Search

Article

x

Highlights

Topics
Article Type

COVER ARTICLE

  

COVER ARTICLE

A high-precision image registration method for multi-channel single molecule localization
Lin Dan-Ying, Gong Zhen-Quan, Huang Li-Lin, Nie Meng-Jiao, Yu Bin, Qu Jun-Le
2024, 73 (6): 068701. doi: 10.7498/aps.73.20231695
Abstract +
Single-molecule localization technology has been widely used in single-particle tracking and super-resolution imaging of biological samples, as it can bypass the diffraction limit of optical systems. Multi-channel single-molecule localization uses multiple imaging channels to simultaneously track different targets or perform multi-color super-resolution imaging, and can also improve the axial depth of single-particle tracking or achieve higher localization precision and density for super-resolution imaging. However, the difference between images in each channel can affect collaborative localization or quantitative analysis, so image registration is a key step in its image data preprocessing. Moreover, due to the high precision of single-molecule localization, its requirements for multi-channel image registration accuracy are also high. Existing technologies generally use control point-based registration methods and often use complicated and precise methods to obtain fiducial images for locating control point pairs to achieve high-precision image registration, which involves high sample or experimental equipment requirements and is difficult to directly extend to other systems. Therefore, developed in this work, is a high-precision image registration method that can directly use randomly distributed fluorescent beads as fiducial samples based on local nonlinear transformation and elimination of mismatched points. By monitoring and iteratively filtering control points in the process of feature matching and transformation model parameter estimation to eliminate control point pairs that are not accurately matched due to inaccurate or poor precision of single-molecule localization, the adverse effects on accurate acquisition and precise matching of control points when using randomly distributed fluorescent beads as fiducial samples are eliminated. At the same time, a second-order polynomial fitting based on local weighted mean is used for estimating the transformation model parameter to better adapt to the existence of local nonlinear deformation between different channels. The results show that using this method only requires three iterations to find and eliminate control point pairs that are not accurately located and matched, thereby achieving more accurate transformation model parameter and improving the registration accuracy by an order of magnitude, achieving a registration accuracy of about 6 nm in a complex dual-channel single-molecule localization imaging system based on orthogonal astigmatism.

SPECIAL TOPIC——Two-dimensional magnetism and topological spin physics • COVER ARTICLE

  

COVER ARTICLE

Tuning magnetic properties of two-dimensional antiferromagnetic MPX3 by organic cations intercalation
Mi Meng-Juan, Yu Li-Xuan, Xiao Han, Lü Bing-Bing, Wang Yi-Lin
2024, 73 (5): 057501. doi: 10.7498/aps.73.20232010
Abstract +
Electrical control of magnetism of two-dimensional (2D) antiferromagnetic (AFM) materials combines the advantages of controlling magnetism by purely electrical means, compatibility with semiconductor process, low energy consumption, heterogeneous integration of 2D materials with van der Waals (vdW) interface, and AFM materials with no stray field, resistance to external magnetic field interference, and high intrinsic frequency, and thus becomes a research focus in the field. The carrier concentration control is the main mechanism of electrical control of magnetism, and has been proved to be an effective way to control the magnetic properties of materials. The intralayer-antiferromagnetic materials have net-zero magnetic moments, and it is a challenging task to measure their regulated magnetic properties. Therefore, there is limited research on the electrical control of magnetism of intralayer-antiferromagnetic materials, and their potential mechanisms are not yet clear. Based on the diversity of organic cations, the present work systematically modulates the carrier concentrations of 2D intralayer-antiferromagnetic materials MPX3 (M = Mn, Fe, Ni; X = S, Se) by utilizing organic cations intercalation, and investigates the influence of electron doping on their magnetic properties. Phase transitions between AFM-ferrimagnetic (FIM)/ferromagnetic (FM) depending on carrier concentration changes are observed in MPX3 materials, and the corresponding regulation mechanism is revealed through theoretical calculations. This research provides new insights into the carrier-controlled magnetic phase transition of 2D magnetic materials, and opens up a pathway for studying the correlation between the electronic structure and magnetic properties of 2D magnets, and designing novel spintronic devices as well.

COVER ARTICLE

  

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.

