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Vol. 73, No. 18 (2024)

2024-09-20
SPECIAL TOPIC—Machine learning in biomolecular modelling
Progress in protein pre-training models integrating structural knowledge
Tang Tian-Yi, Xiong Yi-Ming, Zhang Rui-Ge, Zhang Jian, Li Wen-Fei, Wang Jun, Wang Wei
2024, 73 (18): 188701. doi:10.7498/aps.73.20240811
Abstract +
The AI revolution, sparked by natural language and image processing, has brought new ideas and research paradigms to the field of protein computing. One significant advancement is the development of pre-training protein language models through self-supervised learning from massive protein sequences. These pre-trained models encode various information about protein sequences, evolution, structures, and even functions, which can be easily transferred to various downstream tasks and demonstrate robust generalization capabilities. Recently, researchers have further developed multimodal pre-trained models that integrate more diverse types of data. The recent studies in this direction are summarized and reviewed from the following aspects in this paper. Firstly, the protein pre-training models that integrate protein structures into language models are reviewed: this is particularly important, for protein structure is the primary determinant of its function. Secondly, the pre-trained models that integrate protein dynamic information are introduced. These models may benefit downstream tasks such as protein-protein interactions, soft docking of ligands, and interactions involving allosteric proteins and intrinsic disordered proteins. Thirdly, the pre-trained models that integrate knowledge such as gene ontology are described. Fourthly, we briefly introduce pre-trained models in RNA fields. Finally, we introduce the most recent developments in protein designs and discuss the relationship of these models with the aforementioned pre-trained models that integrate protein structure information.
Effect of electrolyte concentration on bubble evolution and mass transfer characteristics on surface of photoelectrode
Wang Meng-Sha, Xu Qiang, Nie Teng-Fei, Luo Xin-Yi, Guo Lie-Jin
2024, 73 (18): 188201. doi:10.7498/aps.73.20240533
Abstract +
In the photoelectrochemical water splitting reaction system, bubbles will cover the reaction area on the photoelectrode surface, affecting the reaction impedance and gas-liquid mass transfer. A laser irradiation system is built and it is coupled with an electrochemical workstation and high-speed microscopic imaging system. The evolution behavior and mass transfer characteristics of single O2bubble on the TiO2photoelectrode are studied at different electrolyte concentrations (Na2SO4, 0.1–2.0 mol/L). With the increase of electrolyte concentration from 0.1 mol/L to 2.0 mol/L, the solution resistance and bubble additional resistance decrease, and the overpotential in the stable growth stage of bubble decreases from 0.113 V to –0.089 V. The bubble will cause the fluctuation of overpotential in the nucleation, growth and detachment stages, which is consistent with the impedance change caused by the change of dissolved oxygen concentration in the liquid phase. By analyzing the correlation between gas evolution efficiency and bubble coverage, it is found that the increase of electrolyte concentration will lead the bubble coverage and gas evolution efficiency to decrease simultaneously. By calculating the Sherwood dimensionless number, the results show that the total convective mass transfer coefficient increases with the electrolyte concentration increasing. Single-phase natural convection plays a dominant role in the process of gas product transfer, and its mass transfer coefficient is one order of magnitude larger than that of bubble-induced convection. In summary, by adjusting the electrolyte concentration, the bubble on the gas evolution photoelectrode surface can be effectively removed and the mass transfer of the system can be optimized, which is of great significance in improving the efficiency of photoelectrochemical water splitting.
