Exact zeros of fidelity in finite-size systems as a signature for probing quantum phase transitions

The fidelity is widely used to detect quantum phase transition, which is characterized by either a sharp change of fidelity or the divergence of fidelity susceptibility in the thermodynamical limit when the phase-driving parameter is across the transition point. In this work, we unveil that the occurrence of exact zero of fidelity in finite-size systems can be applied to detect quantum phase transitions. In general, the fidelity $\mathcal{F}(\gamma,\tilde{\gamma})$ always approaches zero in the thermodynamical limit, due to the Anderson orthogonality catastrophe, no matter whether the parameters of two ground states ($\gamma$ and $\tilde{\gamma}$) are in the same phase or different phases, and this makes it difficult to distinguish whether an exact zero of fidelity exists by finite-size analysis. To overcome the influence of orthogonality catastrophe, we study finite-size systems with twist boundary conditions, which can be introduced by applying a magnetic flux, and demonstrate that exact zero of fidelity can be always accessed by tuning the magnetic flux when $\gamma$ and $\tilde{\gamma}$ belong to different phases. On the other hand, no exact zero of fidelity can be observed if $\gamma$ and $\tilde{\gamma}$ are in the same phase. We demonstrate the applicability of our theoretical scheme by studying concrete examples, including the Su-Schrieffer-Heeger model, Creutz model and Haldane model. Our work provides a practicable way to detect quantum phase transition via the calculation of fidelity of finite-size systems.Comment: 9 pages, 8 figure

Dynamical singularity of the rate function for quench dynamics in finite size quantum systems

The dynamical quantum phase transition is characterized by the emergence of nonanalytic behaviors in the rate function, corresponding to the occurrence of exact zero points of Loschmidt echo in the thermodynamical limit. In general, exact zeros of Loschmidt echo are not accessible in a finite size quantum system except for some fine-tuned quench parameters. In this work, we study the realization of dynamical singularity of the rate function for finite size systems under the twist boundary condition, which can be introduced by applying a magnetic flux. By tuning the magnetic flux, we illustrate that exact zeros of Loschmidt echo can be always achieved when the postquench parameter is across the underlying equilibrium phase transition point, and thus the rate function of a finite size system is divergent at a series of critical times. We demonstrate our scheme by considering the Su-Schrieffer-Heeger model and the Creutz model as concrete examples. Our result unveils that the emergence of dynamical singularity in the rate function can be viewed as a signature for detecting dynamical quantum phase transition in finite size systems. We also unveil that the critical times in our theoretical scheme are independent on the systems size, and thus it provides a convenient way to determine the critical times by tuning the magnetic flux to achieve the dynamical singularity of the rate function.Comment: 8 pages, 6 figure

Signature of nonequilibrium quantum phase transition in the long time average of Loschmidt echo

We unveil the role of the long time average of Loschmidt echo in the characterization of nonequilibrium quantum phase transitions by studying sudden quench processes across quantum phase transitions in various quantum systems. While the dynamical quantum phase transitions are characterized by the emergence of a series of zero points at critical times during time evolution, we demonstrate that nonequilibrium quantum phase transitions can be identified by nonanalyticities in the long time average of Loschmidt echo. The nonanalytic behaviours are illustrated by a sharp change in the long time average of Loschmidt echo or the corresponding rate function or the emergence of divergence in the second derivative of rate function when the driving quench parameter crosses the phase transition points. The connection between the second derivative of rate function and fidelity susceptibility is also discussed.Comment: 7 pages, 7 figure

The C-terminal selenenylsulfide of extracellular/non-reduced thioredoxin reductase endows this protein with selectivity to small-molecule electrophilic reagents under oxidative conditions

Mammalian cytosolic thioredoxin reductase (TrxR1) serves as an antioxidant protein by transferring electrons from NADPH to various substrates. The action of TrxR1 is achieved via reversible changes between NADPH-reduced and non-reduced forms, which involves C-terminal selenolthiol/selenenylsulfide exchanges. TrxR1 may be released into extracellular environment, where TrxR1 is present mainly in the non-reduced form with active-site disulfide and selenenylsulfide bonds. The relationships between extracellular TrxR1 and tumor metastasis or cellular signaling have been discovered, but there are few reports on small-molecule compounds in targeted the non-reduced form of TrxR1. Using eight types of small-molecule thiol-reactive reagents as electrophilic models, we report that the selenenylsulfide bond in the non-reduced form of TrxR1 functions as a selector for the thiol-reactive reagents at pH 7.5. The non-reduced form of TrxR1 is resistant to hydrogen peroxide/oxidized glutathione, but is sensitive to certain electrophilic reagents in different ways. With 5,5′-dithiobis-(2-nitrobenzoic acid) (DTNB) and S-nitrosoglutathione (GSNO), the polarized selenenylsulfide bond breaks, and selenolate anion donates electron to the dynamic covalent bond in DTNB or GSNO, forming TNB-S-Se-TrxR1 complex or ON-Se-TrxR1 complex. The both complexes lose the ability to transfer electrons from NADPH to substrate. For diamide, the non-reduced TrxR1 actually prevents irreversible damage by this oxidant. This is consistent with the regained activity of TrxR1 through removal of diamide via dialysis. Diamide shows effective in the presence of human cytosolic thioredoxin (hTrx1), Cys residue(s) of which is/are preferentially affected by diamide to yield disulfide, hTrx1 dimer and the mixed disulfide between TrxR1-Cys497/Sec498 and hTrx1-Cys73. In human serum samples, the non-reduced form of TrxR1 exists as dithiothreitol-reducible polymer/complexes, which might protect the non-reduced TrxR1 from inactivation by certain electrophilic reagents under oxidative conditions, because cleavage of these disulfides can lead to regain the activity of TrxR1. The details of the selective response of the selenenylsulfide bond to electrophilic reagents may provide new information for designing novel small-molecule inhibitors (drugs) in targeted extracellular/non-reduced TrxR1