SPECIAL TOPIC—Heat conduction and its related interdisciplinary areas • COVER ARTICLE

  

COVER ARTICLE

Thermal protection characteristics of non-enclosed thermal cloak
Miao Yu-Zhao, Tang Gui-Hua
2024, 73 (3): 034401. doi: 10.7498/aps.73.20231262
Abstract +
The aerodynamic heat of hypersonic vehicle nose cone can reach tens of MW/m2 during flight, which could be transferred to the interior of hypersonic vehicle in the form of conduction and radiation. High efficient thermal insulation technology is of significance in keeping internal electronic components working safely. Thermal metamaterials can regulate the macroscopic heat flow path, and they are developing rapidly and have a wide application prospect in the field of thermal protection. In this work, a non-enclosed point transformation thermal cloak is designed to guide heat flow around hypersonic vehicle nose cone by using the transformation multithermotics, which can control thermal conduction and radiation simultaneously. A multi-layer structure is designed as cloak’s simplified approximation due to the anisotropic parameters. Based on the software COMSOL, the thermal protection characteristics and heat transfer mechanism of the point transformation cloak and multi-layer structure are studied numerically. The results show that heat can flow around the object in the form of conduction and radiation in both point transformation thermal cloak and multi-layer structure, so the heat transferred to the inner area decreases. Comparing with the thermal insulation material, the heating rate of the protected area slows down, and the temperature in the front of the hypersonic vehicle nose cone is significantly reduced. However, the improvement of the thermal protection performance of point transformation cloak and multi-layer structures requires that the solid thermal conductivity and radiative thermal conductivity of the material are lower than those of the original thermal insulation material. To solve this problem, a non-enclosed region transformation thermal cloak is further proposed. The solid thermal conductivity and radiative thermal conductivity of region transformation thermal cloak are non-singular, which could be higher than those of the original thermal insulation material. Numerical simulation results show that the region transformation thermal cloak can guide heat flow around object, so the thermal protection capability is improved significantly. Comparing with the thermal insulation materials, the temperature of the front of the hypersonic vehicle nose cone is reduced by 100 K, and the temperature of the inner central zone of the hypersonic vehicle nose cone is reduced by 10 K. The non-enclosed region transformation thermal cloak provides a new approach to realizing thermal protection and is suitable for complex target areas, showing great application potential in thermal protection.

COVER ARTICLE

  

COVER ARTICLE

Significant role of thermal effects in current-induced exchange bias field switching at antiferromagnet/ferromagnet interface
He Yu, Chen Wei-Bin, Hong Bin, Huang Wen-Tao, Zhang Kun, Chen Lei, Feng Xue-Qiang, Li Bo, Liu Guo, Sun Xiao-Han, Zhao Meng, Zhang Yue
2024, 73 (2): 027501. doi: 10.7498/aps.73.20231374
Abstract +
The current-induced switching of in-plane exchange bias field (Heb) has many advantages, such as switching without assistance of external magnetic field, excellent immunity to magnetic field, and robust magnetic anisotropy. However, the blocking temperature of the nanoscale antiferromagnet/ferromagnet (AFM/FM) heterostructure is relatively low and susceptible to thermal effects. Therefore, the Joule heating theoretically plays a substantial role in the switching of Heb driven by current, but its underlying mechanism requires further investigation and verification. We prepare a series of Pt/IrMn/Py heterostructures with varying antiferromagnet IrMn thicknesses and systematically investigate the role of thermal effects in current-driven Heb switching. These results demonstrate that under millisecond-level current pulses, Joule heating heats the device above the blocking temperature, leading to the decoupling of exchange coupling at AFM/FM interface. Simultaneously, the Oersted field and spin-orbit torque field generated by the current switch the ferromagnetic moments, and then a new Heb will be induced along the direction of the ferromagnetic moments in the cooling process. Furthermore,in the switching process of Heb, the anisotropic magnetoresistance curve of the AFM/FM heterostructure exhibits a temperature-dependent two-step magnetization reversal phenomenon. Theoretical analysis indicates that this phenomenon arises from the competitive relationship between exchange bias coupling at AFM/FM interface and direct exchange coupling between the ferromagnetic moments. The findings of this study elucidate the crucial role of thermal effects in the current-driven switching of Heb, thereby contributing to the advancement of spintronic devices based on electrically controlled Heb.

SPECIAL TOPIC—Two-dimensional magnetism and topological spin physics • COVER ARTICLE

  

COVER ARTICLE

Magnon Hall effect
Jin Zhe-Jun-Yu, Zeng Zhao-Zhuo, Cao Yun-Shan, Yan Peng
2024, 73 (1): 017501. doi: 10.7498/aps.73.20231589
Abstract +
Hall effect is an ancient but highly potential subfield in condensed matter physics, and its origin can be traced back hundreds of years. In 1879, Hall made a momentous discovery that when a current-carrying conductor is placed in a magnetic field, the Lorentz force pushes its electrons to one side of the conductor. This intriguing phenomenon was dubbed Hall effect. Since then, a series of novel Hall effects have been discovered, including anomalous Hall effect, quantum Hall effect, spin Hall effect, topological Hall effect, and planar Hall effec. Notably, Hall effects play an important role in realizing the information transport, since it can realize the mutual conversion of current in different directions. In bosonic systems such as magnons, a series of magnon Hall effects have been found, jointly driving the development of the magnon-based spintronics. In this perspective, we review the researches of the Hall effect in magnonic system in recent years, and briefly introduce its modern semi-classical theories, including virtual electromagnetic field theory and scattering theory. Furthermore, we introduce the different magnon Hall effects and clarify the physics behind them. Finally, the prospect of magnon Hall effect is discussed.

