Accelerating imaging research at large-scale scientific facilities through scientific computing.

To date, computed tomography experiments, carried-out at synchrotron radiation facilities worldwide, pose a tremendous challenge in terms of the breadth and complexity of the experimental datasets produced. Furthermore, near real-time three-dimensional reconstruction capabilities are becoming a crucial requirement in order to perform high-quality and result-informed synchrotron imaging experiments, where a large amount of data is collected and processed within a short time window. To address these challenges, we have developed and deployed a synchrotron computed tomography framework designed to automatically process online the experimental data from the synchrotron imaging beamlines, while leveraging the high-performance computing cluster capabilities to accelerate the real-time feedback to the users on their experimental results. We have, further, integrated it within a modern unified national authentication and data management framework, which we have developed and deployed, spanning the entire data lifecycle of a large-scale scientific facility. In this study, the overall architecture, functional modules and workflow design of our synchrotron computed tomography framework are presented in detail. Moreover, the successful integration of the imaging beamlines at the Shanghai Synchrotron Radiation Facility into our scientific computing framework is also detailed, which, ultimately, resulted in accelerating and fully automating their entire data processing pipelines. In fact, when compared with the original three-dimensional tomography reconstruction approaches, the implementation of our synchrotron computed tomography framework led to an acceleration in the experimental data processing capabilities, while maintaining a high level of integration with all the beamline processing software and systems.

Solid-liquid-gas reaction accelerated by gas molecule tunnelling-like effect.

Solid-liquid-gas reactions are ubiquitous and are encountered in both nature and industrial processes1-4. A comprehensive description of gas transport in liquid and following reactions at the solid-liquid-gas interface, which is substantial in regard to achieving enhanced triple-phase reactions, remains unavailable. Here, we report a real-time observation of the accelerated etching of gold nanorods with oxygen nanobubbles in aqueous hydrobromic acid using liquid-cell transmission electron microscopy. Our observations reveal that when an oxygen nanobubble is close to a nanorod below the critical distance (~1 nm), the local etching rate is significantly enhanced by over one order of magnitude. Molecular dynamics simulation results show that the strong attractive van der Waals interaction between the gold nanorod and oxygen molecules facilitates the transport of oxygen through the thin liquid layer to the gold surface and thus plays a crucial role in increasing the etching rate. This result sheds light on the rational design of solid-liquid-gas reactions for enhanced activities.

Hydrated cation-π interactions of π-electrons with hydrated Li+, Na+, and K+ cations.

Cation-π interactions are essential for many chemical, biological, and material processes, and these processes usually involve an aqueous salt solution. However, there is still a lack of a full understanding of the hydrated cation-π interactions between the hydrated cations and the aromatic ring structures on the molecular level. Here, we report a molecular picture of hydrated cation-π interactions, by using the calculations of density functional theory (DFT). Specifically, the graphene sheet can distort the hydration shell of the hydrated K+ to interact with K+ directly, which is hereafter called water-cation-π interactions. In contrast, the hydration shell of the hydrated Li+ is quite stable and the graphene sheet interacts with Li+ indirectly, mediated by water molecules, which we hereafter call the cation-water-π interactions. The behavior of hydrated cations adsorbed on a graphene surface is mainly attributed to the competition between the cation-π interactions and hydration effects. These findings provide valuable details of the structures and the adsorption energy of hydrated cations adsorbed onto the graphene surface.

S-shaped velocity deformation induced by ionic hydration in aqueous salt solution flow.

Ionic hydration shells are the most noticeable microscopic feature in an aqueous salt solution, and have attracted attention due to their possible contribution to its flow behavior. In this paper, we find by molecular dynamic simulations that an S-shaped velocity profile is induced by the ionic hydration shells in the nano channel flow. Our theoretical analysis implies a linear relationship between the energy density inside the first hydration shell of the ions and the deformation strength of the velocity profiles of aqueous salt solutions, where the deformation strength is quantified by the curvature length defined by the linear deviation extended from the velocity profile. Our simulation results confirm that such a linear relationship holds for chloride salt solutions with monatomic cations, e.g., K, Na, Ca, Mg, Al and the Na/Ca models by varying the valence number of Na and Ca in the salt solutions. Furthermore, the influence of the flow velocity and the channel width upon the velocity deformation strength are also investigated. Our results indicate that the calculated curvature length provides a numerical evaluation for nano flow behavior and would be helpful in nanofluidic device design.

