High-throughput computational materials screening of transition metal peroxides.

Semiconductor materials of abnormal stoichiometric ratio often exhibit unique properties, yet it is still a challenge to determine the structures of such materials in an efficient way. Herein, we propose a method for structurally biased screening according to the coordination numbers and the numbers of Wyckoff positions, balancing the atom local environment and the global symmetry of structures. Based on first-principles calculations, we have predicted two metastable peroxides P21/c-ScO2 and Pmmn-TiO3 with more than six coordination points. For these two structures, the most stable intrinsic defect is the oxygen vacancy (VO) at the peroxide anion (O2-2), which induces the absence of antibonding orbital formed by O2-2 near the valence band maximum. With the introduction of VO, the decrease of coordination numbers leads to charge recombination, and results in the appearance of an ordered phase TiO2.5 with stronger Ti-O orbital hybridization. The proposed method presents a promising and feasible approach for the screening of novel compounds.

Room-Temperature Magnetic Phase Transition in an Electrically Tuned van der Waals Ferromagnet.

Finding tunable van der Waals (vdW) ferromagnets that operate at above room temperature is an important research focus in physics and materials science. Most vdW magnets are only intrinsically magnetic far below room temperature and magnetism with square-shaped hysteresis at room temperature has yet to be observed. Here, we report magnetism in a quasi-2D magnet Cr_{1.2}Te_{2} observed at room temperature (290 K). This magnetism was tuned via a protonic gate with an electron doping concentration up to 3.8×10^{21} cm^{-3}. We observed nonmonotonic evolutions in both coercivity and anomalous Hall resistivity. Under increased electron doping, the coercivities and anomalous Hall effects (AHEs) vanished, indicating a doping-induced magnetic phase transition. This occurred up to room temperature. DFT calculations showed the formation of an antiferromagnetic (AFM) phase caused by the intercalation of protons which induced significant electron doping in the Cr_{1.2}Te_{2}. The tunability of the magnetic properties and phase in room temperature magnetic vdW Cr_{1.2}Te_{2} is a significant step towards practical spintronic devices.

Electric Control of Exchange Bias Effect in FePS3-Fe5GeTe2 van der Waals Heterostructures.

Manipulating the exchange bias (EB) effect using an electronic gate is a significant goal in spintronics. The emergence of van der Waals (vdW) magnetic heterostructures has provided improved means to study interlayer magnetic coupling, but to date, these heterostructures have not exhibited electrical gate-controlled EB effects. Here, we report electrically controllable EB effects in a vdW heterostructure, FePS3-Fe5GeTe2. By applying a solid protonic gate, the EB effects were repeatably electrically tuned. The EB field reaches up to 23% of the coercivity and the blocking temperature ranges from 30 to 60 K under various gate-voltages. The proton intercalations not only tune the average magnetic exchange coupling but also change the antiferromagnetic configurations in the FePS3 layer. These result in a dramatic modulation of the total interface exchange coupling and the resultant EB effects. The study is a significant step toward vdW heterostructure-based magnetic logic for future low-energy electronics.

Progress on regulatory elements of plant plastid genetic engineering.

With the advancement of plant synthetic biology, plastids have emerged as an optimal platform for the heterologous production of numerous commercially valuable secondary metabolites and therapeutic proteins. In comparison on nuclear genetic engineering, plastid genetic engineering offers unique advantages in terms of efficient expression of foreign genes and biological safety. However, the constitutive expression of foreign genes in the plastid system may impede plant growth. Therefore, it is imperative to further elucidate and design regulatory elements that can achieve precise regulation of foreign genes. In this review, we summarize the progress made in developing regulatory elements for plastid genetic engineering, including operon design and optimization, multi-gene coexpression regulation strategies, and identification of new expression regulatory elements. These findings provide valuable insights for future research.

Electronic structure, defect properties, and optimization of the band gap of the earth-abundant and low-toxicity photovoltaic absorber Cu3SbS4.

