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Background:Lysine lipoylation which is a rare and highly conserved post-translational modification of proteins has been considered as one of the most important processes in the biological field. To obtain a comprehensive understanding of regulatory mechanism of lysine lipoylation, the key is to identify lysine lipoylated sites. The experimental methods are expensive and laborious. Due to the high cost and complexity of experimental methods, it is urgent to develop computational ways to predict lipoylation sites.Methodology:In this work, a predictor named LipoSVM is developed to accurately predict lipoylation sites. To overcome the problem of an unbalanced sample, synthetic minority over-sampling technique (SMOTE) is utilized to balance negative and positive samples. Furthermore, different ratios of positive and negative samples are chosen as training sets.Results:By comparing five different encoding schemes and five classification algorithms, LipoSVM is constructed finally by using a training set with positive and negative sample ratio of 1:1, combining with position-specific scoring matrix and support vector machine. The best performance achieves an accuracy of 99.98% and AUC 0.9996 in 10-fold cross-validation. The AUC of independent test set reaches 0.9997, which demonstrates the robustness of LipoSVM. The analysis between lysine lipoylation and non-lipoylation fragments shows significant statistical differences.Conclusion:A good predictor for lysine lipoylation is built based on position-specific scoring matrix and support vector machine. Meanwhile, an online webserver LipoSVM can be freely downloaded from https://github.com/stars20180811/LipoSVM.

It has recently been found that nonsymmorphic symmetries can bring many exotic band crossings. Here, based on symmetry analysis, we predict that materials with time-reversal symmetry in the space group of Pbca (No. 61) possess rich symmetry-enforced band crossings, including nodal surfaces, fourfold degenerate nodal lines and hourglass Dirac loops, which appear in triplets as ensured by the cyclic permutation symmetry. We take Pbca AgF2 as an example in real systems and studied its band structures with ab initio calculations. Specifically, in the absence of spin-orbit coupling (SOC), besides the above-mentioned band degeneracies, this system features a nodal chain and a nodal armillary sphere penetrating the Brillouin zone (BZ). While with SOC, we find a new configuration of the hourglass Dirac loop/chain with the feature traversing the BZ, which originates from the splitting of a Dirac loop confined in the BZ. Furthermore, guided by the bulk-surface correspondence, we calculated the surface states to explore these bulk nodal phenomena. The evolution of these interesting nodal phenomena traversing the BZ under two specific uniaxial strains is also discussed.

Weyl semimetal defines a material with three-dimensional Dirac cones, which appear in pair due to the breaking of spatial inversion or time reversal symmetry. Superconductivity is the state of quantum condensation of paired electrons. Turning a Weyl semimetal into superconducting state is very important in having some unprecedented discoveries. In this work, by doing resistive measurements on a recently recognized Weyl semimetal TaP under pressures up to about 100 GPa, we show the concurrence of superconductivity and a structure transition at about 70 GPa. It is found that the superconductivity becomes more pronounced when decreasing pressure and retains when the pressure is completely released. High-pressure x-ray diffraction measurements also confirm the structure phase transition from I41 md to P-6m2 at about 70 GPa. More importantly, ab-initial calculations reveal that the P-6m2 phase is a new Weyl semimetal phase and has only one set of Weyl points at the same energy level. Our discovery of superconductivity in TaP by high pressure will stimulate investigations on superconductivity and Majorana fermions in Weyl semimetals. Under pressure, Weyl semimetals can become superconductive; in TaP, the superconducting transition is associated with a phase transition. Weyl semimetals are topological materials hosting massless quasiparticles, the Weyl fermions. A team of researchers led by Hai-Hu Wen at Nanjing University, in collaboration with colleagues from other Chinese institutes and the US, investigated the effect of applying high pressures to tantalum phosphide, discovering that the material undergoes a structural phase transition under pressure, becoming superconductive. Theoretical calculations and x-ray diffraction measurements clarify the structure of the new phase. Interestingly, the superconductive behaviour becomes more pronounced as the pressure is decreased, and the sample remains superconductive after the pressure is released. Inducing superconductivity in Weyl semimetals is interesting because it can result in the observation of exotic phenomena, such as the appearance of Majorana fermions.

