Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one...Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one of the main tasks in modern biophysics. Coarse-grained methods play an increasingly important role in the simulation of protein folding, especially for large proteins. In recent years, we proposed a novel coarse-grained method derived from the topological soliton model, in terms of the backbone Cα chain. In this review, we will first systematically address the theoretical method of topological soliton. Then some successful applications will be displayed, including the thermodynamics simulation of protein folding, the property analysis of dynamic conformations, and the multi-scale simulation scheme. Finally, we will give a perspective on the development and application of topological soliton.展开更多
In the Phase Ⅱ Project at the Hefei Light Source, a fourth-harmonic ＂Landau＂ cavity will be operated in order to suppress the coupled-bunch instabilities and increase the beam lifetime of the Hefei storage ring. In...In the Phase Ⅱ Project at the Hefei Light Source, a fourth-harmonic ＂Landau＂ cavity will be operated in order to suppress the coupled-bunch instabilities and increase the beam lifetime of the Hefei storage ring. Instabilities limit the utility of the higher-harmonic cavity when the storage ring is operated with a small momentum compaction. Analytical modeling and simulations show that the instabilities result from Robinson mode coupling. In the analytic modeling, we operate an algorithm to consider the Robinson instabilities. To study the evolution of unstable behavior, simulations have been performed in which macroparticles are distributed among the buckets. Both the analytic modeling and simulations agree for passive operation of the harmonic cavity.展开更多
文摘Proteins are important biological molecules whose structures are closely related to their specific functions. Understanding how the protein folds under physical principles, known as the protein folding problem, is one of the main tasks in modern biophysics. Coarse-grained methods play an increasingly important role in the simulation of protein folding, especially for large proteins. In recent years, we proposed a novel coarse-grained method derived from the topological soliton model, in terms of the backbone Cα chain. In this review, we will first systematically address the theoretical method of topological soliton. Then some successful applications will be displayed, including the thermodynamics simulation of protein folding, the property analysis of dynamic conformations, and the multi-scale simulation scheme. Finally, we will give a perspective on the development and application of topological soliton.
基金Supported by National Natural Science Foundation of China(10979045,11175180,11175182)
文摘In the Phase Ⅱ Project at the Hefei Light Source, a fourth-harmonic ＂Landau＂ cavity will be operated in order to suppress the coupled-bunch instabilities and increase the beam lifetime of the Hefei storage ring. Instabilities limit the utility of the higher-harmonic cavity when the storage ring is operated with a small momentum compaction. Analytical modeling and simulations show that the instabilities result from Robinson mode coupling. In the analytic modeling, we operate an algorithm to consider the Robinson instabilities. To study the evolution of unstable behavior, simulations have been performed in which macroparticles are distributed among the buckets. Both the analytic modeling and simulations agree for passive operation of the harmonic cavity.
