Session Y7: Control of Light with Bacteriorhodopsin

Earle K. Plyler Prize Talk: Stark Realities

Stark spectroscopy is the effect of an electric field on a spectrum. Measurements of the Stark effect give information on the change in dipole moment and polarizability for a spectroscopic transition. The great majority of Stark effect measurements have been and still are made in the gas phase where spectroscopic transitions are very narrow and a Stark splitting can be readily measured. There are many fewer examples of Stark spectroscopy measurements in condensed phases, largely because of the perceived difficulty of applying a large electric field. While this is the case for liquid samples, where molecular alignment and low breakdown voltages complicate the measurement, it is simple to immobilize the molecule of interest, either by embedding it in a thin polymer film or by freezing the solvent. The latter is completely general and any sample that forms a high quality optical glass, including protein samples, can be studied. In this talk I will present an overview of applications of Stark effects to diverse systems. We divide the phenomenon into two broad classes: classical Stark effects, where the applied field acts as a perturbation shifting a transition; and non-classical Stark effects, where the applied field affects the intrinsic absorption lineshape and/or populations of states. Classical Stark effects provide quantitative information on the dipolar nature of excited states for electronic or vibrational transitions. Once calibrated, the spectroscopic transition can be used to probe electric fields in organized complex systems such as proteins and changes in those fields accompanying mutations, catalysis, ligand binding and folding. Vibrational Stark effects are particularly useful in this context, and this has led to diverse strategies for introducing unique and sensitive probes for electrostatic fields in proteins. Non-classical Stark effects embrace the many effects that electric fields can have on reaction dynamics, particularly involving electron transfer, either photoinduced or in mixed valence systems. For such systems, the electric field can alter the absorption or emission lineshape substantially because the potential surface depends upon the field and the spectrum depends on the shape of the potential. Examples of each type will be presented.   

Protein-Based Three-Dimensional Memories and Associative Processors

The field of bioelectronics has benefited from the fact that nature has often solved problems of a similar nature to those which must be solved to create molecular electronic or photonic devices that operate with efficiency and reliability. Retinal proteins show great promise in bioelectronic devices because they operate with high efficiency ($\sim $0.65{\%}), high cyclicity ($>$10$^{7})$, operate over an extended wavelength range (360 -- 630 nm) and can convert light into changes in voltage, pH, absorption or refractive index. This talk will focus on a retinal protein called bacteriorhodopsin, the proton pump of the organism \textit{Halobacterium salinarum}. Two memories based on this protein will be described. The first is an optical three-dimensional memory. This memory stores information using volume elements (voxels), and provides as much as a thousand-fold improvement in effective capacity over current technology. A unique branching reaction of a variant of bacteriorhodopsin is used to turn each protein into an optically addressed latched AND gate. Although three working prototypes have been developed, a number of cost/performance and architectural issues must be resolved prior to commercialization. The major issue is that the native protein provides a very inefficient branching reaction. Genetic engineering has improved performance by nearly 500-fold, but a further order of magnitude improvement is needed. Protein-based holographic associative memories will also be discussed. The human brain stores and retrieves information via association, and human intelligence is intimately connected to the nature and enormous capacity of this associative search and retrieval process. To a first order approximation, creativity can be viewed as the association of two seemingly disparate concepts to form a totally new construct. Thus, artificial intelligence requires large scale associative memories. Current computer hardware does not provide an optimal environment for creating artificial intelligence due to the serial nature of random access memories. Software cannot provide a satisfactory work-around that does not introduce unacceptable latency. Holographic associative memories provide a useful approach to large scale associative recall. Bacteriorhodopsin has long been recognized for its outstanding holographic properties, and when utilized in the Paek and Psaltis design, provides a high-speed real-time associative memory with variable thresholding and feedback. What remains is to make an associative memory capable of high-speed association and long-term data storage. The use of directed evolution to create a protein with the necessary unique properties will be discussed.   