We present in situ high-pressure synchrotron x-ray diffraction (XRD) and electrical transport measurements on quasi-one-dimensional single-crystal $\mathrm{Ti}{\mathrm{S}}_{3}$ up to 29.9--39.0 GPa in diamond-anvil cells, coupled with first-principles calculations. Counterintuitively, the conductive behavior of semiconductor $\mathrm{Ti}{\mathrm{S}}_{3}$ becomes increasingly insulating with pressure until ${P}_{C1}\ensuremath{\sim}12\phantom{\rule{0.16em}{0ex}}\mathrm{GPa}$, where extremes in all three axial ratios are observed. Upon further compression to ${P}_{C2}\ensuremath{\sim}22\phantom{\rule{0.16em}{0ex}}\mathrm{GPa}$, the XRD data evidence a structural phase transition. Based on our theoretical calculations, this structural transition is determined to be isosymmetric, i.e., without change of the structural symmetry ($P{2}_{1}/m$), mainly resulting from rearrangement of the dangling ${\mathrm{S}}_{2}$ pair along the $a$ axis.

We have grown nearly freestanding single-layer $1{T}^{\ensuremath{'}}\ensuremath{-}\mathrm{WT}{\mathrm{e}}_{2}$ on graphitized $6H$-SiC(0001) by using molecular beam epitaxy (MBE), and characterized its electronic structure with scanning tunneling microscopy/spectroscopy (STM/STS). The existence of topological edge states at the periphery of single-layer $\mathrm{WT}{\mathrm{e}}_{2}$ islands was confirmed. Surprisingly, a bulk band gap at the Fermi level and insulating behaviors were also found in single-layer $\mathrm{WT}{\mathrm{e}}_{2}$ at low temperature, which are likely associated with an incommensurate charge order transition. The realization of two-dimensional topological insulators (2D TIs) in single-layer transition-metal dichalcogenide provides a promising platform for further exploration of the 2D TIs' physics and related applications.

Among the family of TMDs, ReS2 takes a special position, which crystalizes in a unique distorted low-symmetry structure at ambient conditions. The interlayer interaction in ReS2 is rather weak, thus its bulk properties are similar to that of monolayer. However, how does compression change its structure and electronic properties is unknown so far. Here using ab initio crystal structure searching techniques, we explore the high-pressure phase transitions of ReS2 extensively and predict two new high-pressure phases. The ambient pressure phase transforms to a "distorted-1T" structure at very low pressure and then to a tetragonal I41/amd structure at around 90 GPa. The "distorted-1T" structure undergoes a semiconductor-metal transition (SMT) at around 70 GPa with a band overlap mechanism. Electron-phonon calculations suggest that the I41/amd structure is superconducting and has a critical superconducting temperature of about 2 K at 100 GPa. We further perform high-pressure electrical resistance measurements up to 102 GPa. Our experiments confirm the SMT and the superconducting phase transition of ReS2 under high pressure. These experimental results are in good agreement with our theoretical predictions., 25 pages, 6 figures, accepted by npj Quantum Materials

Using ab initio calculations based on density-functional theory and effective model analysis, we propose that the trigonal YH3(Space Group: P-3c1) at ambient pressure is a node-line semimetal when spin-orbit coupling (SOC) is ignored. This trigonal YH3 has very clean electronic structure near Fermi level and its nodal lines locate very closely to the Fermi energy, which makes it a perfect system for model analysis. Symmetry analysis shows that the nodal ring in this compound is protected by the glide-plane symmetry, where the band inversion of |Y+,dxz> and |H1-,s> orbits at Gamma point is responsible for the formation of the nodal lines. When SOC is included, the line nodes are prohibited by the glide-plane symmetry, and a small gap (~5 meV) appears, which leads YH3 to be a strong topological insulator with Z2 indices (1,000). Thus the glide-plane symmetry plays an opposite role in the formation of the nodal lines in cases without and with SOC. As the SOC-induced gap is so small that can be neglected, this P-3c1 YH3 may be a good candidate for experimental explorations on the fundamental physics of topological node-line semimetals. We find the surface states of this P-3c1 phase are somehow unique and may be helpful to identify the real ground state of YH3 in the experiment., 9 pages, 3 figures

