which estimates Ωβδ, the ratio of the number of second harmonic photons generated by ...

Quantum effects, thermal statistics and reliability of nanoscale molecular and semiconductor devices

The reliability of nanoscale molecular and semiconductor devices is analysed in terms of generalized error prediction algorithms. The authors statistical procedures predict the reliability of a device based on the assignment of three independent variables. The first variable, P(1) is the probability of determining the state of the device if only one molecule (or information carrier) is present. The second variable N is the number of molecules (or information carriers) operating to assign the state of the device (that is, the number of quantized entities within the ensemble). The third variable xi lim is the limiting logarithmic reliability factor which is a function of the entire system and the environment in which it must operate. Statistical procedures are also presented which allow one to determine the total system reliability based on the assignment of the desired mean-time-between-failures (DMTBF) and the individual reliabilities of the components. Sample reliability analyses are carried out on three devices to determine the minimum number of molecules N that must be included in the ensemble to achieve an error probability of less than 10-10.

Spatial Light Modulators And Optical Associative Memories Based On Bacteriorhodopsin

In this paper we present an overview of current research on the development of spatial light modulators and optical associative memories based on bacteriorhodopsin. The spatial light modulator is a thesholding type and uses oriented bacteriorhodopsin in chemically optimized polymer matrices. The associative memory uses bacteriorhodopsin to store reference holograms and is based on the closed loop autoassociative design of Paek and Psaltis [Opt. Eng. 26, 428-433 (1987)l which includes both feedback and thresholding. We demonstrate that bacteriorhodopsin provides an outstanding photochromic material for use in optically coupled devices of the type investigated here.

Bioelectronics, three-dimensional memories and hybrid computers

The promise of new architectures and more cost-effective miniaturization has prompted interest in hybrid molecular and semiconductor computers. Nature has already optimized some molecules for such applications. We examine here the use of the protein bacteriorhodopsin in associative and three-dimensional memories and the potential for making hybrid computer systems which combine semiconductor and biomolecular components.<<ETX>>

Bit error sources in 3D optical memory: experiments and models

The photoactive protein, bacteriorhodopsin (BR), may be used as the recording medium in optical three-dimensional memories. Experiments with a sequential, one-photon read/write scheme have shown promising results. In this scheme a planar laser beam activates a narrow slice of the medium, so that the bit patterns of the slice can be read independently of the rest of the memory. This gives rise to a paged memory architecture with approximately 100 Megabytes/page. Experimental images taken of the activated pages show bit patterns subject to degradation, which may be attributed to intensity variations within the activation beam. These intensity gradients are believed to be the result of refraction within the memory page. Writing a bit in the memory changes the index of refraction within the activated memory volume illuminated by the write beam. Bit error rates are directly related to the proportion of 0s and 1s written into the memory page, with minimum error rates recorded at a 50/50 ratio. In addition to experiments with prototype BR memories, we report on a computer model for the activation phase of the memory read cycle. This model may be used to study various schemes for placing the bits within a memory page and ensuring that the distribution of 0s and 1s is uniform.

Protein-based volumetric memories

This paper will explore the use of the protein, bacteriorhodopsin, as the photoactive recording medium in an optical three-dimensional memory. Although this protein has been used previously as the photoactive medium in a number of three-dimensional architectures (e.g., holographic and two- photon), a sequential one-photon volumetric architecture employing a photochemical branching reaction characteristic of the protein is currently showing the most promise. This unique branching reaction allows for long-term data storage by the protein, and rigorously excludes unwanted photochemistry. During the past two years, two prototypes have been constructed, and the preliminary results look promising. The use of chemical modification and genetic engineering of the protein has improved data reliability by roughly five-fold, but reliability remains an issue. Some of the key problems will be discussed. In addition, the use of gray-scale and polarization multiplexing to increase the storage capacity will be examined.

Origins Of The Quantum Efficiency Duality In The Primary Photochemical Event Of Bacteriorhodopsin

Experimental and theoretical evidence is presented which suggests that two distinct forms of light-adapted bacteriorhodopsin may exist. We propose that these two forms have characteristic photocycles with significantly different primary quantum yields. INDO-PSDCI molecular orbital procedures and semiempirical molecular dynamics simulations predict that one ground state geometry of bR undergoes photochemistry with a primary quantum yield, Φ1, of ~ 0.27, and that a second ground state geometry, with a slightly displaced counterion, yields Φ1 ~ 0.74. This theoretical model is supported by the observation that literature measurements of Φ1 tend to fall into one of two categories- those that observe Φ1 ~ 0.33 or below, and those that observe Φ1 ~ 0.6 or above. The observation that all photostationary state measurements of the primary quantum yield give values near 0.3, and all direct measurements of the quantum yield result in values near 0.6, suggests that photochemical back reactions may select the bacteriorhodopsin conformation with the lower quantum yield. The two photocycles may have developed as a natural biological requirement that the bacterium have the capacity to adjust the efficiency of the photocycle in relation to the intensity of light and/or membrane electrochemical gradient

Mathematical Problems Arising in Molecular Electronics: Global Geometry and Dynamics of the Double-Well Potential

In a demonstration that no physical limitations to computers arise from quantum mechanics and the uncertainty principle, Feynman 1 constructed Hamiltonians for spin systems which performed any desired sequence of logical operations. Although this work showed that there are no intrinsic reasons circuits could not be built at the molecular scale, numerous problems remain in constructing molecular analogs to the standard electronics building blocks: transmission lines, amplifiers, gates and switches. Numerous molecules or molecular systems have been proposed to serve these functions, but such questions such as interconnections, noise isolation, and immunity to thermal and quantum fluctuations remain unanswered. As with the engineering of computers in bulk matter, the engineering of computers in molecular systems requires attention to the detailed dynamics of the system. Part of the problem is at the foundations. Aside from numerical calculations, which are presently beyond the bounds of computer technology, and are likely to remain so for some time hence, the dynamics of large molecules are inaccessible to precise quantitative prediction. On the other hand, an analytical theory of molecular dynamics presents some serious technical challenges and conceptual difficulties. Rapid progress toward a science of information processing at the molecular level awaits the resolution of these fundamental difficulties.

Potential application of optical phased arrays in two-photon three-dimensional optical memories

The potential use of optical phased arrays to address individual bits within a volumetric memory medium is examined by using phase sensitive ray tracing procedures. We demonstrate that a 200 element linear array with cylindrical microlens collimation is capable of addressing two-photon ((lambda) equals 1 micrometers ) activated irradiated volumes of approximately 64 micrometers 3, comparable to the volumetric elements that can be addressed via standard crossed-beam two-photon excitation. The two key advantages of using phased arrays is speed of addressing and the elimination of cleaning pulses. Both advantages dramatically improve read/write speeds as well as signal-to-noise performance of two-photon volumetric memories. We examine four different configurations including collimated linear and spherical arrays as well as binary and pure phased two-dimensional arrays. Although phased arrays with the necessary characteristics have not as yet been constructed, we hope that the present demonstration of their potential advantages will enhance interest in the development of phased arrays for application in volumetric memories.© (1993) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.