Optical Fourier and Holographic Techniques for Medical Image Processing with Bacteriorhodopsin

The biological photochrome bacteriorhodopsin (bR) shows many intrinsic optical and physical properties. The active chromophore~in bR is a retinal group which absorbs light and goes through a photocycle. The unique feature of the system is its flexibility -- the photocycle can be~optically controllable since the process of photoisomerization can go in both directions depending on wavelength, intensity and polarization of the incident light, opening a variety of possibilities for manipulating amplitude, phase, polarization and index of refraction of the incident light. Over the years we studied the basic nonlinear optics and successfully exploited the unique properties for several optical spatial filtering techniques with applications in medical image processing. For nonlinear Fourier filtering, the photo-controlled light modulating characteristics of bR films are exploited. At the Fourier plane, the spatial frequency information carried by a blue probe beam at 442 nm is selectively manipulated in the bR film by changing the position and intensity of a yellow control beam at 568 nm. In transient Fourier holography, photoisomerizative gratings are recorded and reconstructed in bR films. Desired spatial frequencies are obtained by matching the reference beam intensity to that of the particular frequency band in object beam. A novel feature of the technique is the ability to transient display of selected spatial frequencies in the reconstructing process which enables radiologists to study the features of interest in time scale.~The results offer useful information to radiologists for early detection of breast cancer. Some of the highlights will be presented.   

Light manipulation with Bacteriorhodopsin membrane self-assembled on high-Q photonic structures

Resonant photonic structures such as ring resonators and photonic crystal nanocavities interact evanescently with biological material assembled on a reflecting interface. Quality (Q-) factors $\sim$10$^6$ and sub-wavelength modal (V-) volumes significantly enhance the interaction so that tuning of microcavity resonances by only few molecules is feasible. Since only few constituents are required, the molecular-photonic interface can be fashioned from self-organizing principles that govern interaction of organic and biological polymers. We demonstrate this bottom-up approach with photochromic Bacteriorhodopsin membrane which we self-assemble on various microcavities. The hybrid molecular-photonic architectures exhibit high Q/V-values and are sensitive to photoinduced molecular transitions and other non-linearities which we utilize for demonstrations of all-optical switching, routing and molecular analysis.   

The Integration of Bacteriorhodopsin Proteins with Semiconductor Heterostructure Devices

Bioelectronics has emerged as one of the most rapidly developing fields among the active frontiers of interdisciplinary research. A major thrust in this field is aimed at the coupling of the technologically-unmatched performance of biological systems, such as neural and sensing functions, with the well developed technology of microelectronics and optoelectronics. To this end we have studied the integration of a suitably engineered protein, \textit{bacteriorhodopsin} (BR), with semiconductor optoelectronic devices and circuits. Successful integration will potentially lead to ultrasensitive sensors with polarization selectivity and built-in preprocessing capabilities that will be useful for high speed tracking, motion and edge detection, biological detection, and artificial vision systems. In this presentation we will summarize our progresses in this area, which include fundamental studies on the transient dynamics of photo-induced charge shift in BR and the coupling mechanism at protein-semiconductor interface for effective immobilizing and selectively integrating light sensitive proteins with microelectronic devices and circuits, and the device engineering of BR-transistor-integrated optical sensors as well as their applications in phototransceiver circuits. \newline \newline Work done in collaboration with Pallab Bhattacharya, Jonghyun Shin, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI; Robert R. Birge, Department of Chemistry, University of Connecticut, Storrs, CT 06269; and Gy\"{o}rgy V\'{a}r\'{o}, Institute of Biophysics, Biological Research Center of the Hungarian Academy of Science, H-6701 Szeged, Hungary.   

All-Optical Switching in Bacteriorhodopsin Based on Excited-State Absorption

Switching light with light is of tremendous importance for both fundamental and applied science. The advent of nano-bio-photonics has led to the design, synthesis and characterization of novel biomolecules that exhibit an efficient nonlinear optical response, which can be utilized for designing all-optical biomolecular switches. Bacteriorhodopsin (bR) protein found in the purple membrane of \textit{Halobacterium halobium }has been the focus of intense research due to its unique properties that can also be tailored by physical, chemical and genetic engineering techniques to suit desired applications. The talk would focus on our recent results on all-optical switching in bR and its mutants, based on excited-state absorption, using the pump-probe technique. We would discuss the all-optical control of various features of the switching characteristics such as switching contrast, switching time, switching pump intensity, switched probe profile and phase, and relative phase-shift. Optimized conditions for all-optical switching that include optimized values of the small-signal absorption coefficient (for cw case), the pump pulse width and concentration for maximum switching contrast (for pulsed case), would be presented. We would discuss the desired optimal spectral and kinetic properties for device applications. We would also discuss the application of all-optical switching to design low power all-optical computing devices, such as, spatial light modulators, logic gates and multiplexers and compare their performance with other natural photoreceptors such as pharaonis phoborhodopsin, proteorhodopsin, photoactive yellow protein and the blue light plant photoreceptor phototropin.