Two rhombic ice phases from aqueous salt solutions under graphene confinement.

Water exhibits rich ice phases depending upon its respective formation conditions, and in particular, the two-dimensional ice with nonhexagonal symmetry adsorbed on solids relates to the exceptional arrangement of water molecules. Despite extensive reporting of two-dimensional ice on various solid surfaces, the geometry and thermodynamics of ice formation from an aqueous salt solution are still unknown. In this Letter, we show the formation of single- and two-phase mixed two-dimensional rhombic ice from aqueous salt solutions with different concentrations under strong compressed confinement of graphene at ambient temperature by using classical molecular dynamics simulations and first-principles calculations. The two rhombic ice phases exhibit identical geometry and thermodynamic properties, but different projections of the oxygen atoms against solid surface symmetry, where they relate to the stable and metastable arrangements of water molecules confined between two graphene layers. A single-phase rhombic ice would grow from the confined saturated aqueous solutions since the previously stable rhombic molecular arrangement becomes an unstable high-energy state by introducing salt ions nearby. Our result reveals different rhombic ice phases growing from pure water and aqueous solutions, highlighting the deciding role of salt ions in the ice formation process due to their common presence in liquids.

Enhancing antibacterial properties by regulating valence configurations of copper: a focus on Cu-carboxyl chelates.

Optimizing the antibacterial effectiveness of copper ions while reducing environmental and cellular toxicity is essential for public health. A copper chelate, named PAI-Cu, is skillfully created using a specially designed carboxyl copolymer (a combination of acrylic and itaconic acids) with copper ions. PAI-Cu demonstrates a broad-spectrum antibacterial capability both in vitro and in vivo, without causing obvious cytotoxic effects. When compared to free copper ions, PAI-Cu displays markedly enhanced antibacterial potency, being about 35 times more effective against Escherichia coli and 16 times more effective against Staphylococcus aureus. Moreover, Gaussian and ab initio molecular dynamics (AIMD) analyses reveal that Cu+ ions can remain stable in the carboxyl compound's aqueous environment. Thus, the superior antibacterial performance of PAI-Cu largely stems from its modulation of copper ions between mono- and divalent states within the Cu-carboxyl chelates, especially via the carboxyl ligand. This modulation leads to the generation of reactive oxygen species (˙OH), which is pivotal in bacterial eradication. This research offers a cost-effective strategy for amplifying the antibacterial properties of Cu ions, paving new paths for utilizing copper ions in advanced antibacterial applications.

Initiating Reversible Aqueous Copper-Tellurium Conversion Reaction with High Volumetric Capacity through Electrolyte Engineering.

Pursuing conversion-type cathodes with high volumetric capacity that can be used in aqueous environments remains rewarding and challenging. Tellurium (Te) is a promising alternative electrode due to its intrinsic attractive electronic conductivity and high theoretical volumetric capacity yet still to be explored. Herein, the kinetically/thermodynamically co-dominat copper-tellurium (Cu-Te) alloying phase-conversion process and corresponding oxidation failure mechanism of tellurium are investigated using in situ synchrotron X-ray diffraction and comprehensive ex situ characterization techniques. By virtue of the fundamental insights into the tellurium electrode, facile and precise electrolyte engineering (solvated structure modulation or reductive antioxidant addition) is implemented to essentially tackle the dramatic capacity loss in tellurium, affording reversible aqueous Cu-Te conversion reaction with an unprecedented ultrahigh volumetric capacity of up to 3927 mAh cm-3 , a flat long discharge plateau (capacity proportion of ≈81%), and an extraordinary level of capacity retention of 80.4% over 2000 cycles at 20 A g-1 of which lifespan thousand-fold longer than Cu-Te conversion using CuSO4 -H2 O electrolyte. This work paves a significant avenue for expanding high-performance conversion-type cathodes toward energetic aqueous multivalent-ion batteries.