THE PHYSICS OF ELEMENTARY PARTICLES AND FIELDS
Dual-band semi-Dirac cones in two-dimensional photonic crystal and zero-index material
Ji Yu-Xuan, Zhang Ming-Kai, Li Yan
2024, 73 (18): 181101. doi:10.7498/aps.73.20240800
Abstract +
Semi-Dirac cones, a type of unique dispersion relation, always exhibit a series of interesting transport properties, such as electromagnetic topological transitions and anisotropic electromagnetic transmission. Recently, dual-band semi-Dirac cones have been found in three-dimensional photonic crystals, presenting great potential in electromagnetic wave regulation. However, to the best of our knowledge, there has been no report on dual-band semi-Dirac cones and their applications in two-dimensional photonic crystals, and most of two-dimensional systems have only realized semi-Dirac cones at a single frequency. Therefore, we are to realize dual-band semi-Dirac cones in two-dimensional photonic crystals. In this work, a type of two-dimensional photonic crystal that comprises a square lattice of elliptical cylinders embedded in air is proposed. By rotating the elliptical cylinders and adjusting their sizes appropriately, accidental degeneracy at two different frequencies is achieved simultaneously in the center of the Brillouin zone. Using ${\boldsymbol{k}} \cdot {\boldsymbol{p}}$ perturbation theory, the dispersion relations near the two degenerate points are proved to be nonlinear in one direction, and linear in other directions. These results indicate that the double accidental degenerate points are two semi-Dirac points with different frequencies, and two different semi-Dirac cones, i.e. dual-band semi-Dirac cones, are realized simultaneously in our designed photonic crystal. More interestingly, the dual-band semi-Dirac cones exhibit opposite linear and nonlinear dispersion relation along the major axis and the minor axis of the ellipse, respectively. And our photonic crystal can be equivalent to an impedance-matched double-zero index material in the direction of linear dispersion and a single-zero index material in the direction of nonlinear dispersion, which is demonstrated by the perfect transmission in the straight waveguide and wavefront shaping capabilities of electromagnetic waves. Based on the different properties of the equivalent zero-refractive-indices near the frequencies of two semi-Dirac point, the designed Y-type waveguide can be used to realize frequency separation by leading out the plane waves of different frequencies along different ports. We believe that our work is meaningful in broadening the exploration of the band structures of two-dimensional photonic crystals and providing greater convenience for regulating electromagnetic waves.
ELECTROMAGNETISM, OPTICS, ACOUSTICS, HEAT TRANSFER, CLASSICAL MECHANICS, AND FLUID DYNAMICS
System multi-scale analysis of temperature control for spaceborne electronic devices
Li Xin-Ze, Tang Gui-Hua, Wang Zi-Han, Feng Jian-Chao, Zhang Xiao-Feng
2024, 73 (18): 184401. doi:10.7498/aps.73.20240685
Abstract +
To improve the simulation resolution and accuracy in thermal analysis of spaceborne electronic devices and the temperature control performance of passive thermal control devices, a system multi-scale model is established, thereby obtaining the temperature field and heat flux of electronic devices inside the satellite on different scales as illustrated in the below figure. The temperature fluctuation mechanism inside the satellite is analyzed on different physical scales. The thermal analysis resolution of spaceborne electronic equipment is improved, and a method to reduce the power fluctuation of spaceborne equipment is proposed based on the results of system multi-scale thermal analysis. The results indicate that the accuracy deviation between the multi-scale model of the system and the actual model is less than 9%. However, the system multi-scale model saves 99.67% of the mesh generation time, which greatly improves the computation efficiency. The system multi-scale model can capture the thermal information about device-level chip microstructures at a lower computational cost. The system-level model can evaluate the temperature control and insulation performance of passive thermal control materials on a macroscale. The temperature fluctuation amplitude of the platform compartment is 7.95 K, while the temperature fluctuation amplitude of the load compartment decreases to 2.43 K after the temperature of the composite phase change insulation material has been controlled, which is 69.43% lower than that of the platform compartment. Compared with traditional vacuum insulation panels, the composite phase change materials are very superior in controlling the temperature of the chamber and suppressing temperature fluctuations. The temperature fluctuation signal after being insulated by the composite phase change insulation materials shows a characteristic of shifting to the high-frequency domain. After selecting the cabins that require key insulation and temperature control through multiple regression analysis, a simplified model at device level is employed to obtain temperature fields under different thermal control device layouts as a training dataset. A neural network genetic algorithm is used to predict the optimal installation position of passive thermal control device on the device scale and a thermal control layout scheme is obtained, which reduces the maximum temperature fluctuation of the device by 2.74 K. If the temperature uniformity coefficient is taken as the optimization goal, the temperature of each device on PCB board can be reduced to 14.39% of the average temperature of all devices through optimizations.