Searching for an earth-abundant and environment-friendly absorber for thin-film solar cells that provides similar power conversion efficiency to CdTe and Cu(In,Ga)Se2 is of great importance for large-scale applications. Success would change the world's solar energy supply to an even more sustainable material resource. In this paper, we have studied by first-principles calculations the electronic structure and defect properties of the promising absorber Cu3SbS4. Its electronic properties, like direct band gap, high absorption coefficient, and light carrier effective masses, satisfy the requirements for an absorber except for its somewhat too small band gap energy. Sulfur and copper vacancies are easily formed defects in Cu3SbS4, where the S vacancy shrinks the band gap and degrades the material. This probably explains the experimental findings of a rather poor device performance. The suitable preparation conditions for Cu3SbS4 as an absorber are anticipated to be Cu-poor, Sb-moderate, and S-rich conditions. Herein, isovalent element alloying is demonstrated to be an effective way to increase the gap energy and thereby improve the material properties.

Theoretical study on ferroelectric nitrides with super-wurtzite structures for solar energy conversion applications.

Polarized structured nitride semiconductors are attractive due to their unique and environment-friendly electronic properties. The stability, ferroelectricity and photocatalytic and photovoltaic properties of super-wurtzite Mg2XN3 (X = Bi, Mo, Nb, Sb, Ta, Tc and W) were determined based on first principles calculations in this study. The calculated results indicate that Mg2XN3 (X = Sb, Ta, Bi and Nb) are stable polar nitrides by phonon frequencies, elastic coefficients and ferroelectric analysis. Mg2XN3 (X = Sb, Ta and Nb) with large ferroelectric polarization strength could absorb ultraviolet light to promote photocatalytic water splitting for hydrogen production. Mg2BiN3 is a new excellent photovoltaic candidate due to its ideal energy band, high electron mobility, high absorption coefficient and large ferroelectric polarization strength.

Gate-Controlled Magnetic Phase Transition in a van der Waals Magnet Fe5GeTe2.

Magnetic van der Waals (vdW) materials are poised to enable all-electrical control of magnetism in the two-dimensional limit. However, tuning the magnetic ground state in vdW itinerant ferromagnets by voltage-induced charge doping remains a significant challenge, due to the extremely large carrier densities in these materials. Here, by cleaving the vdW itinerant ferromagnet Fe5GeTe2 (F5GT) into 5.4 nm (around two unit cells), we find that the ferromagnetism (FM) in F5GT can be substantially tuned by the thickness. Moreover, by utilizing a solid protonic gate, an electron doping concentration of above 1021 cm-3 has been exhibited in F5GT nanosheets. Such a high carrier accumulation exceeds that possible in widely used electric double-layer transistors (EDLTs) and surpasses the intrinsic carrier density of F5GT. Importantly, it is accompanied by a magnetic phase transition from FM to antiferromagnetism (AFM). The realization of an antiferromagnetic phase in nanosheet F5GT suggests the promise of applications in high-temperature antiferromagnetic vdW devices and heterostructures.

Artificial intelligence-based multi-objective optimization protocol for protein structure refinement.

MOTIVATION: Protein structure refinement is an important step of protein structure prediction. Existing approaches have generally used a single scoring function combined with Monte Carlo method or Molecular Dynamics algorithm. The one-dimension optimization of a single energy function may take the structure too far away without a constraint. The basic motivation of our study is to reduce the bias problem caused by minimizing only a single energy function due to the very diversity of different protein structures. RESULTS: We report a new Artificial Intelligence-based protein structure Refinement method called AIR. Its fundamental idea is to use multiple energy functions as multi-objectives in an effort to correct the potential inaccuracy from a single function. A multi-objective particle swarm optimization algorithm-based structure refinement is designed, where each structure is considered as a particle in the protocol. With the refinement iterations, the particles move around. The quality of particles in each iteration is evaluated by three energy functions, and the non-dominated particles are put into a set called Pareto set. After enough iteration times, particles from the Pareto set are screened and part of the top solutions are outputted as the final refined structures. The multi-objective energy function optimization strategy designed in the AIR protocol provides a different constraint view of the structure, by extending the one-dimension optimization to a new three-dimension space optimization driven by the multi-objective particle swarm optimization engine. Experimental results on CASP11, CASP12 refinement targets and blind tests in CASP 13 turn to be promising. AVAILABILITY AND IMPLEMENTATION: The AIR is available online at: www.csbio.sjtu.edu.cn/bioinf/AIR/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Three-Dimensional Dirac Phonons with Inversion Symmetry.

