Computationally Guided Monomerization of Red Fluorescent Proteins of the Class Anthozoa

Red fluorescent proteins (RFPs) have attracted significant engineering focus because of the promise of near infrared fluorescent proteins, whose light penetrates biological tissue, and which would allow imaging inside of vertebrate animals. The RFP landscape, which numbers ~200 members, is mostly populated by engineered variants of four native RFPs, leaving the vast majority of native RFP biodiversity untouched. This is largely due to the fact that native RFPs are obligate tetramers, limiting their usefulness as fusion proteins. Monomerization has imposed critical costs on these evolved tetramers, however, as it has invariably led to loss of brightness, and often to many other adverse effects on the fluorescent properties of the derived monomeric variants. Here we have attempted to understand why monomerization has taken such a large toll on Anthozoa class RFPs, and to outline a clear strategy for their monomerization. We begin with a structural study of the far-red fluorescence of AQ143, one of the furthest red emitting RFPs. We then try to separate the problem of stable and bright fluorescence from the design of a soluble monomeric β-barrel surface by engineering a hybrid protein (DsRmCh) with an oligomeric parent that had been previously monomerized, DsRed, and a pre-stabilized monomeric core from mCherry. This allows us to use computational design to successfully design a stable, soluble, fluorescent monomer. Next we took HcRed, which is a previously unmonomerized RFP that has far-red fluorescence (λemission = 633 nm) and attempted to monomerize it making use of lessons learned from DsRmCh. We engineered two monomeric proteins by pre-stabilizing HcRed’s core, then monomerizing in stages, making use of computational design and directed evolution techniques such as error-prone mutagenesis and DNA shuffling. We call these proteins mGinger0.1 (λem = 637 nm / Φ = 0.02) and mGinger0.2 (λem = 631 nm Φ = 0.04). They are the furthest red first generation monomeric RFPs ever developed, are significantly thermostabilized, and add diversity to a small field of far-red monomeric FPs. We anticipate that the techniques we describe will be facilitate future RFP monomerization, and that further core optimization of the mGingers may allow significant improvements in brightness.

Relay lens-free birefringence-customized stackable beam-steering modules for optical interconnects

A previously suggested birefringence-customized modular optical interconnect technique is extended for lens-free relay operation. Various lens-free relay imaging models are developed. We claim that the lens-free relay system is important in simplifying an optical interconnect system whenever the imaging conditions permit. To verify the validity of various proposed concepts, we experimentally implemented some 8 x 8 optical permutation modules. High-power efficiency and low channel cross talk were experimentally observed. In general, the larger the channel spacing, the less the cross talk. A quantitative cross-talk measurement of the lens-free relay system shows that, for a fixed channel width of 0.5 mm and channel spacings of 0.5, 1, and 2 mm, a less than -20-dB cross-talk performance can be guaranteed for lens-free relay distances of 40, 280, and 430 mm, respectively. (C) 1998 Optical Society of America.

Distortion of beam shape by a rotating double-prism wide-angle laser beam scanner

We describe the rigorous results of a wide-angle laser beam scanner, obtained with the help of the vector refraction theory. Using the rigorous results, the distortion of the beam shape is discussed. The distortion to the beam varies with the different relative angles of double prisms. The scanner expands the beam in some directions while it contracts the beam in other directions. According to the conservation of energy, the distribution of the laser intensity is changed as well. (c) 2006 Society of Photo-Optical Instrumentation Engineers.

The effect of the rotating double-prism wide-angle laser beam scanner on the beam shape

In this paper, we describe a wide-angle laser beam scanner and the rigorous result of the wide-angle laser beam scanner was obtained with the help of the vector refraction theory. Using the rigorous results, the distortion of the beam shape was discussed. The distortion of the beam shape is varying with the different relative angles of the double prisms. According to the conservation of the energy, the distribution of the laser intensity is changed too. (c) 2005 Elsevier GmbH. All rights reserved.

Influence of recording conditions on crossed-beam photorefractive gratings in doubly doped LiNbO3 crystals

The influence of the recording conditions, including the widths of the recording beams, the width ratio of the recording beams, and the recording angles, on the properties of crossed-beam photorefractive gratings in doubly doped LiNbO3 crystals is studied. A theoretical model that combines the band transport model with two-dimensional coupled-wave theory is proposed. The numerical calculations of the space-charge field, the intensity profiles of the diffracted beam, and the diffraction efficiency are presented. (C) 2006 Optical Society of America.

Aberration measurement of projection optics in lithographic tools based on two-beam interference theory

The degradation of image quality caused by aberrations of projection optics in lithographic tools is a serious problem in optical lithography. We propose what we believe to be a novel technique for measuring aberrations of projection optics based on two-beam interference theory. By utilizing the partial coherent imaging theory, a novel model that accurately characterizes the relative image displacement of a fine grating pattern to a large pattern induced by aberrations is derived. Both even and odd aberrations are extracted independently from the relative image displacements of the printed patterns by two-beam interference imaging of the zeroth and positive first orders. The simulation results show that by using this technique we can measure the aberrations present in the lithographic tool with higher accuracy. (c) 2006 Optical Society of America.