Unravelling Twin Topotactic/Nontopotactic Reactive TiSe2 Cathodes for Aqueous Batteries.

Titanium selenide (TiSe2 ), a model transition metal chalcogenide material, typically relies on topotactic ion intercalation/deintercalation to achieve stable ion storage with minimal disruption of the transport pathways but has restricted capacity (<130 mAh g-1 ). Developing novel energy storage mechanisms beyond conventional intercalation to break capacity limits in TiSe2 cathodes is essential yet challenging. Herein, the ion storage properties of TiSe2 are revisited and an unusual thermodynamically stable twin topotactic/nontopotactic Cu2+ accommodation mechanism for aqueous batteries is unraveled. In situ synchrotron X-ray diffraction and ex situ microscopy jointly demonstrated that topotactic intercalation sustained the ion transport framework, nontopotactic conversion involved localized multielectron reactions, and these two parallel reactions are miraculously intertwined in nanoscale space. Comprehensive experimental and theoretical results suggested that the twin-reaction mechanism significantly improved the electron transfer ability, and the reserved intercalated TiSe2 structure anchored the reduced titanium monomers with high affinity and promoted efficient charge transfer to synergistically enhance the capacity and reversibility. Consequently, TiSe2 nanoflake cathodes delivered a never-before-achieved capacity of 275.9 mAh g-1 at 0.1 A g-1 , 93.5% capacity retention over 1000 cycles, and endow hybrid batteries (TiSe2 -Cu||Zn) with a stable energy supply of 181.34 Wh kg-1 at 2339.81 W kg-1 , offering a promising model for aqueous ion storage.

Experimental study on inhibitory effects of diallyl sulfide on growth and invasion of human osteosarcoma MG-63 cells.

The inhibitory effects of diallyl sulfide (DAS) derived from allicin on in vitro and in vivo proliferation of human osteosarcoma MG-63 cells and the action mechanism, and the influence of DAS on invasive capability of MG-63 cells were investigated in order to search for the novel medicines for osteosarcoma. In the in vitro experiment, MG-63 cells were treated with different concentrations of DSA, and the morphological changes of MG-63 cells were observed under an inverted phase microscope. MTT method was used to assay the proliferation of MG-63 cells. Semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) was used to detect the VEGF mRNA expression level in MG-63 cells. By using Transwell invasion assay, the influence of DAS on invasive ability of MG-63 cells was tested. In the in vivo experiment, the nude mice MG-63 cells tumor-bearing model was established, and different concentrations of DAS were injected beside the tumor. Twenty-one days after treatment, the mice were killed, the tumor size and tumor inhibition rate were calculated. The microvessel density (MVD) was determined by using immunohistochemistry. In the in vitro experiment, different concentrations of DAS could obviously inhibit proliferation of MG-63 cells in a time- and concentration-dependent manner. RT-PCR revealed that the expression levels of VEGF mRNA in DSA groups (different concentrations) were significant reduced as compared with those in control group (all P<0.05). Transwell invasion assay indicated that in 20 and 40 µg/mL DAS groups, the number of migratory cells was 91.4±8.3 and 81.8±7.4 respectively, which was significantly declined as compared with that in control group (150.4±14.7, both P<0.05). In the in vivo experiment, DAS could significantly suppress the growth of MG-63 tumor-bearing tissue. Immunohistochemistry demonstrated that different concentrations (20 and 40 µg/mL) of DAS could significantly decrease MVD of MG-63 tumor-bearing tissue (all P<0.05). It was suggested that DAS could inhibit the growth of MG-63 cells probably by suppressing the expression of VEGF mRNA.

Effect of ω-3 polyunsaturated fatty acid on toll-like receptors in patients with severe multiple trauma.