Dirac semimetals associated with bulk Dirac fermions are well known in topological electronic systems. In sharp contrast, three-dimensional (3D) Dirac phonons in crystalline solids are still unavailable. Here we perform symmetry arguments and first-principles calculations to systematically investigate 3D Dirac phonons in all space groups with inversion symmetry. The results show that there are two categories of 3D Dirac phonons depending on their protection mechanisms and positions in momentum space. The first category originates from the four-dimensional irreducible representations at the high symmetry points. The second category arises from the phonon branch inversion, and the symmetry guarantees Dirac points to be located along the high symmetry lines. Furthermore, we reveal that nonsymmorphic symmetries and the combination of inversion and time-reversal symmetries play essential roles in the emergence of 3D Dirac phonons. Our work not only offers a comprehensive understanding of 3D Dirac phonons but also provides significant guidance for exploring Dirac bosons in both phononic and photonic systems.

Gate-Tuned Interlayer Coupling in van der Waals Ferromagnet Fe_{3}GeTe_{2} Nanoflakes.

The weak interlayer coupling in van der Waals (vdW) magnets has confined their application to two dimensional (2D) spintronic devices. Here, we demonstrate that the interlayer coupling in a vdW magnet Fe_{3}GeTe_{2} (FGT) can be largely modulated by a protonic gate. With the increase of the protons intercalated among vdW layers, interlayer magnetic coupling increases. Because of the existence of antiferromagnetic layers in FGT nanoflakes, the increasing interlayer magnetic coupling induces exchange bias in protonated FGT nanoflakes. Most strikingly, a rarely seen zero-field cooled (ZFC) exchange bias with very large values (maximally up to 1.2 kOe) has been observed when higher positive voltages (V_{g}≥4.36 V) are applied to the protonic gate, which clearly demonstrates that a strong interlayer coupling is realized by proton intercalation. Such strong interlayer coupling will enable a wider range of applications for vdW magnets.

Synthesis and Catalytic Properties of Porous Metal Silica Materials Templated and Functionalized by Extended Coordination Cages.

A practically applicable strategy is developed to rationally immobilize easily accessed and highly dispersed redox-active metal oxides into porous metal silica (PMS) materials templated and functionalized by porous metal-ligand moieties. On the basis of this strategy, the highly active porous catalyst PMS-1 is successfully targeted for aerobic oxidation of cyclohexane with conversion up to 14.6%, which is much superior to the current industrially adopted catalysts (less than 4% cyclohexane conversion) that use harsh conditions. This promising approach to explore highly active heterogeneous catalysts for inert C-H bond activation should lead to the further discovery of numerous industrially useful catalysts for the oxidation of inert hydrocarbon raw materials.

Energy landscape of Au13: a global view of structure transformation.

It has long been a challenge in physics and chemistry to acquire a global picture of the energy landscape of a specific material, as well as the kinetic transformation process between configurations of interest. Here we have presented a comprehensive approach to deal with the structure transformation problem, along with the illustration of the energy landscape, as exemplified with the case of Au13. A configuration space based on interatomic distances was proposed and demonstrated to have a strong correlation between structure and energy, with application in structure analysis to screen for trial transition pathways. As several representative configurations and their transition pathways ascertained and by projecting on a plane, a visual two-dimensional contour map was sketched revealing the unique energy landscape of Au13. It shows that the 2D and 3D clusters form two funnels in the high-dimensional configuration space, with a transition pathway with a 0.976 eV barrier bridging them.

Motif based high-throughput structure prediction of superconducting monolayer titanium boride.

Two-dimensional boron structures, due to their diverse properties, have attracted great attention because of their potential applications in nanoelectronic devices. A series of TiBn (2 ≤ n ≤ 13) monolayers are efficiently constructed through our motif based method and theoretically investigated through high-throughput first-principles calculations. The configurations are generated based on the motifs of boron dimeric/triangular/quadrilateral fragments and multi-coordinate titanium-centered boron molecular wheels. Besides previously reported TiB4 and TiB9 which were discovered by the global search method, we predict that high symmetry monolayer TiB7 (Cmmm), which is octa-coordinate titanium boride, is dynamically stable. The TiB7 monolayer is a BCS superconductor with a transition temperature Tc of up to 8.3 K. The motif based approach is proved to be efficient in searching stable structures with prior knowledge so that the potentially stable transition metal monolayers can be quickly constructed by using basic cluster motifs. As an efficient way of discovering materials, the method is easily extended to predict other types of materials which have common characteristic patterns in the structure.