The high pressure phase diagrams of TaAs family (NbP, NbAs, TaP and TaAs) are explored systematically using crystal structure search together with first-principles calculations. Our calculations show that NbAs and TaAs have similar phase diagrams and possess the same structural phase transition sequence of I41md $\rightarrow$ P-6m2 $\rightarrow$ P21/c $\rightarrow$ Pm-3m, with a bit different transition pressures. The phase transition sequence of NbP and TaP are somewhat different from that of NbAs and TaAs. In which new structures emerge, for instance, the Cmcm structure in NbP and the Pmmn structure in TaP. It is found interestingly that in the electronic structure of the high-pressure phase P-6m2-NbAs, there are Weyl points and triple degenerate points coexisted, similar to the high-pressure P-6m2-TaAs., Comment: 17 pages, 6 figures. (Email: jiansun@nju.edu.cn)

The structure and superconductivity of $\mathrm{WT}{\mathrm{e}}_{2}$ under pressure are investigated using ab initio calculations combined with high-pressure synchrotron x-ray diffraction and Raman spectroscopy. We find that the emergence of superconductivity in $\mathrm{WT}{\mathrm{e}}_{2}$ under pressure can be attributed to the phase transition from ambient ${T}_{d}$ phase to the monoclinic $1T$\ensuremath{'} structure phase at around 4--5 GPa, which is associated with a sliding of the $\mathrm{WT}{\mathrm{e}}_{2}$ layers, resulting in a critical point in the changes of Te-Te interlayer distance. This phase transition introduces an inversion center and eliminates the topological Weyl fermions in the ${T}_{d}$ structure. Electron-phonon coupling calculations predict a similar ${T}_{c}$ as the reported value, implying that $\mathrm{WT}{\mathrm{e}}_{2}$ might belong to conventional normal Bardeen-Cooper-Schrieffer superconductors.

We report a new pressure-induced phase in TaAs with different Weyl fermions than the ambient structure with the aid of theoretical calculations, experimental transport and synchrotron structure investigations up to 53 GPa. We show that TaAs transforms from an ambient $I{4}_{1}md$ phase ($t\text{\ensuremath{-}}\mathrm{TaAs}$) to a high-pressure hexagonal $P\text{\ensuremath{-}}6m2\text{ }$ ($h\text{\ensuremath{-}}\mathrm{TaAs}$) phase at 14 GPa, along with changes of the electronic state from containing 24 Weyl nodes distributed at two energy levels to possessing 12 Weyl nodes at an isoenergy level, which substantially reduces the interference between the surface and bulk states. The new pressure-induced phase can be reserved upon releasing pressure to ambient condition, which allows one to study the exotic behavior of a single set of Weyl fermions, such as the interplay between surface states and other properties.

To help our understanding of the structural and superconducting transitions in ferropnictides, partial phonon density of states (PDOS) of iron in a single-crystal $\mathrm{SrF}{\mathrm{e}}_{2}\mathrm{A}{\mathrm{s}}_{2}$ pnictide have been investigated from both out-of-plane and in-plane polarizations with respect to the basal plane of the crystal structure using nuclear resonant inelastic x-ray scattering in a high-pressure diamond anvil cell at ambient temperature. The partial PDOS of iron in the pnictide crystal changes dramatically at approximately 8 GPa, which can be associated with the tetragonal (T) to collapsed tetragonal (CT) isostructural transition as evidenced in high-pressure x-ray diffraction measurements and theoretical calculations. Across the T-CT phase transition, analysis of the PDOS spectra shows a rapid stiffening of the optical phonon modes and a dramatic increase of the Lamb-M\"ossbauer factor (${f}_{\mathrm{LM}}$) and mean force constant which can be associated with the rapid decrease of the $c$ axis and the anomalous expansion of the $a$ axis. Theoretically calculated Fe partial PDOS and lattice parameters of $\mathrm{SrF}{\mathrm{e}}_{2}\mathrm{A}{\mathrm{s}}_{2}$ further reveal the strong correlation between the lattice parameters and phonons. Our results show that the T-CT transition can induce significant changes in the vibrational, elastic, and thermodynamic properties of $\mathrm{SrF}{\mathrm{e}}_{2}\mathrm{A}{\mathrm{s}}_{2}$ single crystal at high pressure.

