ALBERT

Description: Model evaluation is a necessary step for better prediction and design of 3D RNA structures. For proteins, this has been widely studied and the knowledge-based statistical potential has been proved to be one of effective ways to solve this problem. Currently, a few knowledge-based statistical potentials have also been proposed to evaluate predicted models of RNA tertiary structures. The benchmark tests showed that they can identify the native structures effectively but further improvements are needed to identify near-native structures and those with non-canonical base pairs. Here, we present a novel knowledge-based potential, 3dRNAscore, which combines distance-dependent and dihedral-dependent energies. The benchmarks on different testing datasets all show that 3dRNAscore are more efficient than existing evaluation methods in recognizing native state from a pool of near-native states of RNAs as well as in ranking near-native states of RNA models.

Description: Author(s): Y. Liu (刘育), D. F. Shao (邵定夫), L. J. Li, W. J. Lu, X. D. Zhu, P. Tong, R. C. Xiao, L. S. Ling, C. Y. Xi, L. Pi, H. F. Tian, H. X. Yang, J. Q. Li, W. H. Song, X. B. Zhu, and Y. P. Sun Transition-metal dichalcogenides (TMDs) M X 2 ( M = Ti , Nb , Ta ; X = S , Se , Te ) exhibit a rich set of charge density wave (CDW) orders, which usually coexist and/or compete with superconductivity. The mechanisms of CDWs and superconductivity in TMDs are still under debate. Here we perform an investigation on a t… [Phys. Rev. B 94, 045131] Published Thu Jul 21, 2016

Description: Author(s): C. Xiao, M. Maier, X. N. Du, P. Gerhard, L. Groening, S. Mickat, and H. Vormann Knowledge of the transverse four-dimensional beam rms parameters is essential for applications that involve lattice elements that couple the two transverse degrees of freedom (planes). Of special interest is the elimination of interplane correlations to reduce the projected emittances. A dedicated r… [Phys. Rev. Accel. Beams 19, 072802] Published Tue Jul 19, 2016

Description: Magnetic islands have been implemented in the gyrokinetic toroidal code to study the effects of the islands on microturbulence. The pressure profile flattening is verified in the simulation with the islands. Simulations of ion temperature gradient instability find that different toroidal modes are linearly coupled together and that toroidal spectra become broader when the island width increases. The real frequencies and growth rates of different toroidal modes approach each other with the averaged value independent of the island width. The linear mode structures are enhanced at the island separatrices and weakened at the island centers, consistent with the flattening of the pressure profile inside the islands.

Description: 〈span〉〈div〉ABSTRACT〈/div〉Borehole Radar (BHR) uses ultra-wideband electromagnetic (EM) waves to image discontinuities in formations. It has been a major bottleneck to extend BHR applications to obtain a clear and high-resolution radar profile in a complex and noisy environment, which increases ambiguity in the geology interpretation. To avoid this increased ambiguity in the geology interpretation, we proposed a scheme based on the empirical mode decomposition (EMD) and complex signal analysis theory to process the BHR data with low signal to noise ratio (SNR). The scheme includes four steps. First, the original radar profile is pre-processed to avoid mode confusion and noise interference to the radar echo. Next, the EMD method is used to process a single-channel radar dataset and to analyze the frequency components of the radar signal. Various intrinsic modes of the pre-processing radar profile are also obtained by using EMD. Finally, we reconstruct the intrinsic mode profile, which contains information about the formation, calculate the complex signals of the reconstructed radar profile using the Hilbert transform, extract the three instantaneous attributes (instantaneous amplitude, instantaneous phase, and instantaneous frequency), and draw the separate instantaneous attributes profiles. This processing scheme provides both the conventional time-distance profile also in addition to the three instantaneous attributes. The additional attributes reduce ambiguity when evaluating the original radar profile and avoid the deviation relying solely on a conventional time-distance profile. An actual radar profile, which was obtained by a BHR system in a limestone fracture zone, is used to verify the effectiveness of instantaneous attributes for improving interpretation accuracy. The results demonstrate that the EMD method is superior in processing the BHR signal under a low SNR and has the capability to separate the high-low components of the radar echo effectively.〈/span〉