This study examined the effects of ω-3 polyunsaturated fatty acid (ω-3PUFA) on the expression of toll-like receptor 2 (TLR2), toll-like receptor 4 (TLR4) and some related inflammatory factors in peripheral blood mononuclear cells (PBMCs) of patients with early-stage severe multiple trauma. Thirty-two patients who were admitted to the Department of Traumatic Surgery, Tongji Hospital (Wuhan, China) between May 2010 and November 2010, and diagnosed as having severe multiple trauma with a injury severity score (ISS) no less than 16, were enrolled in the study and divided into two groups at random (n=16 in each): ω-3PUFA group and control group in which routine parenteral nutrition supplemented with ω-3PUFA or not was administered to the patients in two groups for consecutive 7 days. Peripheral blood from these patients was collected within 2 h of admission (day 0), and 1, 3, 5 and 7 days after the nutritional support. PBMCs were isolated and used for detection of the mRNA and protein expression of TLR2 and TLR4 by using real-time PCR and flow cytometry respectively, the levels of NF-κB by quantum dots-based immunofluorescence assay, the levels of TNF-α, IL-2, IL-6 and COX-2 by ELISA, respectively. The results showed that the mRNA and protein expression of TLR2 and TLR4 in PBMCs was significantly lower in ω-3PUFA group than in control group 5 and 7 days after nutrition support (both P<0.05). The levels of TNF-α, IL-2, IL-6 and COX-2 were found to be substantially decreased in PBMCs in ω-3PUFA group as compared with control group at 5th and 7th day (P<0.05 for all). It was concluded that ω-3PUFA can remarkably decrease the expression of TLR2, TLR4 and some related inflammatory factors in NF-κB signaling pathway in PBMCs of patients with severe multiple trauma, which suggests that ω-3PUFA may suppress the excessive inflammatory response meditated by the TLRs/NF-κB signaling pathway.

Adjustable diffusion enhancement of water molecules in a nanoscale water bridge.

The emergence of nanofluidics in the last few decades has led to the development of various applications such as water desalination, ultrafiltration, osmotic energy conversion, etc. In particular, understanding water molecule transport in nanotubes is of importance for designing novel ultrafiltration and filtering devices. In this paper, we use an electric field to form a nanoscale water bridge as an artificial water channel to connect two separate disjoint nanotubes by molecular dynamics simulations. The extended length of the water bridge under different electric field strengths could adjust the diffusion process of the water molecules crossing the two disjoint nanotubes and the diffusion coefficients could be remarkably enhanced up to 4 times larger than the value in bulk water. By analyzing the structure of the water bridge, it is found that the diffusion enhancement originates from the strengthened interactions and the increase of hydrogen bonds between the water molecules due to the restrained reorientation from the external electric field. Our result provides a promising insight for realizing an efficient mass transport between various disjoint nanochannels.

Phonon-Induced Ratchet Motion of a Water Nanodroplet on a Supported Black Phosphorene.

Phonons are not supposed to carry any physical momentum as lattice vibrational modes; thus, it is believed no mass transport could be induced by phonons. In this Letter, we show that a ratchet motion of a water nanodroplet could be induced on a two-dimensional puckered lattice like black phosphorene (BP) by exciting its flexural phonons through a moving substrate. The water nanodroplet exhibits a forward motion along the armchair or a backward motion along the zigzag directions on a BP lattice that is supported on a substrate possessing a relative armchair or zigzag forward motion with BP. Through the analysis of the structure and vibrational density states of BP, it is found that in-plane lattice displacement asymmetry and the in-plane vibration asymmetry are induced by the excited flexural phonons, which determine the water nanodroplet motion as an anisotropic Brownian motor. Simulations of the nanodroplet motion as functions of the substrate relative motion speed and direction and also the substrate coupling strength with BP are performed. Results of the nanodroplet ratchet motion exhibit good agreement with the theoretical predications from calculating the Brownian motor asymmetry. Our findings reveal a promising mass transport strategy and a further understanding of phonon-related interactions in crystalline solids.

Suppressed-to-enhanced thermal transport in a Fermi-Pasta-Ulam superlattice: Mediation roles of solitons and phonons.

