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COVER ARTICLE

Full-atomistic molecular dynamics analysis of p53 active tetramer
Zhou Han, Geng Yi-Zhao, Yan Shi-Wei
2024, 73 (4): 048701. doi: 10.7498/aps.73.20231515
Abstract +
p53 is a tumor suppressor protein that plays a crucial role in inhibiting cancer development and maintaining the genetic integrity. Within the cell nucleus, four p53 molecules constitute a stable tetrameric active structure through highly cooperative interactions, bind to DNA via its DNA-binding domain, and transcriptionally activate or inhibit their target genes. However, in most human tumor cells, there are numerous p53 mutations. The majority of these mutations are formed in the p53 DNA-binding domain, importantly, the p53 DNA-binding domain is critical for p53 to form the tetrameric active structures and to regulate the transcription of its downstream target genes. In this work, the all-atom molecular dynamics simulation is conducted to investigate the mechanism of interaction within the wild-type p53 tetramers. This study indicates that the symmetric dimers on either side of the DNA are stable ones, keeping stable structures before and after DNA binding. The binding of two monomers on the same side of the DNA depends on protein-protein interaction provided by two contact surfaces. DNA scaffold stabilizes the tetrameric active structure. Such interactions crucially contribute to the tetramer formation. This study clarifies the internal interactions and key residues within the p53 tetramer in dynamic process, as well as the critical sites at various interaction interfaces. The findings of this study may provide a significant foundation for us to further understand the p53’s anticancer mechanisms, to explore the effective cancer treatment strategies, and in near future, to develop the effective anti-cancer drugs.

EDITOR'S SUGGESTION

Topological phase in one-dimensional momentum space lattice of ultracold atoms without chiral symmetry
Zeng Chao, Mao Yi-Yi, Wu Ji-Zhou, Yuan Tao, Dai Han-Ning, Chen Yu-Ao
2024, 73 (4): 040301. doi: 10.7498/aps.73.20231566
Abstract +
Symmetry plays a crucial role in understanding topological phases in materials. In one-dimensional systems, such as the Su-Schrieffer-Heeger (SSH) model, chiral symmetry is thought to ensure the quantization of the Zak phase and the nontrivial topological phase. However, our work demonstrates that the one-dimensional lattice system with broken chiral symmetry can still possess quantized Zak phase and nontrivial topological phase. Specifically, we use a Bose-Einstein condensate of 87Rb atoms in a momentum space lattice of ultracold atoms to effectively simulate a one-dimensional Zigzag model of 26 sites, which intrinsically breaks the chiral symmetry by additional next-nearest-neighbor coupling. To ensure the existence of the nontrivial topological phase, where the Zak phase can be measured from the time-averaged displacement during the system’s evolution, we need to preserve the inversion symmetry by modulating laser power so that all next-nearest-neighbor coupling strengths are equal. Furthermore, by changing the ratio of nearest-neighbor coupling strengths, we observe a topological phase transition from a nontrivial topological phase to a trivial topological phase at the point where the ratio equals 1. Our work demonstrates that the ultracold atom system provides a controllable platform for studying the symmetrical phase and topological phase, with the potential to explore nonlinear topological phenomena by increasing the interactions among atoms. In addition, our system can be used to investigate other interesting topological phenomena with more complex models, such as critical phenomena at the phase transitions and flat band structures in the extended SSH model with long-range coupling. By controlling the coupling strengths, we can also explore the influence of different symmetries on the topological properties of extended SSH models in the future. Moreover, our platform makes it possible to studythe models with more energy bands, such as the Aharonov-Bohm caging model with a three-level structure, which shows peculiar flat-band properties. This work provides opportunities for various studies in the fields of symmetry, topology, and the interaction of controllable quantum systems.