Diffraction properties of volume holographic gratings for an ultrashort pulsed beam with different polarization states readout

The diffraction properties of volume holographic gratings are studied when the gratings are illuminated by an ultrashort pulsed beam with different polarization states. The developed coupled wave theory of Kogelnik is used. Considering the dispersion effect of the grating media, solutions for the diffracted and transmitted intensities, diffraction efficiencies and the bandwidths of the gratings are given in transmission volume holographic gratings and reflection volume holographic gratings. The bandwidths of the gratings are reduced by the dispersion effect of the grating media. They also have different influences on the diffraction of an ultrashort pulsed beam with different polarization states. For different values of the ratio of the spectral bandwidth of the input pulse to that of the grating, the changes of the spectral and temporal distributions of the diffracted intensities, as well as the diffraction efficiencies of the gratings are shown.

Distortion of beam shape by a rotating double-prism wide-angle laser beam scanner

We describe the rigorous results of a wide-angle laser beam scanner, obtained with the help of the vector refraction theory. Using the rigorous results, the distortion of the beam shape is discussed. The distortion to the beam varies with the different relative angles of double prisms. The scanner expands the beam in some directions while it contracts the beam in other directions. According to the conservation of energy, the distribution of the laser intensity is changed as well. (c) 2006 Society of Photo-Optical Instrumentation Engineers.

Absolute oscillator strengths for iron, copper, cadmium and gold measured by the atomic beam method

Absolute f-values for 7 transitions in the first spectra of 4 elements have been measured using the atomic beam absorption technique. The equivalent widths of the absorption lines are measured with a photoelectric scanner and the atomic beam density is determined by continuously weighing a part of it with a sensitive automatic microbalance. The complete theory is presented and corrections are calculated to cope with gas absorption by the deposit on the microbalance pan and atoms which do not stick to the pan. An additional correction for the failure of the assumption of effusive flow in the formation of the atomic beam at large densities has been measured experimentally.

The following f-values were measured:

Fe: f_λ3720 = 0.0430 ± 8%

Cu: f_λ3247 = 0.427 ± 4.5%, f_λ3274 = 0.206 ± 4.7%, f_λ2492 = 0.0037 ± 9%

Cd: f_λ3261 = 0.00190 ± 7%, f_λ2288 = 1.38 ± 12%

Au: f_λ2428 = 0.283 ± 5.3%

Comparison with other accurately measured f-values, where they exist, shows agreement within experimental errors.

The resolution of the thermodynamic paradox and the theory of guided wave propagation in anisotropic media

The resolution of the so-called thermodynamic paradox is presented in this paper. It is shown, in direct contradiction to the results of several previously published papers, that the cutoff modes (evanescent modes having complex propagation constants) can carry power in a waveguide containing ferrite. The errors in all previous “proofs” which purport to show that the cutoff modes cannot carry power are uncovered. The boundary value problem underlying the paradox is studied in detail; it is shown that, although the solution is somewhat complicated, there is nothing paradoxical about it.

The general problem of electromagnetic wave propagation through rectangular guides filled inhomogeneously in cross-section with transversely magnetized ferrite is also studied. Application of the standard waveguide techniques reduces the TM part to the well-known self-adjoint Sturm Liouville eigenvalue equation. The TE part, however, leads in general to a non-self-adjoint eigenvalue equation. This equation and the associated expansion problem are studied in detail. Expansion coefficients and actual fields are determined for a particular problem.

Diffraction of an ultrashort pulsed beam with arbitrary polarization state from a volume holographic grating in LiNbO3 crystals

Based on a modified coupled wave theory of Kogelnik, we have studied the diffraction of an ultrashort pulsed beam with an arbitrary polarization state from a volume holographic grating in photorefractive LiNbO3 crystals. The results indicate that the diffracted intensity distributions in the spectral and temporal domains and the diffraction efficiency of the grating are both changed by the polarization state and spectral bandwidth of the input pulsed beam. A method is given of choosing the grating parameters and input conditions to obtain a large variation range of the spectral bandwidth of the diffracted pulsed beam with an appropriate diffraction efficiency. Our study presents a possibility of using a volume holographic grating recorded in anisotropic materials to shape a broadband ultrashort pulsed beam by modulating its polarization state.

Laser beam shaping system with a radial birefringent filter

Reshaping of a Gaussian laser beam into a uniform or other intensity distribution is required for various applications. The laser beam shaping system with a radial birefringent filter is presented in this paper. With such a system the Gaussian beams can be transformed into uniform or annular beams. The theory and simulation of the proposed systems are described in detail. The primary advantage of such a system is that the out beam pro. le can be tunable with the rotation of the radial birefringent element.