Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation.

BACKGROUND: Resolution estimation is the main evaluation criteria for the reconstruction of macromolecular 3D structure in the field of cryoelectron microscopy (cryo-EM). At present, there are many methods to evaluate the 3D resolution for reconstructed macromolecular structures from Single Particle Analysis (SPA) in cryo-EM and subtomogram averaging (SA) in electron cryotomography (cryo-ET). As global methods, they measure the resolution of the structure as a whole, but they are inaccurate in detecting subtle local changes of reconstruction. In order to detect the subtle changes of reconstruction of SPA and SA, a few local resolution methods are proposed. The mainstream local resolution evaluation methods are based on local Fourier shell correlation (FSC), which is computationally intensive. However, the existing resolution evaluation methods are based on multi-threading implementation on a single computer with very poor scalability. RESULTS: This paper proposes a new fine-grained 3D array partition method by key-value format in Spark. Our method first converts 3D images to key-value data (K-V). Then the K-V data is used for 3D array partitioning and data exchange in parallel. So Spark-based distributed parallel computing framework can solve the above scalability problem. In this distributed computing framework, all 3D local FSC tasks are simultaneously calculated across multiple nodes in a computer cluster. Through the calculation of experimental data, 3D local resolution evaluation algorithm based on Spark fine-grained 3D array partition has a magnitude change in computing speed compared with the mainstream FSC algorithm under the condition that the accuracy remains unchanged, and has better fault tolerance and scalability. CONCLUSIONS: In this paper, we proposed a K-V format based fine-grained 3D array partition method in Spark to parallel calculating 3D FSC for getting a 3D local resolution density map. 3D local resolution density map evaluates the three-dimensional density maps reconstructed from single particle analysis and subtomogram averaging. Our proposed method can significantly increase the speed of the 3D local resolution evaluation, which is important for the efficient detection of subtle variations among reconstructed macromolecular structures.

Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization.

BACKGROUND: Cryo-electron tomography (Cryo-ET) is an imaging technique used to generate three-dimensional structures of cellular macromolecule complexes in their native environment. Due to developing cryo-electron microscopy technology, the image quality of three-dimensional reconstruction of cryo-electron tomography has greatly improved. However, cryo-ET images are characterized by low resolution, partial data loss and low signal-to-noise ratio (SNR). In order to tackle these challenges and improve resolution, a large number of subtomograms containing the same structure needs to be aligned and averaged. Existing methods for refining and aligning subtomograms are still highly time-consuming, requiring many computationally intensive processing steps (i.e. the rotations and translations of subtomograms in three-dimensional space). RESULTS: In this article, we propose a Stochastic Average Gradient (SAG) fine-grained alignment method for optimizing the sum of dissimilarity measure in real space. We introduce a Message Passing Interface (MPI) parallel programming model in order to explore further speedup. CONCLUSIONS: We compare our stochastic average gradient fine-grained alignment algorithm with two baseline methods, high-precision alignment and fast alignment. Our SAG fine-grained alignment algorithm is much faster than the two baseline methods. Results on simulated data of GroEL from the Protein Data Bank (PDB ID:1KP8) showed that our parallel SAG-based fine-grained alignment method could achieve close-to-optimal rigid transformations with higher precision than both high-precision alignment and fast alignment at a low SNR (SNR=0.003) with tilt angle range ±60∘ or ±40∘. For the experimental subtomograms data structures of GroEL and GroEL/GroES complexes, our parallel SAG-based fine-grained alignment can achieve higher precision and fewer iterations to converge than the two baseline methods.

Surface photovoltage phase spectra for analysing the photogenerated charge transfer and photocatalytic activity of ZnFe2O4-TiO2 nanotube arrays.