Atom Classification Model for Total Energy Evaluation of Two-Dimensional Multicomponent Materials.

The tunable properties of materials originate from variety of structures; however, it is still a challenge to give an accurate and fast evaluation of stabilities for screening numerous candidates. Herein, we propose an atom classification model to describe the multicomponent materials based on the structural recognition, in which the atoms are classified to estimate the total energies. Taking two-dimensional planar C1-xBx and C1-2x(BN)x as examples, we have found that the test error of total energies is about 3 meV per atom. Notably, the distributions of classified atoms demonstrate the evolution of configurations as a function of temperature, providing a clearer picture of phase transition. In addition, our method is universal, which can be flexibly extended to the bulk structures with more components.

First-Principles Study of Aziridinium Lead Iodide Perovskite for Photovoltaics.

The long-term stability remains one of the main challenges for the commercialization of the rapidly developing hybrid organic-inorganic perovskite solar cells. Herein, we investigate the electronic and optical properties of the recently reported hybrid halide perovskite (CH2 )2 NH2 PbI3 (AZPbI3 ), which exhibits a much better stability than the popular halide perovskites CH3 NH3 PbI3 and HC(NH2 )2 PbI3 , by using density functional theory (DFT). We find that AZPbI3 possesses a band gap of 1.31 eV, ideal for single-junction solar cells, and its optical absorption is comparable with those of the popular CH3 NH3 PbI3 and HC(NH2 )2 PbI3 materials in the whole visible-light region. In addition, the conductivity of AZPbI3 can be tuned from efficient p-type to n-type, depending on the growth conditions. Besides, the charge-carrier mobilities and lifetimes are unlikely hampered by deep transition energy levels, which have higher formation energies in AZPbI3 according to our calculations. Overall, we suggest that the perovskite AZPbI3 is an excellent candidate as a stable high-performance photovoltaic absorber material.

Eudesmane-type sesquiterpene diols directly synthesized by a sesquiterpene cyclase in Tripterygium wilfordii.

Cryptomeridiol, a typical eudesmane diol, is the active principle component of the antispasmodic Proximol. Although it has been used for many years, the biosynthesis pathway of cryptomeridiol has remained blur. Among terpenoid natural products, terpenoid cyclases are responsible for cyclization and generation of hydrocarbon backbones. The cyclization is mediated by carbocationic cascades and ultimately terminated via deprotonation or nucleophilic capture. Isoprene precursors are, respectively, converted into hydrocarbons or hydroxylated backbones. A sesquiterpene cyclase in Tripterygium wilfordii (TwCS) was determined to directly catalyze (E,E)-farnesyl pyrophosphate (FPP) to unexpected eudesmane diols, primarily cryptomeridiol. The function of TwCS was characterized by a modular pathway engineering system in Saccharomyces cerevisiae The major product determined by NMR spectroscopy turned out to be cryptomeridiol. This unprecedented production was further investigated in vitro, which verified that TwCS can directly produce eudesmane diols from FPP. Some key residues for TwCS catalysis were screened depending on the molecular model of TwCS and mutagenesis studies. As cryptomeridiol showed a small amount of volatile and medicinal properties, the biosynthesis of cryptomeridiol was reconstructed in S. cerevisiae Optimized assays including modular pathway engineering and the CRISPR-cas9 system were successfully used to improve the yield of cryptomeridiol in the S. cerevisiae The best engineered strain TE9 (BY4741 erg9::Δ-200-176 rox1::mut/pYX212-IDI + TwCS/p424-tHMG1) ultimately produced 19.73 mg/l cryptomeridiol in a shake flask culture.

Transcripts of antibacterial peptides in chicken erythrocytes infected with Marek's disease virus.

