Refining near-native protein-protein docking decoys by local resampling and energy minimization

How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.

Mineral provinces and material provenance of the surficial sediments near the Zhongsha Islands in the South China Sea

Characteristics and distribution patterns of elastic minerals (0.063 similar to 0.125 mm) in bottom sediments represent a significant indicator for the identification of the origin of sediment. One hundred and fourteen surface sediment samples, which were collected from the area near the Zhongsha Islands in the South China Sea, were analysed to identify the mineral suites and their distributions in the study area. The area can be divided into three mineral provinces: ( I) a province of biogenic minerals, which mainly originate from the Zhongsha Atoll; ( H) a province of volcanogenic minerals, which are mainly derived from local basaltic seamounts and small-scale volcanoes that are probably erupting, with some influences from the island-are volcanic region around the South China Sea; and (II) a mixed mineral province whose material source includes biogenic minerals, volcanogenic minerals and terrigenous minerals; the last province can be subdivided into a mixed mineral sub-province of the northeastern part of the study area, in which terrigenous minerals are mainly derived from China's Mainland and do not exceed 17 degrees N, and a mixed mineral sub-province of the southeastern part of the study area, in which terrigenous minerals are derived from Kalimantan and Indochina Peninsula and might be further transported into the deep sea basin through submarine canyons.

Formation of Fe-oxyhydroxides from the East Pacific Rise near latitude 13 degrees N: Evidence from mineralogical and geochemical data

The mineralogical and geochemical characteristics of Fe-oxyhydroxide samples from one dredge station (long. 103 degrees 54.48'W, lat. 12 degrees 42.30'N, water depth 2655 m) on the East Pacific Rise near lat 13 degrees N were analyzed by XRD, ICP-AES, and ICP-MS. Most Fe-oxyhydroxides are amorphous, with a few sphalerite microlites. In comparison with Fe-oxyhydroxides from other fields, the variable ranges in the chemical composition of Fe-oxyhydroxide samples are very narrow; their Fe, Si, and Mn contents were 39.90%, 8.92%, and 1.59%, respectively; they have high Cu (0.88%-1.85%) and Co (65x10(-6)-704x10(-6)) contents, and contain Co+Cu+Zn+Ni > 1.01%. The trace-element (As, Co, Ni, Cu, Zn, Ba, Sr) and major-element (Fe, Ca, Al, Mg) contents of these samples are in the range of hydrothermal sulfide from the East Pacific Rise near 13 degrees N, reflecting that this type of Fe-oxyhydroxide constitutes a secondary oxidation product of hydrothermal sulfide. The Fe-oxyhydroxide samples from one dredge station on the East Pacific Rise near 13 degrees N are lower in Sigma REE (5.44x10(-6)-17.01x10(-6)), with a distinct negative Ce anomaly (0.12-0.28). The Fe-oxyhydroxide samples have similar chondrite-normalized rare-earth-element (REE) patterns to that of seawater, and they are very different from the REE composition characteristics of hydrothermal plume particles and hydrothermal fluids, showing that the REEs of Fe-oxyhydroxide are a major constituent of seawater and that the Fe-oxyhydroxides can become a sink of REE from seawater. The quick settling of hydrothermal plume particles resulted in the lower REE content and higher Mn content of these Fe-oxyhydroxides, which are captured in part of the V and P from seawater by adsorption. The Fe-oxyhydroxides from one dredge station on the East Pacific Rise near 13 degrees N were formed by secondary oxidation in a low temperature, oxygenated environment. In comparison with the elemental (Zn, Cd, Pb, Fe, Co, Cu) average content of hydrothermal sulfide samples from the East Pacific Rise near 13 degrees N, the Zn, Cd, and Pb contents of the Fe-oxyhydroxides are lower, and their Fe, Co, and Cu contents are higher.

Periodical mixing of MORB magmas near East Pacific Rise 13N: evidence from modeling and zoned plagioclase phenocrysts