SPECIAL TOPIC—Machine learning in biomolecular simulations • COVER ARTICLE

  

COVER ARTICLE

Exploring proten’s conformational space by using encoding layer supervised auto-encoder
Chen Guang-Lin, Zhang Zhi-Yong
2023, 72 (24): 248705. doi: 10.7498/aps.72.20231060
Abstract +
Protein function is related to its structure and dynamic change. Molecular dynamics simulation is an important tool for studying protein dynamics by exploring its conformational space, however, conformational sampling is a nontrivial issue, because of the risk of missing key details during sampling. In recent years, deep learning methods, such as auto-encoder, can couple with MD to explore conformational space of protein. After being trained with the MD trajectories, auto-encoder can generate new conformations quickly by inputting random numbers in low dimension space. However, some problems still exist, such as requirements for the quality of the training set, the limitation of explorable area and the undefined sampling direction. In this work, we build a supervised auto-encoder, in which some reaction coordinates are used to guide conformational exploration along certain directions. We also try to expand the explorable area by training through the data generated by the model. Two multi-domain proteins, bacteriophage T4 lysozyme and adenylate kinase, are used to illustrate the method. In the case of the training set consisting of only under-sampled simulated trajectories, the supervised auto-encoder can still explore along the given reaction coordinates. The explored conformational space can cover all the experimental structures of the proteins and be extended to regions far from the training sets. Having been verified by molecular dynamics and secondary structure calculations, most of the conformations explored are found to be plausible. The supervised auto-encoder provides a way to efficiently expand the conformational space of a protein with limited computational resources, although some suitable reaction coordinates are required. By integrating appropriate reaction coordinates or experimental data, the supervised auto-encoder may serve as an efficient tool for exploring conformational space of proteins.

SPECIAL TOPIC—Modification of material properties by defects and dopants • COVER ARTICLE

  

COVER ARTICLE

Non-adiabatic dynamic study of S vacancy formation in MoS2
Wang Yue, Ma Jie
2023, 72 (22): 226101. doi: 10.7498/aps.72.20230787
Abstract +
Defect is one of the central issues in semiconductors. MoS2 is sensitive to irradiation and can be damaged by electron beams, accompanied with the generation of sulfur vacancies. However, the dynamics for the defect generation process is still unclear. In this work, we employ the time-dependent density functional theory to simulate the process of a sulfur atom sputtering from the MoS2, producing a sulfur vacancy defect in the lattice. We find that there exists a strong non-adiabatic effect in the process.During the formation of the sulfur vacancy, there exist electron transitions which can be described by the Landau-Zener model. As the sulfur atom leaves away from the lattice, two energy levels from the valence bands rise up and one energy level from the conduction band falls down. When the spin-orbit coupling (SOC) is not considered, those levels do not couple with each other. However, when the SOC is taken into account, electrons can transit between those levels. The transition probability is related to the kinetic energy of the sputtered sulfur atom. As the kinetic energy of the sulfur atom increases, the non-adiabatic electron transitions are enhanced. The evolution of the energy levels is also strongly dependent on the kinetic energy of the sputtered sulfur atom, which is induced by the non-adiabatic electron transition. It is worth noting that the SOC plays a key role in sputtering sulfur atoms, although the system produces no magnetic moments in the whole process.The non-adiabatic effect enhances the energy barrier of the sulfur sputtering. As the initial kinetic energy of the sputtered sulfur atom increases, the energy barrier increases, and exhibits a jump around the initial kinetic energy of ~22 eV, which can be explained by the non-adiabatic electron occupation and the Coulomb repulsion. Beside the energy barrier, the non-adiabatic effect also modifies the charge distribution. When the kinetic energy of the sputtered sulfur atom is relatively low, more electrons occupy the pz level; when the kinetic energy is relatively high, more electrons occupy the pxy level instead. The sputtered sulfur atom always carries a bit more electrons, leaving holes around the vacancy defect.Our work reveals the dynamics of the sulfur sputtering and vacancy formation in MoS2, particularly the non-adiabatic effect in the process. It builds the theoretical foundation for defect engineering.

