Structural changes of purple membrane and bacteriorhodopsin during its denaturation induced by high pH

Bacteriorhodopsin (bR) trimers naturally form two-dimensional hexagonal crystals in purple membrane (PM), which make it very stable. However, the dnaturation of bR was found to occur during a very narrow pH range when the pH was increased above 12.0, as indicated by inactivation of the photochemical cycle observed by flash photolysis kinetic spectra. Here, atomic force microscopy was used to study the surface structural changes of PM during the denaturation process induced by high pH. Together with the absorption and fluorescence spectra, it was found that the structural changes could be divided into three steps. First, some hydrophobic amino acids of bR become exposed to the aqueous environment and PM loses its 2D crystalline structure, transforming into the so-called "nonisland" structure. Second, bR molecules are extracted out of membrane and form protrusions on the surface like islands in the sea; therefore, the "nonisland" structure transforms into the "island" structure. Finally, most bRs break off from the membrane and form large depositions.     

Theoretical study of the effect of water in the process of proton transfer of glycinamide

For the purpose of investigating the tautomerism from glycinamide (G) to glycinamidic acid (G*) induced by proton transfer, we carried out a study of structural interconversion of the two tautomers and the relative stabilizing influences of water during the tautomerization process. Throughout the study, we used density functional theory (DFT) calculations at the B3LYP/6-311++G** level of theory, also considering the correction functions, that is, the effect of basis set superposition error (BSSE). Totally, 42 geometries, including fourteen important transition states, were optimized, and their geometric parameters have also been discussed in detail. Water molecules were gradually put in three different regions in the vicinity of G and its tautomer G*. The calculation results indicate that water in two of these regions can protect G from tautomerizing to G*, while in another region, water can assist in the tautomerism; this reveals that water molecules have stabilization and mutagenicity effects for G simultaneously.     

A partition coefficient calculation method with the SFED model

The Solvation Free Energy Density (SFED) model, a solvation model proposed by No et al. was modified to give better solvation free energies of the molecules having high polarizable groups. The SFED at a point around the molecule was represented by a linear combination of four basis functions, the contribution from the cavitation free energy of a solvent, and a constant. As an application of the SFED model, the linear expansion coefficients of the Hydration Free Energy Density (HFED) and the 1-Octanol Free Energy Density (1-OFED) were determined. Both calculated hydration free energy and 1-octanol solvation free energy of selected 95 organic molecules agreed well with experimental values. The standard errors were 0.47 and 0.39 kcal/mol, respectively. 1-Octanol/water partition coefficients (P) of the molecules were calculated from the difference of the HFE and 1-OFE of the molecules. At the same time, the logP density (LPD) of a molecule was represented by the same basis functional form with the SFED model. The logP of a molecule can be obtained by the integration of the LPD of the molecule. The coefficients of the basis functions were determined by using experimental logP as constraints through an optimization procedure. Both logPs calculated from the free energy difference and from the LPD agreed well with the experimental data. The absolute mean errors were obtained as 0.34 and 0.32, respectively.     

Atomic-scale imaging of wall-by-wall breakdown and concurrent transport measurements in multiwall carbon nanotubes

We report the atomic-scale imaging with concurrent transport measurements of the breakdown of individual multiwall carbon nanotubes inside a transmission electron microscope equipped with a piezomanipulator. We found unexpectedly three distinct breakdown sequences: namely, from the outermost wall inward, from the innermost wall outward, and alternatively between the innermost and the outmost walls. Remarkably, a significant amount of current drop was observed when an innermost wall is broken, proving unambiguously that every wall is conducting. Moreover, the breakdown of each wall in any sequence initiates in the middle of the nanotube, not at the contact, proving that the transport is not ballistic.     