Managing thermal transport in nanostructured materials possesses both theoretical and application value in thermoelectric and microelectronics design. Though a suppressed thermal conductivity could be easily achieved through disorder-induced phonon scattering in a superlattice, it is challenging to enhance thermal transport in a periodically designed lattice. In this paper, we show the possibility of mediating thermal conductivity from a suppressed to an enhanced value in a Fermi-Pasta-Ulam ß superlattice with periodic cells of arithmetically increased nonlinearity. When the cell length is increased, thermal conductivity in the superlattice crosses over a suppressed region into an enhanced one and it is even higher than in a homogeneous lattice with the same nonlinearity strength. The mediation originates from the long-lived nonlinear wave packets as solitons across the disorder-induced interface between cells of the superlattice, while at the same time the normal vibrational modes as phonons are suppressed. Our result shows a promising strategy to manipulate thermal transport over a wide range in a superlattice with strong nonlinearity.

Two-state diffusive mobility of slow and fast transport of water in narrow nanochannels.

Transport of water in narrow nanochannels as a single-file chain is involved in various biological activities and nanofluidic applications. However, although the consistent dipole orientation of the water molecules is intensively studied, its effect upon the transport behavior is still unknown. In this Rapid Communication, we find two states of slow and fast transport coexist in the single-file water in the presence of channel defects that break the collective dipole orientation. A low diffusive mobility is found for the dipole orientation inconsistent configurations while mobility approximately two times higher is found for the consistent ones. The two-state diffusion process relies on the different hydrogen bond connections, which possess overlapped structures, enabling a spontaneous transition. The slow state is insensitive to the increased defect number while the fast state is reduced accordingly. The two states exhibit different lifetime and temperature dependences that demonstrate a possibility for manipulation. Our result implies the possibility of two-state diffusion process of water in nanofluid phenomena due to the common presence of defects in nanochannels.

Efficient selection methods for black phosphorene nanoribbons.

Black phosphorene (BP) has shown anisotropic, electronic, mechanical, and thermal properties for various promising applications in recent years. To take full advantage of this unique anisotropy in its further functional design and application, it is of paramount importance to separate BP with well-defined chirality quickly and precisely. In this paper, we propose three efficient methods to separate BP ribbons with different chiralities by utilizing their strong chirality-dependent bending stiffness. Our results show that the bending stiffness in the zigzag direction is 4 times larger than that in the armchair direction. The mechanical anisotropy and bending-binding competition are used to realize chirality-dependent design. To fold, wrap or scroll the BP nanoribbons, it is necessary to overcome the bending stiffness by applying the binding energy between the BP nanoribbons and the contact surfaces. Due to the mechanical anisotropy, the BP nanoribbons could easily be folded, wrapped and scrolled along the armchair direction rather than the zigzag direction. Therefore, we introduce this characteristic in our chirality separation designs as, the self-folding model to fold up the armchair BP nanoribbons by nanoparticles, the suspension-bridge sieve model to pull down the armchair BP nanoribbons, and the nanorod-roller model to scroll up the armchair nanoribbons. Our separation methods in this research can be extended to other 2D materials with anisotropic mechanical properties. We hope our findings would offer a novel route for the manufacturing of BP-based electronic devices and self-assembly of nano-devices.

Betavoltaic Enhancement Using Defect-Engineered TiO2 Nanotube Arrays through Electrochemical Reduction in Organic Electrolytes.

Utilizing high-energy beta particles emitted from radioisotopes for long-lifetime betavoltaic cells is a great challenge due to low energy conversion efficiency. Here, we report a betavoltaic cell fabricated using TiO2 nanotube arrays (TNTAs) electrochemically reduced in ethylene glycol electrolyte (EGECR-TNTAs) for the enhancement of the betavoltaic effect. The electrochemical reduction of TNTAs using high cathodic bias in organic electrolytes is indeed a facile and effective strategy to induce in situ self-doping of oxygen vacancy (OV) and Ti3+ defects. The black EGECR-TNTAs are highly stable with a significantly narrower band gap and higher electrical conductivity as well as UV-vis-NIR light absorption. A 20 mCi of 63Ni betavoltaic cell based on the reduced TNTAs exhibits a maximum ECE of 3.79% with open-circuit voltage of 1.04 V, short-circuit current density of 117.5 nA cm-2, and a maximum power density of 39.2 nW cm-2. The betavoltaic enhancement can be attributed to the enhanced charge carrier transport and separation as well as multiple exciton generation of electron-hole pairs due the generation of OV and Ti3+ interstitial bands below the conductive band of TiO2.