SPECIAL TOPIC—Energetic particles in magnetic confinement fusion plasma • COVER ARTICLE

  

COVER ARTICLE

Tomography of fast ion distribution function under neutral beam injection and ion cyclotron resonance heating on EAST
Sun Yan-Xu, Huang Juan, Gao Wei, Chang Jia-Feng, Zhang Wei, Shi Chang, Li Yun-He
2023, 72 (21): 215203. doi: 10.7498/aps.72.20230846
Abstract +
In magnetic confinement fusion devices, velocity-space tomography of fast-ion velocity distribution function is crucial for investigating fast-ion distribution and transport. In the neutral beam injection (NBI) and ion cyclotron resonance heating (ICRF) synergistic heating experiments in Experimental Advanced Superconducting Tokamak (EAST), high-energy particles with energy exceeding the particle energy in NBI are observed. Simulations of synergistic effect on fast-ion velocity distribution function given by TRANSP also show the existence of particles with energy higher than the particle energy in NBI. To investigate the behaviors of fast ion distribution and calculate the velocity distribution functions under different heating conditions, the first-order Tikhonov regularization tomographic inversion method with higher inversion accuracy is introduced by comparing various regularization techniques. The limitations of the dual-view fast-ion Dα (FIDA) diagnostic measurements in velocity space are addressed by incorporating prior information such as null measurement and the known peaks and effectively mitigate the occurrence of artifacts. This method is first employed in the case of NBI heating. The NBI peak is successfully reconstructed at the expected location in velocity space, which shows significant improvement in the inversion results. In order to further validate the synergistic effect of NBI-ICRF heating and study the mechanism of fast ion distribution under synergistic heating, the combination of FIDA and neutron emission spectrometer (NES) is applied to the first-order Tikhonov regularization tomographic inversion method for enhancing the coverage of velocity space, through which the issue of artifacts in the inversion results is significantly improved, and thus the precision of the obtained fast-ion velocity distribution functions is enhanced. Based on the benefit described above, the method of combining NES diagnosis and FIDA diagnosis is used to obtain fast-ion velocity distribution functions in the NBI and ICRF synergistic heating discharge. The synergistic heating effect is manifested in the fast-ion velocity distribution. The availability of this inversion method in reconstructing fast-ion velocity distribution functions during high-performance operation of NBI-ICRF synergistic heating in the EAST experiment is confirmed. In the next-step EAST research, high performance discharge will demand more efficiency NBI and ICRF synergistic heating, the present work builds the stage for investigating the underlying mechanism of synergistic heating and the intricate behaviors associated with fast ion distribution and transport.

COVER ARTICLE

  

COVER ARTICLE

Phase separation phenomenon in mixed system composed of low- and high-inertia active particles
Wang Jing, Jiao Yang, Tian Wen-De, Chen Kang
2023, 72 (19): 190501. doi: 10.7498/aps.72.20230792
Abstract +
Active matter refers to a class of substance capable of autonomously moving by harnessing energy from its surrounding environment. The substance exhibits unique non-equilibrium phenomenon, and hence has attracted great attention in the scientific community. Many active matters, such as bacteria, cells, micro-swimmers, and self-propelled colloidal particles, operate in viscous environments and their motions are described usually by using overdamped models. Examples include overdamped active Brownian particle (ABP) model for self-propelled colloidal particles in solution and run-and-tumble (RTP) model for swimming bacteria. In recent years, increasing studies focus on the influence of inertia on the behavior of active matter. Vibrating robots, runners, flying insects, and micro-fliers are typical of active systems under the underdamped condition. The motions of these active matters can be modelled by underdamped Langevin equation, known as the active inertial particle (AIP) model. Previous studies have demonstrated that like the scenarios in ABP systems, motility-induced phase separation (MIPS) phenomena also happen in AIP systems under certain density conditions. However, due to the strong collision-and-rebound effect, aggregation of AIP particles and hence the MIPS are impeded. In complex living/application environments, mixture of different active agents is often seen. Some studies on mixed systems of active matter show that the composition is an important quantity, which influences the phase separation phenomena. In this paper, we study the phase separation phenomena in a mixed system composed of low- and high-inertia active particles by underdamped Langevin dynamics simulations. We find that compared with single-component system, the mixed system is unexpectedly favorable for the occurrence of phase separation at a moderate overall concentration and a certain range of component fraction, while unfavorable for phase separation at a high overall concentration. The underlying mechanism is that the presence of a small number of the high-inertia particles could accelerate the motion of the low-inertia particles, thus facilitating their aggregation and promoting the phase separation. However, when the fraction of the high-inertia particles is large, frequent elastic collisions would disturb the aggregation of the low-inertia particles and suppress the occurrence of phase separation. Our results provide a new insight into the collective behavior of active materials and also a reference for their design and applications.
  • 1
  • 2
  • 3
  • 4
  • 5
  • ...
  • 10
  • 11