EDITOR'S SUGGESTION

Growth of Bi2O2Se nanowires and their superconducting quantum interference devices
Liu Huai-Yuan, Xiao Jian-Fei, Lü Zhao-Zheng, Lü Li, Qu Fan-Ming
2024, 73 (4): 047803. doi: 10.7498/aps.73.20231600
Abstract +
Bi2O2Se is a new type of semiconductor material, which has the advantages of high carrier mobility, air stability, strong spin-orbit coupling, etc. It has a variety of synthesis methods and a wide range of applications. In the past few years, many explorations have been made in the synthesis, large-size growth, and applications of Bi2O2Se. It has been applied to field effect transistors, infrared photodetectors, semiconductor devices, heterojunctions, spin electronics, etc. Since nanowire has a larger surface area-to-volume ratio than nano-film, nanowire may have greater advantages in gate regulation and strong spin-orbit coupling, and these properties can play a crucial role in certain fields. However, most of the studies focused on its two-dimensional films, and there are less researches of its one-dimensional counterpart. In this work, a method of growing Bi2O2Se one-dimensional nanowires by chemical vapor deposition in a three-temperature-zone tubular furnace is introduced. High-quality suspended Bi2O2Se nanowires are obtained. In addition, the effects on the Bi2O2Se nanowire growth of the position of the mica substrates, i.e, different horizontal positions and vertical heights in the quartz boat, are studied, and the optimal conditions for the growth are summarized. The nanowires are characterized by atomic force microscope and energy dispersive spectrometer to show the information about the size and component. Then, superconducting quantum interference device based on the Bi2O2Se nanowires is constructed, and the superconducting quantum interference in a magnetic field is observed, which provides a way to broaden the application of Bi2O2Se nanowires.

EDITOR'S SUGGESTION

Breathers of Gerdjikov-Ivanov equation under background of elliptic function
Yao Hui, Zhang Hai-Qiang, Xiong Wei-Yue
2024, 73 (4): 040201. doi: 10.7498/aps.73.20231590
Abstract +
As one specific type of local solutions of nonlinear evolution equation, the breathers have the characteristic of envelope oscillation structure. This kind of oscillation is periodic. According to the periodicity of the distribution and evolution directions, there are three kinds of breathers, namely, the Kuznetsov-Ma breather (KMB), the Akhmediev breather (AB), and the general breather (GB). In recent years, the propagation of envelope breathers under the periodic background has been observed in many nonlinear physical fields, including nonlinear optical fibers and hydrodynamics. It is believed that the breathers can arise due to the modulational instability of the periodic waves, and they demonstrate many rich physical properties and dynamic behaviors of interactions. Therefore, recently great attention has been paid to the breathers under the periodic background in nonlinear science. As an important integrable model, the Gerdjikov-Ivanov (GI) equation can be used to describe various nonlinear phenomena in many physical fields such as in the quantum field theory, weak nonlinear dispersive water wave, and nonlinear optics. It is very meaningful to solve various types of solutions of this model to describe the propagation of nonlinear waves. As far as we know, the breather solutions for the GI equation have not been given under the elliptic function background. In this study, firstly, elliptic function solutions of the GI equation are solved by the modified squared wave (MSW) function approach and the traveling wave transformation. Then, we obtain the basic solution of the Lax pair corresponding to the Jacobi elliptic function seed solution. Based on the elliptic function transformation formulas and the integral formulas, the potential function solution can be expressed in terms of the Weierstrass elliptic function. Secondly, by the once iterated Darboux transformation, three types of breather solutions under the elliptic function background are constructed including the GB, the KMB and the AB. In addition, we analyze the dynamic behaviors of these three kinds of breathers, and present their three-dimensional space-time structures. By the twice iterated Darboux transformation, under the dn-periodic background we exhibit three types of interactions between two breathers, i.e. a GB and a KMB, an AB and a KMB, and a GB and an AB. Finally, we also present three types of interactions between two breathers under the general periodic background.