BACKGROUND: Chicken erythrocytes are involved in immunity through binding of toll-like receptors (TLRs) with their ligands to activate downstream signaling and lead to cytokine production in erythrocytes. Some avian ß-defensins (AvBDs) are constitutively expressed in tissues and some others can be induced by various bacteria and viruses. However, the expression of AvBDs in erythrocytes has not yet been studied extensively. RESULTS: The transcripts of eight AvBDs (AvBD1 to AvBD7, and AvBD9) and liver-expressed antimicrobial peptide-2 (LEAP-2) were found in normal chicken erythrocytes. The expression levels of AvBD2, 4 and 7 were significantly increased (P < 0.01), whereas the levels of AvBD1, 6 and 9 were significantly decreased (P < 0.01) after Marek's disease virus (MDV) infection. The mRNA expression level of LEAP-2 was not significantly changed after MDV infection. Highest viral nucleic acid (VNA) of MDV in the feather tips among the tested time points was found at 14 days post-infection (d.p.i.). In addition, 35 MD5-related gene segments were detected in the erythrocytes at 14 d.p.i. by transcriptome sequencing. CONCLUSIONS: These results suggest that the AvBDs in chicken erythrocytes may participate in MDV-induced host immune responses.

Theoretical investigations on diamondoids (CnHm, n = 10-41): Nomenclature, structural stabilities, and gap distributions.

Combining the congruence check and the first-principles calculations, we have systematically investigated the structural stabilities and gap distributions of possible diamondoids (CnHm) with the carbon numbers (n) from 10 to 41. A simple method for the nomenclature is proposed, which can be used to distinguish and screen the candidates with high efficiency. Different from previous theoretical studies, the possible diamondoids can be enumerated according to our nomenclature, without any pre-determination from experiments. The structural stabilities and electronic properties have been studied by density functional based tight binding and first-principles methods, where a nearly linear correlation is found between the energy gaps obtained by these two methods. According to the formation energy of structures, we have determined the stable configurations as a function of chemical potential. The maximum and minimum energy gaps are found to be dominated by the shape of diamondoids for clusters with a given number of carbon atoms, while the gap decreases in general as the size increases due to the quantum confinement.

Cloning and functional analysis of two sterol-C24-methyltransferase 1 (SMT1) genes from Paris polyphylla.

The biosynthetic pathways of phytosterols and steroidal saponins are located in two adjacent branches which share cycloartenol as substrate. The rate-limiting enzyme S-adenosyl-L-methionine-sterol-C24-methyltransferase 1 (SMT1) facilitates the metabolic flux toward phytosterols. It catalyzes the methylation of the cycloartenol in the side chain of the C24-alkyl group, to generate 24(28)-methylene cycloartenol. In this study, we obtained two full-length sequences of SMT1 genes from Pari polyphylla, designated PpSMT1-1 and PpSMT1-2. The full-length cDNA of PpSMT1-1 was 1369 bp long with an open reading frame (ORF) of 1038 bp, while the PpSMT1-2 had a length of 1222 bp, with a 1005 bp ORF. Bioinformatics analysis confirmed that the two cloned SMTs belong to the SMT1 family. The predicted function was further validated by performing in vitro enzymatic reactions, and the results showed that PpSMT1-1 encodes a cycloartenol-C24-methyltransferase, which catalyzes the conversion of cycloartenol to 24-methylene cycloartenol, whereas PpSMT1-2 lacked this catalytic activity. The tissue expression patterns of the two SMTs revealed differential expression in different organs of Paris polyphylla plants of different developmental stage and age. These results lay the foundation for detailed genetic studies of the biosynthetic pathways of steroid compounds, which constitute the main class of active substances found in P. polyphylla.

[Establishment of a genetic transformation system for hairy root culture of Erigeron breviscapus].

The electroporation method was performed to transfer plasmid DNA of PBI-1300 carrying GFP gene into Agrobacterium rhizogenes C58C1 strains. Mediated by A. rhizogenes C58C1, the GFP gene were transformed into Erigeron breviscapus aseptic leaves by leaf disc method, then the hairy roots were induced and the infected hairy roots were screened by hygromycin resistance. The chromosomal DNA of the hairy root was used as the templates for the PCR amplification with the GFP-specific primers and then the expected amplified DNA bands appeared, the green fluorescent of GFP in the cut hairy roots was observed by two-photon microscope. These results indicated that GFP gene was integrated into the genome of E. breviscapus and was expressed stably. This study laid the groundwork for foreign gene high-efficiency expression inthe genetic transformation system for hairy root culture of E. breviscapus.