As a new type of topological materials, ZrTe5 shows many exotic properties under extreme conditions. Using resistance and ac magnetic susceptibility measurements under high pressure, while the resistance anomaly near 128 K is completely suppressed at 6.2 GPa, a fully superconducting transition emerges. The superconducting transition temperature Tc increases with applied pressure, and reaches a maximum of 4.0 K at 14.6 GPa, followed by a slight drop but remaining almost constant value up to 68.5 GPa. At pressures above 21.2 GPa, a second superconducting phase with the maximum Tc of about 6.0 K appears and coexists with the original one to the maximum pressure studied in this work. In situ high-pressure synchrotron X-ray diffraction and Raman spectroscopy combined with theoretical calculations indicate the observed two-stage superconducting behavior is correlated to the structural phase transition from ambient Cmcm phase to high-pressure C2/m phase around 6 GPa, and to a mixture of two high-pressure phases of C2/m and P-1 above 20 GPa. The combination of structure, transport measurement, and theoretical calculations enable a complete understanding of the emerging exotic properties in 3D topological materials under extreme environments.

By using scanning tunneling microscopy (STM) / spectroscopy (STS), we systematically characterize the electronic structure of lightly doped 1T-TiSe2, and demonstrate the existence of the electronic inhomogeneity and the pseudogap state. It is found that the intercalation induced lattice distortion impacts the local band structure and reduce the size of the charge density wave (CDW) gap with the persisted 2x2 spatial modulation. On the other hand, the delocalized doping electrons promote the formation of pseudogap. Domination by either of the two effects results in the separation of two characteristic regions in real space, exhibiting rather different electronic structures. Further doping electrons to the surface confirms that the pseudogap may be the precursor for the superconducting gap. This study suggests that the competition of local lattice distortion and the delocalized doping effect contribute to the complicated relationship between charge density wave and superconductivity for intercalated 1T-TiSe2., Comment: 12 pages, 5 figures

Due to fundamental interest and potential applications in quantum computation, tremendous efforts have been invested to study topological superconductivity. However, bulk topological superconductivity seems to be difficult to realize and its mechanism is still elusive. Several possible routes to induce topological superconductivity have been proposed, including proximity efforts, doping or pressurizing a topological insulator or semimetal. Among them, the pressurizing is considered to be a clean way to tune the electronic structures. Here we report the discovery of a pressure-induced topological and superconducting phase of SnSe, a material which is highly focused recently due to its superior thermoelectric properties. In situ high-pressure electrical transport and synchrotron X-ray diffraction measurements show that the superconductivity emerges along with the formation of a CsCl-type structural symmetry of SnSe above around 27 GPa, with a maximum critical temperature of 3.2 K at 39 GPa. Based on ab initio calculations, this CsCl-type SnSe is predicted to be a Dirac line nodes (DLN) semimetal in the absence of spin-orbit coupling, whose DLN states are protected by the coexistence of time-reversal and inversion symmetries. These results make CsCl-type SnSe an interesting model platform with simple crystal symmetry to study the interplay of topological physics and superconductivity., Comment: 32 pages, 7 figures, 2 tables

To explore new superconductors beyond the copper-based and iron-based systems is very important. The Ru element locates just below the Fe in the periodic table and behaves like the Fe in many ways. One of the common thread to induce high temperature superconductivity is to introduce moderate correlation into the system. In this paper, we report the significant enhancement of superconducting transition temperature from 3.84K to 5.77K by using a pressure only of 1.74 GPa in LaRu2P2 which has an iso-structure of the iron-based 122 superconductors. The ab-initio calculation shows that the superconductivity in LaRu2P2 at ambient pressure can be explained by the McMillan's theory with strong electron-phonon coupling. However, it is difficult to interpret the significant enhancement of Tc versus pressure within this picture. Detailed analysis of the pressure induced evolution of resistivity and upper critical field Hc2(T) reveals that the increases of Tc with pressure may be accompanied by the involvement of extra electronic correlation effect. This suggests that the Ru-based system has some commonality as the Fe-based superconductors., 21 pages, 12 figures including suppl. materials