Ksak: A high-throughput tool for alignment-free phylogenetics

Phylogenetic tools are fundamental to the studies of evolutionary relationships. In this paper, we present Ksak, a novel high-throughput tool for alignment-free phylogenetic analysis. Ksak computes the pairwise distance matrix between molecular sequences, using seven widely accepted k-mer based distance measures. Based on the distance matrix, Ksak constructs the phylogenetic tree with standard algorithms. When benchmarked with a golden standard 16S rRNA dataset, Ksak was found to be the most accurate tool among all five tools compared and was 19% more accurate than ClustalW2, a high-accuracy multiple sequence aligner. Above all, Ksak was tens to hundreds of times faster than ClustalW2, which helps eliminate the computation limit currently encountered in large-scale multiple sequence alignment. Ksak is freely available at https://github.com/labxscut/ksak

Daidzein alleviates high glucose-induced pyroptosis of renal tubular epithelial cells

Objective To investigate the impact of daidzein (DAI) on the pyroptosis of renal tubular epithelial cells induced by high glucose by regulating NOD-like receptor protein 3 (NLRP3)/caspase-1 signal pathway. Methods HK-2 cells were divided into control group (NC group) (5.5 mmol/L D-glucose), HG group(30 mmol/L D-glucose), DAI-L, DAI-M, DAI-H groups (HK-2 cells were incubated with 30 mmol/L D-glucose and 25, 50, 100 μmol/L DAI,respectively), and DAI-H+LPS group (HK-2 cells were incubated with 30 mmol/L D-glucose, 100 μmol/L DAI and 1 μg/mL LPS). MTT assay was applied to detect the cytotoxicity and proliferation of HK-2 cells; the apoptosis of HK-2 cells was detected by flow cytometry. The level of interleukin-1β (IL-1β) and inter-leukin-18 (IL-18) in HK-2 cells was detected by ELISA. The morphology of pyroptosis cells was observed by scanning electron microscope. Immunofluorescence staining was applied to detect pyroptosis related proteins. The expression of NLRP3, cleaved casase-1 and GSDMD-N was detected by Western blot. Results In NC group, the cells were spherical with regular boundaries, while in HG group, the cells swelled and became larger with irregular boundaries; the OD value (490 nm) of HK-2 cells in HG group was obviously lower than that in NC group(P＜0.05), the apoptosis rate, IL-1β, IL-18 contents, NLRP3, cleaved casase-1, GSDMD-N protein level of HK-2 cells were obviously higher (P＜0.05); After DAI treatment, the swelling of cells was alleviated, the A value (490 nm) of HK-2 cells increased significantly (P＜0.05), the apoptosis rate of HK-2 cells, IL-1 β, IL-18 content, NLRP3, cleaved-caspase-1 and GSDMD-N protein levels were significantly decreased(P＜0.05) and the therapeutic effect of DAI was dose-dependent; LPS eliminated the beneficial effect of DAI-H on high glucose induced apoptosis of renal tubular epithelial cells. Conclusions DAI may alleviate pyroptosis of renal tubular epithelial cells induced by high glucose through inhibition of NLRP3/caspase-1 signaling pathway

Zwitterionic base-stabilized digermadistannacyclobutadiene and tetragermacyclobutadiene

The syntheses of a zwitterionic base-stabilized digermadistannacyclobutadiene and tetragermacyclobutadiene supported by amidinates and low-valent germanium amidinate substituents are described. The reaction of the amidinate GeI dimer, [LGe:]2 (1, L=PhC(NtBu)2), with two equivalents of the amidinate tin(II) chloride, [LSnCl] (2), and KC8 in tetrahydrofuran (THF) at room temperature afforded a mixture of the zwitterionic base-stabilized digermadistannacyclobutadiene, [L2Ge2Sn2L′2] (3; L′=LGe:), and the bis(amidinate) tin(II) compound, [L2Sn:] (4). Compound 3 can also be prepared by the reaction of 1 with [LArSnCl] (5, LAr=tBuC(NAr)2, Ar=2,6-iPr2C6H3) in THF at room temperature. Moreover, the reaction of 1 with the “onio-substituent transfer” reagent [4-NMe2-C5H4NSiMe3]OTf (8) in THF and 4-(N,N-dimethylamino)pyridine (DMAP) at room temperature afforded a mixture of the zwitterionic base-stabilized tetragermacyclobutadiene, [L4Ge6] (9), the amidinium triflate, [PhC(NHtBu)2]OTf (10), and Me3SiSiMe3 (11). X-ray structural data and theoretical studies show conclusively that compounds 3 and 9 have a planar and rhombic charge-separated structure. They are also nonaromatic