The transfer properties of the photogenerated charge carriers in TiO2 nanotube arrays (TNAs) and ZnFe2O4 modified TiO2 nanotube arrays (ZFO-TNAs) were investigated by surface photovoltage phase spectra. The modification of ZnFe2O4 on TNAs will lead to a new process of photogeneration of charge carriers. When irradiated with UV or visible light, before ZnFe2O4 modification photogenerated holes can transfer to the surface of TNAs; while after ZnFe2O4 modification, a process of photogenerated electrons transferring to the surface occurred. The different detected photogenerated charge transfer processes agree well with the photocatalytic reduction of Cr(VI) and the degradation of methyl orange experiments, which confirmed that the photogenerated holes transferring to the surface of the TNAs or ZFO-TNAs were beneficial for the reactions of photocatalytic reduction and electrons transferring to the surface were beneficial for photocatalytic degradation.

Synthesis, photoelectric properties and photocatalytic activity of the Fe2O3/TiO2 heterogeneous photocatalysts.

Fe(2)O(3)/TiO(2) heterogeneous photocatalysts with different mass ratios of Fe(2)O(3)vs. TiO(2) were synthesized by impregnation of Fe(3+) on the surface of TiO(2) microrods and calcination at 300 degrees C. Scanning electron microscopy (SEM), high resolution transmission electron microscopy (HRTEM), photoluminescence spectra and X-ray diffraction (XRD) have been used to characterize the samples. The photocatalytic activities of Fe(2)O(3)/TiO(2) heterocomposites, pure Fe(2)O(3) and pure TiO(2) were evaluated by the photodegrading efficiency of Orange II under visible light (lambda > 420 nm). The experiments demonstrated that Orange II in aqueous solution was more efficiently photodegraded using Fe(2)O(3)/TiO(2) heterogeneous photocatalysts than either pure Fe(2)O(3) or TiO(2) under visible light irradiation. With an optimal mass ratio of 7:3 in Fe(2)O(3)/TiO(2) the highest rate of Orange II photodegradation was achieved under the experimental conditions. We have also compared the photoelectric properties of Fe(2)O(3)/TiO(2) heterogeneous photocatalysts with that of pure Fe(2)O(3) by surface photovoltage (SPV) and transient photovoltage (TPV) techniques. Based on the photovoltage responses, we discussed the influence of the hetero-interface between Fe(2)O(3) and TiO(2) on transfer characteristics of photogenerated charge carriers. We demonstrated that the formation of heterojunctions between Fe(2)O(3) and TiO(2) for Fe(2)O(3)/TiO(2) composites was pivotal for improving the separation and thus restraining the recombination of photogenerated electrons and holes, which accounts for the enhancement of photocatalytic activity.

Effect of photogenerated charge transfer on the photocatalysis in high-performance hybrid Pt-Co:ZnO nanostructure photocatalyst.

Hybrid Pt-Co:ZnO nanostructure photocatalysts were prepared via a facile two-step synthetic strategy. SPS and TPV investigations demonstrate the existence of the synergetic effect between Pt and Co dopants. Such synergetic effect could make use of visible photons as well as facilitates the separation of photogenerated charges to prevent recombination, effectively prolongating the charges lifetime to participate photocatalytic reaction. The synergetic effect exist in Pt-Co:ZnO inducing as high as 7.7-fold in photovoltaic response and 10-fold in the photo-activity for hybrids compared to Co:ZnO.

Enhancement of photocatalytic H2 evolution on Zn(0.8)Cd(0.2)S loaded with CuS as cocatalyst and its photogenerated charge transfer properties.

CuS/Zn(0.8)Cd(0.2)S composites have been successfully prepared by simple hydrothermal and cation exchange method. The Cu species loaded on Zn(0.8)Cd(0.2)S, together with the intimate contact formed between CuS and Zn(0.8)Cd(0.2)S, was clearly demonstrated with X-ray photoelectron spectroscopy and transmission electron microscopy. The optimized CuS/Zn(0.8)Cd(0.2)S photocatalyst has a high H2 evolution rate of 2792 µmol g(-1) h(-1) at CuS content of 3 wt% and the apparent quantum efficiency of 36.7% at 420 nm. The photophysical mechanism of the photocatalytic activity was investigated with the help of surface photovoltage spectroscopy (SPS) and transient photovoltage (TPV) techniques. The results revealed that photogenerated charge separation efficiency in Zn(0.8)Cd(0.2)S was enhanced and the photogenerated electrons were trapped by the loaded CuS, which benefits photo-reduction. Those were the reasons for significant enhancement in the photocatalytic H2 evolution from water splitting.

