Identifying Proteins of High Designability via Surface-Exposure Patterns

Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique lowest-energy conformation. We find that designability is closely correlated with the pattern of surface exposure of the folded structure. For longer chains, complete enumeration of structures is impractical. Instead, structures can be randomly sampled, and relative designability estimated either from designability within the random sample, or directly from surface-exposure pattern. We compare the surface-exposure patterns of those structures identified as highly designable to the patterns of naturally occurring proteins.Comment: 17 pages, 12 figure

Coherent control at its most fundamental: CEP-dependent electron localization in photodissoziation of a H2+ molecular ion beam target

Measurements and calculations of the absolute carrier-envelope phase (CEP) effects in the photodissociation of the simplest molecule, H2+, with a 4.5-fs Ti:Sapphire laser pulse at intensities up to (4 +- 2)x10^14 Watt/cm^2 are presented. Localization of the electron with respect to the two nuclei (during the dissociation process) is controlled via the CEP of the ultra-short laser pulses. In contrast to previous CEP-dependent experiments with neutral molecules, the dissociation of the molecular ions is not preceded by a photoionization process, which strongly influences the CEP dependence. Kinematically complete data is obtained by time- and position-resolved coincidence detection. The phase dependence is determined by a single-shot phase measurement correlated to the detection of the dissoziation fragments. The experimental results show quantitative agreement with ab inito 3D-TDSE calculations that include nuclear vibration and rotation.Comment: new version includes minore changes and adding the supp_material.pd

Long-term stability studies of a semiconductor photoelectrode in three-electrode configuration

Improving the stability of semiconductor materials is one of the major challenges for sustainable and economic photoelectrochemical water splitting. N-terminated GaN nanostructures have emerged as a practical protective layer for conventional high efficiency but unstable Si and III-V photoelectrodes due to their near-perfect conduction band-alignment, which enables efficient extraction of photo-generated electrons, and N-terminated surfaces, which protects against chemical and photo-corrosion. Here, we demonstrate that Pt-decorated GaN nanostructures on an n+-p Si photocathode can exhibit an ultrahigh stability of 3000 h (i.e., over 500 days for usable sunlight ∼5.5 h per day) at a large photocurrent density (>35 mA cm-2) in three-electrode configuration under AM 1.5G one-sun illumination. The measured applied bias photon-to-current efficiency of 11.9%, with an excellent onset potential of ∼0.56 V vs. RHE, is one of the highest values reported for a Si photocathode under AM 1.5G one-sun illumination. This study provides a paradigm shift for the design and development of semiconductor photoelectrodes for PEC water splitting: stability is no longer limited by the light absorber, but rather by co-catalyst particles

Theoretical Study on Rotational Bands and Shape Coexistence of 183,185,187^{183,185,187}{Tl} in the Particle Triaxial-Rotor Model

By taking the particle triaxial-rotor model with variable moment of inertia, we investigate the energy spectra, the deformations and the single particle configurations of the nuclei $^{183,185,187}$Tl systemically. The calculated energy spectra agree with experimental data quite well. The obtained results indicate that the aligned bands observed in $^{183,185,187}$Tl originate from the $[530]{{1/2}}^{-}$, $[532]{{3/2}}^{-}$, $[660]{{1/2}}^{+}$ proton configuration coupled to a prolate deformed core, respectively. Whereas, the negative parity bands built upon the ${{9/2}}^{-}$ isomeric states in $^{183,185,187}$Tl are formed by a proton with the $[505]{{9/2}}^{-}$ configuration coupled to a core with triaxial oblate deformation, and the positive parity band on the ${{13/2}}^{+}$ isomeric state in $^{187}$Tl is generated by a proton with configuration $[606]{{13/2}}^{+}$ coupled to a triaxial oblate core.Comment: 16 pages, 5 figures. To appear in Physical Review

Intima-Media Thickness: Setting a Standard for a Completely Automated Method of Ultrasound Measurement

The intima – media thickness (IMT) of the common carotid artery is a widely used clinical marker of severe cardiovascular diseases. IMT is usually manually measured on longitudinal B-Mode ultrasound images. Many computer-based techniques for IMT measurement have been proposed to overcome the limits of manual segmentation. Most of these, however, require a certain degree of user interaction. In this paper we describe a new completely automated layers extraction (CALEXia) technique for the segmentation and IMT measurement of carotid wall in ultrasound images. CALEXia is based on an integrated approach consisting of feature extraction, line fitting, and classification that enables the automated tracing of the carotid adventitial walls. IMT is then measured by relying on a fuzzy K-means classifier. We tested CALEXia on a database of 200 images. We compared CALEXia performances to those of a previously developed methodology that was based on signal analysis (CULEXsa). Three trained operators manually segmented the images and the average profiles were considered as the ground truth. The average error from CALEXia for lumen – intima (LI) and media – adventitia (MA) interface tracings were 1.46 ± 1.51 pixel (0.091 ± 0.093 mm) and 0.40 ± 0.87 pixel (0.025 ± 0.055 mm), respectively. The corresponding errors for CULEXsa were 0.55 ± 0.51 pixels (0.035 ± 0.032 mm) and 0.59 ± 0.46 pixels (0.037 ± 0.029 mm). The IMT measurement error was equal to 0.87 ± 0.56 pixel (0.054 ± 0.035 mm) for CALEXia and 0.12 ± 0.14 pixel (0.01 ± 0.01 mm) for CULEXsa. Thus, CALEXia showed limited performance in segmenting the LI interface, but outperformed CULEXsa in the MA interface and in the number of images correctly processed (10 for CALEXia and 16 for CULEXsa). Based on two complementary strategies, we anticipate fusing them for further IMT improvements

The origin of the red luminescence in Mg-doped GaN

Optically-detected magnetic resonance (ODMR) and positron annihilation spectroscopy (PAS) experiments have been employed to study magnesium-doped GaN layers grown by metal-organic vapor phase epitaxy. As the Mg doping level is changed, the combined experiments reveal a strong correlation between the vacancy concentrations and the intensity of the red photoluminescence band at 1.8 eV. The analysis provides strong evidence that the emission is due to recombination in which electrons both from effective mass donors and from deeper donors recombine with deep centers, the deep centers being vacancy-related defects.Comment: 4 pages, 3 figure

Nuclear pairing reduction due to rotation and blocking

Nuclear pairing gaps of normally deformed and superdeformed nuclei are investigated using the particle-number conserving (PNC) formalism for the cranked shell model, in which the blocking effects are treated exactly. Both rotational frequency $\omega$-dependence and seniority (number of unpaired particles) $\nu$-dependence of the pairing gap $\tilde{\Delta}$ are investigated. For the ground-state bands of even-even nuclei, PNC calculations show that in general $\tilde{\Delta}$ decreases with increasing $\omega$, but the $\omega$-dependence is much weaker than that calculated by the number-projected Hartree-Fock-Bogolyubov approach. For the multiquasiparticle bands (seniority $\nu> 2$), the pairing gaps keep almost $\omega$-independent. As a function of the seniority $\nu$, the bandhead pairing gaps $\tilde{\Delta}(\nu,\omega=0)$ decrease slowly with increasing $\nu$. Even for the highest seniority $\nu$ bands identified so far, $\tilde{\Delta}(\nu,\omega=0)$ remains greater than 70% of $\tilde{\Delta}(\nu=0,\omega=0)$.Comment: 15 pages, 5 figure