Defect-induced betavoltaic enhancement in black titania nanotube arrays.

Utilizing high-energy beta particles emitted from radioisotopes for long-lifetime betavoltaic cells is a great challenge due to their low energy conversion efficiency (ECE). Here we report a betavoltaic cell fabricated using black titania nanotube arrays (TiO2 NTAs) by electrochemical anodization and Ar-annealing techniques. The obtained samples show enhanced electrical conductivity as well as Vis-NIR light absorption by the introduction of oxygen vacancy (OV) and Ti3+ defects in reduced TiO2-x NTAs. A 20 mCi63 Ni source was assembled into TiO2 NTAs to form a sandwich-type betavoltaic cell. By I-V measurements, the Ar-annealed TiO2 NTAs at 650 °C exhibited a maximum ECE of 3.65% with Voc = 1.13 V, Jsc = 103.3 nA cm-2, and Pmax = 37 nW cm-2. In comparison with air-annealed TiO2 NTAs, the enhancement of the betavoltaic effect in reduced TiO2-x NTAs can be attributed to the suppression of e-h recombination induced by the generation of OV and Ti3+ defects, serving as electron donors as well as electron traps that not only contribute to the increase of electrical conductance, but also facilitate the charge carrier separation.

Anisotropy Enhancement of Thermal Energy Transport in Supported Black Phosphorene.

Thermal anisotropy along the basal plane of materials possesses both theoretical importance and application value in thermal transport and thermoelectricity. Though common two-dimensional materials may exhibit in-plane thermal anisotropy when suspended, thermal anisotropy would often disappear when supported on a substrate. In this Letter, we find a strong anisotropy enhancement of thermal energy transport in supported black phosphorene. The chiral preference of energy transport in the zigzag rather than the armchair direction is greatly enhanced by coupling to the substrate, up to a factor of approximately 2-fold compared to the suspended one. The enhancement originates from its puckered lattice structure, where the nonplanar armchair energy transport relies on the out-of-plane corrugation and thus would be hindered by the flexural suppression due to the substrate, while the planar zigzag energy transport is not. As a result, thermal conductivity of supported black phosphorene shows a consistent anisotropy enhancement under different temperatures and substrate coupling strengths.

3D flexible water channel: stretchability of nanoscale water bridge.

Artificial water channels can contribute to a better understanding of natural water channels and offer a highly selective, advanced conductance system. Most studies use nanotubes, however it is difficult to fabricate a flexible structure, and the nanosized diameter brings nanoconfinement effects, and nanotube toxicity arouses biosafety concerns. In this paper, we use an electric field to restrain the water molecules to form a nanoscale water bridge as an artificial water channel to connect a separated solid plate by molecular dynamics simulations. We observe strong 3D flexible stretchability in the water bridge, maintaining a variable length and an arbitrary angle for a considerably long time. The stretching of the water bridge enables it to be polarized at an arbitrary angle and the stretchability is linearly dependent upon the polarization strength. More interestingly, we show the possibility of establishing complex water networks, e.g., triangle, rectangle, hexagon, and tetrahedron-tetrahedron water networks. Our results may help realize structurally flexible and environmentally friendly water channels for lab-on-a-chip applications in nanofluidics.

Cytogenetics of a pediatric unclassified sex cord-stromal tumor of the testis: a case report.

Unclassified sex cord-stromal tumors account for a small proportion of pediatric testicular tumors and, while most are clinically benign, some have demonstrated malignant potential. Histological findings do not correlate well with clinical behavior and, while cytogenetics may aid in both diagnosis and predicting clinical behavior, these data on sex cord-stromal tumors are scarce. We describe an unclassified sex cord-stromal tumor occurring in the testis of a prepubertal male without evidence of metastasis that had a previously unreported 54,XY,+3,+7,+9,+12,+13,+18,+19,+20 karyotype.