Application of topological soliton in modeling protein folding: Recent progress and perspective

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.

Soliton mode-locked fiber laser based on topological insulator Bi2Te3 nanosheets at 2 μm

We reported diverse soliton operations in a thulium/holmium-doped fiber laser by taking advantage of a tapered fiber-based topological insulator（TI） Bi2Te3 saturable absorber（SA）.The SA had a nonsaturable loss of 53.5% and a modulation depth of 9.8%.Stable fundamentally mode-locked solitons at 1909.5 nm with distinct Kelly sidebands on the output spectrum,a pulse repetition rate of 21.5 MHz,and a measured pulse width of 1.26 ps were observed in the work.By increasing the pump power,both bunched solitons with soliton number up to 15 and harmonically mode-locked solitons with harmonic order up to 10 were obtained.To our knowledge,this is the first report of both bunched solitons and harmonically mode-locked solitons in a fiber laser at 2 μm region incorporated with TIs.

Soliton solution of the generalized modified BBM equation and the generalized Boussinesq equation

In this paper,we obtained the topological soliton solution of the(1+1)-dimensional generalized modified Benjamin-Bona-Mahony equation and shock wave solution of the generalized Boussinesq equation.We get that solutions by using solitary wave ansatz in terms of tanh^(p) functions.The velocity and the free parameters are the physical parameters in the soliton solutions.They can be obtained as functions of the dependent model coefficients.The domain restriction were also identified in the process.we hope that in nonlinear dynamical system these solutions will be explain some nonlinear physical phenomena.

Soliton and other solutions to the (1+2)-dimensional chiral nonlinear Schrodinger equation

The(1+2)-dimensional chiral nonlinear Schr?dinger equation(2D-CNLSE)as a nonlinear evolution equation is considered and studied in a detailed manner.To this end,a complex transform is firstly adopted to arrive at the real and imaginary parts of the model,and then,the modified Jacobi elliptic expansion method is formally utilized to derive soliton and other solutions of the 2D-CNLSE.The exact solutions presented in this paper can be classified as topological and nontopological solitons as well as Jacobi elliptic function solutions.

Vector valley Hall edge solitons in the photonic lattice with type-Ⅱ Dirac cones

Topological edge solitons represent a significant research topic in the nonlinear topological photonics.They maintain their profiles during propagation,due to the joint action of lattice potential and nonlinearity,and at the same time are immune to defects or disorders,thanks to the topological protection.In the past few years topological edge solitons were reported in systems composed of helical waveguide arrays,in which the time-reversal symmetry is effectively broken.Very recently,topological valley Hall edge solitons have been demonstrated in straight waveguide arrays with the time-reversal symmetry preserved.However,these were scalar solitary structures.Here,for the first time,we report vector valley Hall edge solitons in straight waveguide arrays arranged according to the photonic lattice with innate type-II Dirac cones,which is different from the traditional photonic lattices with type-I Dirac cones such as honeycomb lattice.This comes about because the valley Hall edge state can possess both negative and positive dispersions,which allows the mixing of two different edge states into a vector soliton.Our results not only provide a novel avenue for manipulating topological edge states in the nonlinear regime,but also enlighten relevant research based on the lattices with type-II Dirac cones.