EDITOR'S SUGGESTION

Depiction of Hamiltonian PT-symmetry
Zhang Hui-Jie, He Kan
2024, 73 (4): 040302. doi: 10.7498/aps.73.20230458
Abstract +
The theory of PT-symmetry describes the non-hermitian Hamiltonian with real energy levels, which means that the Hamiltonian H is invariant neither under parity operator P, nor under time reversal operator T, PTH = H. Whether the Hamiltonian is real and symmetric is not a necessary condition for ensuring the fundamental axioms of quantum mechanics: real energy levels and unitary time evolution. The theory of PT-symmetry plays a significant role in studying quantum physics and quantum information science, Researchers have paid much attention to how to describe PT-symmetry of Hamiltonian. In the paper, we define operator F according to the PT-symmetry theory and the normalized eigenfunction of Hamiltonian. Then we first describe the PT-symmetry of Hamiltonian in dimensionless cases after finding the features of commutator and anti-commutator of operator CPT and operator F. Furthermore, we find that this method can also quantify the PT-symmetry of Hamiltonian in dimensionless case. I(CPT, F) = ||[CPT, F]||CPT represents the part of PT-symmetry broken, and J(CPT, F) = ||[CPT, F]||CPT represents the part of PT-symmetry. If I(CPT, F) = ||[CPT, F]||CPT = 0, Hamiltonian H is globally PT-symmetric. Once I(CPT, F) = ||[CPT, F]||CPT ≠ 0, Hamiltonian H is PT-symmetrically broken. In addition, we propose another method to describe PT-symmetry of Hamiltonian based on real and imaginary parts of eigenvalues of Hamiltonian, to judge whether the Hamiltonian is PT symmetric. ReF = 1/4||(CPTF+F)||CPT represents the sum of squares of real part of the eigenvalue En of Hamiltonian H, ImF = 1/4||(CPTFF)||CPT is the sum of imaginary part of the eigenvalue En of a Hamiltonian H. If ImF = 0, Hamiltonian H is globally PT-symmetric. Once ImF ≠ 0, Hamiltonian H is PT-symmetrically broken. ReF = 0 implies that Hamiltonian H is PT-asymmetric, but it is a sufficient condition, not necessary condition. The later is easier to realize in the experiment, but the studying conditions are tighter, and it further requires that CPT $\phi_n $(x) = $\phi_n $(x). If we only pay attention to whether PT-symmetry is broken, it is simpler to use the latter method. The former method is perhaps better to quantify the PT-symmetrically broken part and the part of local PT-symmetry.

DATA PAPERS

  

EDITOR'S SUGGESTION

Nd3+:GdScO3 crystal field energy level and fitting
Fan Ying, Zhang Qing-Li, Gao Jin-Yun, Gao Yu-Xi, Huang Lei, Liu Yao
2024, 73 (4): 044207. doi: 10.7498/aps.73.20231475
Abstract +
Gadolinium scandate (GdScO3) crystal has a perovskite structure, belonging to an orthogonal system, and its space group is Pnma (No. 62). Due to the disordered distributions of Sc3+ and Gd3+ ions, different cation sites can be replaced by doped ions, which indicates that GdScO3 crystal has a high tolerance for structural distortion. Compared with other oxide crystals, GdScO3 crystal has lower phonon energy of about 452 cm–1, which reduces non-radiative relaxation between adjacent energy levels and has strong thermal stability. In addition, GdScO3 crystal birefringence is large, and as a laser material, it can eliminate the adverse effects caused by thermal birefringence, such as thermal depolarization loss. As an active ion, Nd3+(4f3) is an ideal four-level system. Therefore, Nd3+:GdScO3 crystal has a broad application prospect as a laser crystal matrix material. However, the study of Nd3+:GdScO3 crystal field energy level fitting and crystal field parameters has not been reported to the authors’ knowledge. Neodymium-doped gadolinium scandiate (Nd3+:GdScO3) crystal is grown by the Czochralski method. The absorption spectrum in a range of 250—2650 nm is tested at a low temperature (8 K), and the emission spectrum at room temperature is also tested. The experimental energy levels of Nd3+ are analyzed and 66 experimental Stark levels of Nd3+:GdScO3 are identified. For the doped trivalent rare earth ion crystals, the energy level structure of rare earth ion is related to its luminescence characteristics, so it is necessary to study its energy level structure. In recent decades, parametric crystal field models have been widely applied to various rare-earth ion doped garnet crystals. The parametric model is used to analyze and fit the crystal field energy levels of Nd3+ doped orthogonal GdScO3. The fitted root mean square error is 13.17 cm–1. The resulting free ion parameters and crystal field parameters are calculated and analyzed, and the crystal field intensity is calculated. Fitting results show that the parameterized Stark levels are in good agreement with the experimental spectra, and the results are ideal. Comparing with Nd3+:YAP and Nd3+:YAG, the crystal field strength of Nd3+:GdScO3 is weak. The weak crystal field strength may be one of the reasons for the excellent laser properties of Nd3+:GdScO3 crystals. But its microscopic mechanism needs further studying. All the data presented in this paper are openly available at https://www.doi.org/10.57760/sciencedb.15702.