Torsional wave experiments with a new magnetostrictive transducer configuration

For the efficient long-range nondestructive structural health inspection of pipes, guided waves have become widely used. Among the various guided wave modes, the torsional wave is most preferred since its first branch is nondispersive. Our objective in this work is to develop a new magnetostrictive transducer configuration to transmit and receive torsional waves in cylindrical waveguides. The conventional magnetostrictive transducer for the generation and measurement of torsional waves consists of solenoid coils and a nickel strip bonded circumferentially to test pipes. The strip must be premagnetized by a permanent magnet before actual measurements. Because of the premagnetization, the transducer is not suitable for the long-term on-line monitoring of pipes buried underground. To avoid the cumbersome premagnetization and to improve the transduction efficiency, we propose a new transducer configuration using several pieces of nickel strips installed at 45 degrees with respect to the pipe axis. If a static bias magnetic field is also applied, the transducer output can be substantially increased. Several experiments were conducted to study the performance of the proposed transducer configuration. The proposed transducer configuration was also applied for damage detection in an aluminum pipe.     

Rapid optimization of working parameters of microwave-driven multilevel qubits for minimal gate leakage

We propose an effective method to optimize the working parameters (WPs) of microwave-driven quantum gates implemented with multilevel qubits. We show that by treating transitions between each pair of levels independently, intrinsic gate errors due primarily to population leakage to undesired states can be determined by spectroscopic properties of the qubits and minimized by choosing proper WPs. The validity and efficiency of the approach are demonstrated by applying it to optimize the WPs of two coupled rf SQUID flux qubits for controlled-not operation. The result of this independent transition approximation (ITA) is in good agreement with that of dynamic method (DM). The ratio of the speed of ITA to that of DM scales exponentially as 2(n) when the number of qubits n increases.     

Time-of-flight flow imaging using NMR remote detection

A time-of-flight imaging technique is introduced to visualize fluid flow and dispersion through porous media using NMR. As the fluid flows through a sample, the nuclear spin magnetization is modulated by rf pulses and magnetic field gradients to encode the spatial coordinates of the fluid. When the fluid leaves the sample, its magnetization is recorded by a second rf coil. This scheme not only facilitates a time-dependent imaging of fluid flow, it also allows a separate optimization of encoding and detection subsystems to enhance overall sensitivity. The technique is demonstrated by imaging gas flow through a porous rock.     

Faraday-Michelson system for quantum cryptography

Quantum key distribution provides unconditional security for communication. Unfortunately, current experimental schemes are not suitable for long-distance fiber transmission because of phase drift or Rayleigh backscattering. In this Letter we present a unidirectional intrinsically stable scheme that is based on Michelson-Faraday interferometers, in which ordinary mirrors are replaced with 90 degree Faraday mirrors. With the scheme, a demonstration setup was built and excellent stability of interference fringe visibility was achieved over a fiber length of 175 km. Through a 125 km long commercial communication fiber cable between Beijing and Tianjin, the key exchange was performed with a quantum bit-error rate of less than 6%, which is to our knowledge the longest reported quantum key distribution experiment under field conditions.     

Nonlinear propagation of ultraslow pulses in media with electromagnetically induced transparency

The nonlinear behavior of a probe pulse propagating in a medium with electromagnetically induced transparency is studied both numerically and analytically. A new type of nonlinear wave equation is proposed in which the noninstantaneous response of nonlinear polarization is treated properly. The resulting nonlinear behavior of the propagating probe pulse is shown to be fundamentally different from that predicted by the simple nonlinear Schr?dinger-like wave equation that considers only instantaneous Kerr nonlinearity.     

Colored conical emission by means of second harmonic generation in a quadratically nonlinear medium

Colored conical emission was observed experimentally in a thick beta-barium borate crystal as a result of spatiotemporal modulational instability. In the presence of both dispersion and diffraction, colored conical emission showed specific features that were characteristic of the nonlinear dynamics of the strongly coupled fundamental and harmonic fields. Experimental observation directly demonstrated that beam angular spectra were substantially modified as a result of exponential growth of perturbations by means of parametric wave mixing. Seeded amplification of colored conical emission was demonstrated to support ultrabroadband up-conversion.