Description: The fast electron flux driven by Lower Hybrid Wave (LHW) in the scrape-off layer (SOL) in EAST is analyzed both theoretically and experimentally. The five bright belts flowing along the magnetic field lines in the SOL and hot spots at LHW guard limiters observed by charge coupled device and infrared cameras are attributed to the fast electron flux, which is directly measured by retarding field analyzers (RFA). The current carried by the fast electron flux, ranging from 400 to 6000 A/m 2 and in the direction opposite to the plasma current, is scanned along the radial direction from the limiter surface to the position about 25 mm beyond the limiter. The measured fast electron flux is attributed to the high parallel wave refractive index n || components of LHW. According to the antenna structure and the LHW power absorbed by plasma, a broad parallel electric field spectrum of incident wave from the antennas is estimated. The radial distribution of LHW-driven current density is analyzed in SOL based on Landau damping of the LHW. The analytical results support the RFA measurements, showing a certain level of consistency. In addition, the deposition profile of the LHW power density in SOL is also calculated utilizing this simple model. This study provides some fundamental insight into the heating and current drive effects induced by LHW in SOL, and should also help to interpret the observations and related numerical analyses of the behaviors of bright belts and hot spots induced by LHW.

Description: The composition of ultraphytoplankton (〈10 µm) sampled in surface waters (1 m depth) was investigated during summer 2010 in the Bay of Marseille (NW Mediterranean) using flow cytometry. In addition to groups of Synechococcus , Prochlorococcus , picoeukaryotes and nanoeukaryotes, an unidentified additional cluster was observed. The particles forming this cluster had a high abundance (〉7 x 10 4 events mL –1 ), with both orange and red fluorescence intensities like Synechococcus , but with a size signal larger than that of 2 µm fluorospheres (beads). These unknown particles were sorted out by flow cytometry and then observed by epifluorescence microscopy: they appeared to be chain-forming microorganisms, just like trichomes of some diazotroph cyanobacteria with one heterocyst, but not unambiguously distal. The chains observed after cell sorting were not straight, but rather folded. To our knowledge, this is the first report of a possible bloom of such free trichomes. The small sample volume available for the delayed analysis and the limited resolution of our photomicrography did not allow for species identification. The brief occurrence of free trichomes in the Bay of Marseille with such a high abundance remains to be explained. High temperature in summer, induced stratification of the water column and nitrate depletion may be related to this event. High-frequency surveys of ultraphytoplankton assemblages at the single cell level appear to be necessary to observe such phenomenon more efficiently and document their dynamics.

Description: Biochemistry DOI: 10.1021/bi4006418

Description: High-pressure synchrotron Mössbauer (SMS) and X-ray emission (XES) spectroscopic measurements were conducted to investigate the spin and valence states of iron in (Al,Fe)-bearing magnesium silicate glass (Mg 0.79 Fe 0.10 Al 0.10 Si 0.96 O 3 ) up to 126 GPa and 300 K. By analyzing the Fe K β emission spectra using the integrated relative difference (IRD) method, which accounts for the spectral broadening effects, the derived total spin momentum ( S ) of the iron in the glass shows no observable changes with pressure within the experimental uncertainties. A two-doublet fitting model representing two diverse local iron atomic environments was used to satisfactorily simulate the high-pressure SMS spectra of iron in the glass. The doublet with an averaged quadrupole splitting (QS) value of 1.94(±0.25) mm/s and chemical shift (CS) of 1.02(±0.25) mm/s at ambient conditions was assigned to be high-spin Fe 2+ , whereas the second doublet with QS = 0.83(±0.25) mm/s and CS = 0.49(±0.25) mm/s was assigned to be high-spin Fe 3+ . Increasing pressure continuously elevates the QS of Fe 2+ from ~2 mm/s at ambient pressure to 3.5 mm/s at 126 GPa, while Fe 3+ only exhibits a slight increase in the QS to 1.34(±0.25) mm/s. Comparing with previous experimental and theoretical studies on the local geometries and hyperfine parameters of silicate glasses and minerals, we conclude that the occurrence of the extremely high QS of Fe 2+ in our glass above ~40–50 GPa can be associated with the enhanced density and diverse distortions and geometries of the local Fe 2+ environments. Our combined XES and SMS results show that both Fe 2+ and Fe 3+ ions in Al-bearing silicate remain in the high-spin state, rather than undergoing a spin-pairing transition as proposed previously. Assuming that the silicate glass results can be used as an analog for understanding silicate melts, our results here indicate that iron ions likely experience significant changes in the local environments yet remain overall in the high-spin state in silicate melts at the extreme pressure and temperature conditions of the deep mantle.

Description: A plasma current up to 15 kA has been driven with outer ohmic heating (OH) coils in the STOR-M iron core tokamak. Even when the inner OH coil is disconnected, the outer OH coils alone can induce the plasma current as primary windings and initial breakdown are even easier in this coil layout. This result suggests a possibility to use an iron core in a spherical tokamak to start up the plasma current without a central solenoid. The effect of the iron core saturation on the extension of the discharge pulse length has been estimated for further experiments in the STOR-M tokamak.