Enhancement of visible-light-driven photoresponse of Mn/ZnO system: photogenerated charge transfer properties and photocatalytic activity.

A visible-light-active ZnO photocatalyst system in the presence of manganese ions (Mn/ZnO) was prepared via a simple and rapid approach. XRD, XPS, Raman scattering and UV-Vis DRS confirmed the manganese exists in multivalent forms (Mn(3+)/Mn(2+)) in the ZnO lattice, furthermore, ZnO light absorption is extended to the visible region. The photocatalytic activities of the catalysts were evaluated by measuring the photodegrading efficiency of 2,4-dichlorophenol (DCP) under visible light irradiation. With an optimal molar ratio of 5% in Mn/ZnO the highest rate photodegradation was achieved under the experimental conditions. We have characterized the separation and transfer behavior of the photogenerated charges in the visible region by means of surface photovoltage (SPV), surface photocurrent (SPC) and transient photovoltage (TPV) techniques. Based on the comprehensive investigation of the photovoltaic properties of Mn/ZnO photocatalyst, we illustrate the behavior of photogenerated charges have distinct effects on the photocatalytic activity. It is demonstrated that the incorporation of multivalent Mn in ZnO promoted the separation of photogenerated charges, inhibited the recombination of photogenerated carriers, and thus prolonged the charges lifetime to participate in the photocatalytic reaction, resulting in highly efficient photocatalytic activity, which is attributed to the formation of a strong electronic interaction between the multivalent Mn and ZnO.

Photoinduced charge transfer properties and photocatalytic activity in Bi2O3/BaTiO3 composite photocatalyst.

A series of Bi(2)O(3)/BaTiO(3) composite photocatalysts with different mass ratios of Bi(2)O(3) vs BaTiO(3) were prepared by an impregnating-annealing method. X-ray diffraction (XRD), high-resolution transmission electron microscopic (HRTEM), and UV-vis diffuse reflection spectroscopy (DRS) confirmed that Bi(2)O(3) and BaTiO(3) coexisted in the composites. The results of surface photovoltage (SPV) experiments showed enhancements of photovoltaic response in composites, which indicated a higher separation efficiency of photoinduced charges due to the establishment of an efficient interfacial electric field between Bi(2)O(3) and BaTiO(3) in the composites. The consistency of phtocatalytic activity and photovoltaic response intensity of photocatalysts showed that the efficiency interfacial electric field between Bi(2)O(3) and BaTiO(3) played an important role in improving the degradation efficiency of Rhodamine B (RhB). The 60%-Bi(2)O(3)/BaTiO(3) sample with the best activity was found by optimizing the mass ratios of Bi(2)O(3) vs. BaTiO(3). On the basis of the work function (WF) measurements, a reasonable energy band diagram was proposed for BaTiO(3)/Bi(2)O(3) composite. It would be helpful in designing and constructing high efficiency heterogeneous semiconductor photocatalyst.

Fabrication of periodic metal nanowires with microscale mold by nanoimprint lithography.

In this paper, a simple method is demonstrated for fabricating periodic metal nanowires based on the unconventional nanoimprint lithography (NIL) technique. Using this method, sub-100 nm metal nanowires with the rectangular cross-section are fabricated with microscale stamp. Furthermore, the metal nanowires with different widths and heights can be generated by adjusting the imprinting parameters with the same stamp. The metal nanowires prepared with this method can be used for chemical sensing, such as ammonia sensing, and it may have applications in optical signal processing.