EDITOR'S SUGGESTION

Hybrid simulation of radio frequency biased inductively coupled Ar/O2/Cl2 plasmas
Tong Lei, Zhao Ming-Liang, Zhang Yu-Ru, Song Yuan-Hong, Wang You-Nian
2024, 73 (4): 045201. doi: 10.7498/aps.73.20231369
Abstract +
In the etching process, a bias source is usually applied to the substrate of the inductively coupled plasma (ICP) to realize independent modulation of the ion energy and ion flux. In this work, a hybrid model, i.e. a global model combined bi-directionally with a fluid sheath model, is employed to investigate the plasma properties and ion energy distribution function (IEDF) in biased inductively coupled Ar/O2/Cl2 plasmas. The results indicate that at a bias frequency of 2.26 MHz, the Cl ion density and ClO+ ion density first increase with bias voltage rising, and then they decrease, and finally they rise again, which is different from the densities of other charged species, such as O and Cl atoms. At the bias frequency of 13.56 MHz and 27.12 MHz, except Cl and $ {\text{Cl}}_2^ + $ ions, the evolutions of other species densities with bias voltage are similar to the results at lower bias frequency. The evolution of the species densities with bias frequency depends on the bias voltage. For instance, in the low bias voltage range (< 200 V), the densities of charges species, O and Cl atoms increase with bias frequency increasing due to a significant increase in the heating of the plasma by the bias source. However, when the bias voltage is high, say, higher than 300 V, except $ {\text{Cl}}_2^ + $ and Cl ions, the densities of other charged species, O and Cl atoms first decrease with bias frequency increasing and then they increase due to a decrease and then an increase in the heating of the plasma by the bias source. In addition, as the bias frequency increases, the peak separation of IEDF becomes narrow, the high energy peak and low energy peak approach each other and they almost merge into one peak at high bias frequency. The results obtained in this work are of significant importance in improving the etching process.

EDITOR'S SUGGESTION

Isoscalar giant resonances of $^{{\bf{18}}}_{{\boldsymbol{\Lambda\Lambda}}}{\bf{O}}$ in relativistic approach
Wen Jing, Sun Shuai, Cao Li-Gang, Zhang Feng-Shou
2024, 73 (4): 042101. doi: 10.7498/aps.73.20231531
Abstract +
The interactions between hyperon-nucleon and hyperon-hyperon have been an important topic in strangeness nuclear physics, which play an important role in understanding the properties of hypernuclei and equation of state of strangeness nuclear matter. It is very difficult to perform a direct scattering experiment of the nucleon and hyperon because the short lifetime of the hyperon. Therefore, the hyperon-nucleon interaction and the hyperon-hyperon interaction have been mainly investigated experimentally by $\gamma$ spectroscopy of single-$\Lambda$ hypernuclei or double-$\Lambda$ hypernuclei. There are also many theoretical methods developed to describe the properties of hypernuclei. Most of these models focus mostly on the ground state properties of hypernuclei, and have given exciting results in producing the banding energy, the energy of single-particle levels, deformations, and other properties of hypernuclei. Only a few researches adopting Skyrme energy density functionals is devoted to the study of the collective excitation properties of hypernuclei. In present work, we have extended the relativistic mean field and relativistic random phase approximation theories to study the collective excitation properties of hypernuclei, and use the methods to study the isoscalar collective excited state properties of double $\Lambda$ hypernuclei. First, the effect of $\Lambda$ hyperons on the single-particle energy of 16O and $^{18}_{\Lambda\Lambda}{\rm{O}}$ are discussed in the relativistic mean field theory, the calculations are performed within TM1 parameter set and related hyperon-nucleon interaction, and hyperon-hyperon interaction. We find that it gives a larger attractive effect on the ${{\mathrm{s}}}_{1/2}$ state of proton and neutron, while gives a weaker attractive effect on the state around Fermi surface. The self-consistent relativistic random phase approximation is used to study the collectively excited state properties of hypernucleus $^{18}_{\Lambda\Lambda}{\rm{O}}$. The isoscalar giant monopole resonance and quadrupole resonance are calculated and analysed in detail, we pay more attention to the effect of the inclusion of $\Lambda$ hyperons on the properties of giant resonances. Comparing with the strength distributions of 16O, changes of response function of $^{18}_{\Lambda\Lambda}{\rm{O}}$ are evidently found both on the isoscalar giant monopole resonance and quadrupole resonance. It is shown that the difference comes mainly from the change of Hartree energy of particle-hole configuration and the contribution of the excitations of $\Lambda$ hyperons. We find that the hyperon-hyperon residual interactions have small effect on the monopole resonance function and quadrupole response function in the low-energy region, and have almost no effect on the response functions in the high-energy region.