Thirty-six basalt samples from near East Pacific Rise 13N are analyzed for major and trace elements. Different types of zoned plagioclase phenocrysts in basalts are also backscatter imaged, and major element profiles scanned and analyzed for microprobe. Basalts dredged from a restricted area have evolved to different extents (MgO=9.38wt%-6.76wt%). High MgO basalts are modeled for crystallization to MgO of about 7wt%, and resulted in the Ni contents (28 ppm) that are generally lower than that in observed basalts (> 60 ppm). It suggests that low MgO basalts may have experienced more intensive magma mixing. High MgO (9.38wt%) basalt is modeled for self-"mixing-crystallization", and the high Ni contents in low MgO basalts can be generated in small scale and periodical self-mixing of new magma (high MgO). "Mixing-crystallization" processes that low MgO magmas experienced accord with recent 226Ra/230Th disequilibria studies for magma residence time, in which low MgO magmas have experienced more circles of "mixing-crystallization" in relatively longer residence time. Magma mixing is not homogeneous in magma chamber, however, low MgO magmas are closer to stable composition produced by periodical "mixing-crystallization", which is also an important reason for magma diversity in East Pacific Rise. Zoned plagioclase phenocrysts can be divided into two types: with and without high An# cores, both of which have multiple reversed An# zones, suggesting periodical mixing of their host magmas. Cores of zoned plagioclase in low MgO (7.45wt%) basalt differ significantly with their mantle in An#, but are similar in An# with microlite cores (products of equilibrium crystallization) in high MgO (9.38wt%) basalt, which further shows that plagioclase phenocryst cores in low MgO basalts may have formed in their parental magmas before entering into the magma chamber.

Distribution and mobility of metals in agricultural soils near a copper smelter in South China

The distribution and mobility of heavy metals in the paddy soils surrounding a copper smelting plant in south China was investigated. We assessed the degree of metal contamination using an index of geoaccumulation. The metals were divided into two groups: (1) Cu, Zn, Pb and Cd, whose concentrations were heavily affected by anthropogenic inputs, and (2) Ni, Co and Cr, which were mainly of geochemical origin. Concentrations of Cu, Cd, Zn, and Pb in the polluted soils were higher than the Chinese soil quality criteria. The chemical partitioning patterns of Pb, Zn and Cu indicated that Pb was largely associated with the residual and NH2OH HCl extractable fractions. In contrast, Cd was predominantly associated with the MgCl2 extractable fraction. A large proportion of Cu was bound to the acidic H2O2 extractable fractions, while Zn was predominantly found in the residual phase. The fraction of mobile species, which potentially is the most harmful to the environment, was found to be elevated compared to unpolluted soils in which heavy metals are more strongly bound to the matrix. The mobility of the metals was studied by water extraction using a modification of Tessier's procedure, and the order of mobility was Zn > Cd > Cu > Ce > Pb.

Near-Space Wide-Swath Radar Imaging With Multiaperture Antenna

Near-space, defined as the altitude region between 20 and 100 km, offers many capabilities that are not accessible for low Earth-orbit (LEO) satellites or airplanes because it is above storm and not constrained by orbital mechanics and high fuel consumption. Hence, a high flying speed can be obtained for the maneuvering vehicles operating in near-space. This offers a promising solution to simultaneous high-resolution and wide-swath synthetic aperture radar (SAR) imaging. As such, one near-space wide-swath SAR imaging technique is presented in this letter. The system configuration, signal model, and imaging scheme are described. An example near-space SAR system is designed, and its imaging performance is analyzed. Simulation results show that near-space maneuvering vehicle SAR indeed seems to be a promising solution to wide-swath SAR imaging.

Characteristics of low-frequency components of the near-bottom current in the Chinese Pioneer Area

Two deep-sea moorings were deployed respectively in the east area and the west area of Chinese Pioneer Area (CPA) in the tropic east Pacific to monitor the regional deep-sea dynamics below 600 meters above bottom (mab) from July 1997 to Oct. 1999. Results of statistics, spectral estimate and correlation analysis of the low-passed velocity data show that time scales of low-frequency components of the near-bottom currents are 25similar to120 days, in which 51-day period dominates the lower band of the frequency domain. Topographic features have obvious effect on low-frequency currents below 50 mab; modulations of the bottom-intensified sheared mean flow to the low-frequency currents are the dynamic mechanism of the frequency shift that occurs in both the east-area and the west-area.

SUSPENDED SEDIMENT TRANSPORT IN THE OFFSHORE NEAR YANGTZE ESTUARY

Based on the Estuarine, Coastal and Ocean Modeling System with Sediments (ECOMSED) model, a 3-D hydrodynamic-transport numerical model was established for the offshore area near the Yangtze Estuary in the East China Sea. The hydrodynamic module was driven by tide and wind. Sediment module included sediment resuspension, transport and deposition of cohesive and non-cohesive sediment. The settling of cohesive sediment in the water column was modeled as a function of aggregation (flocculation) and deposition. The numerical results were compared with observation data for August, 2006. It shows that the sediment concentration reduces gradually from the seashore to the offshore area. Numerical results of concentration time series in the observation stations show two peaks and two valleys, according with the observation data. It is mainly affected by tidal current. The suspended sediment concentration is related to the tidal current during a tidal cycle, and the maximum concentration appears 1 h-4 h after the current maximum velocity has reached.