EDITOR'S SUGGESTION

Parameterized entanglement measures based on Rényi-α entropy
Dai Wei-Peng, He Kan, Hou Jin-Chuan
2024, 73 (4): 040303. doi: 10.7498/aps.73.20231503
Abstract +
Parameterized entanglement measures have demonstrated their superiority compared with kinds of unparameterized entanglement measures. Entanglement concurrence has been widely used to describe entanglement in quantum experiments. As an entanglement measure it is related to specific quantum Rényi-α entropy. In the work, we propose a parameterized bipartite entanglement measure based on the general Rényi-α entropy, which is named α-logarithmic concurrence. This measure, different from existing parameterized measures, is defined first for pure states, then extended to the mixed states. Furthermore, we verify three necessary conditions for α-logarithmic concurrence to satisfy the entanglement measures. We show that this measure is easy to calculate for pure states. However, for mixed states, analytical calculations are only suitable for special two-qubit states or special higher-dimensional mixed states. Therefore, we devote our efforts to developing the analytical lower bound of the-logarithmic concurrence for general bipartite states. Surprisingly, this lower bound is a function on positive partial transposition criterion and realignment criterion of this mixed state. This shows the connection among the three entanglement measures. The interesting feature is that the lower bound depends on the entropy parameter associated with the detailed state. This allows us to choose appropriate parameter α such that $ G_\alpha({\boldsymbol{\rho}})\gg0$ for experimental entanglement detection of specific state ρ. Moreover, we calculate expressions of the α-logarithmic concurrence for isotropic states, and give a the analytic expressions for isotropic states with $ d = 2$. Finally, the monogamy of the α-logarithmic concurrence is also discussed. We set up a mathematical formulation for the monogamous property in terms of α-logarithmic concurrence. Here we set up the functional relation between concurrence and α-logarithmic concurrence in two qubit systems. Then we obtain some useful properties of this function, and by combining the Coffman–Kundu–Wootters (CKW) inequality, we establish the monogamy inequality about α-logarithmic concurrence. We finally prove that the monogamy inequality holds true for α-logarithmic concurrence.

EDITOR'S SUGGESTION

Probing microstructural heterogeneity of La-based amorphous alloy under versatile mechanical stimuli
Zhang Jian, Hao Qi, Zhang Lang-Ting, Qiao Ji-Chao
2024, 73 (4): 046101. doi: 10.7498/aps.73.20231421
Abstract +
The intrinsic structural heterogeneity of amorphous alloy is closely related to the thermodynamics and dynamical behavior, such as relaxation/crystallization, glass transition and plastic deformation. However, the structural information is submerged into the meta-stable disordered long-range structure, which makes it very difficult to explore the structural heterogeneity of amorphous alloy. A mechanical excitation factor is insufficient to effectively describe the heterogeneity of the microstructure in amorphous alloy, particularly the correlation between structure and dynamics. To explore the essence of the structure in amorphous alloy, it is necessary to consider the different mechanical stimuli. La62Cu12Ni12Al14 amorphous alloy is selected as the model system, dynamic mechanical process is probed by dynamic mechanical analyzer (DMA). The contributions of α relaxation process and β relaxation process are described in the framework of the quasi-point defect theory. Based on the quasi-point defect theory, the α-relaxation and β-relaxation in the La-based amorphous alloy are separated. Tensile strain rate jump measurements are conducted to study the high temperature rheological behavior of amorphous alloy. The contributions of elasticity, anelasticity, and plastic deformation during the homogeneous flow of amorphous alloy are determined within the framework of quasi-point defect theory. The present work aims to reveal the structural heterogeneities of amorphous alloys under the action of dynamics on various temporal scales. The physical background of the activation, propagation and coalescence of defects in amorphous alloy under different mechanical stimuli are reviewed.
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