We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures,...We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.展开更多
By using three-dimensional particle-in-cell simulations, externally injected electron beam acceleration and radiation in donut-like wake fields driven by a Laguerre-Gaussian pulse are investigated. Studies show that i...By using three-dimensional particle-in-cell simulations, externally injected electron beam acceleration and radiation in donut-like wake fields driven by a Laguerre-Gaussian pulse are investigated. Studies show that in the acceleration process the total charge and azimuthal momenta of electrons can be stably maintained at a distance of a few hundreds of micrometers. Electrons experience low-frequency spiral rotation and high-frequency betatron oscillation, which leads to a synchrotron-like radiation. The radiation spectrum is mainly determined by the betatron motion of electrons. The far field distribution of radiation intensity shows axial symmetry due to the uniform transverse injection and spiral rotation of electrons. Our studies suggest a new way to simultaneously generate hollow electron beam and radiation source from a compact laser plasma accelerator.展开更多
The shock wave acceleration of ions driven by laser-heated thermal pressure is studied through one-dimensional particle-in-cell simulation and analysis. The generation of high-energy mono-energetic protons in recent e...The shock wave acceleration of ions driven by laser-heated thermal pressure is studied through one-dimensional particle-in-cell simulation and analysis. The generation of high-energy mono-energetic protons in recent experiments （D. Haberberger et al., 2012 Nat. Phys. 8 95） is attributed to the use of exponentially decaying density profile of the plasma target. It does not only keep the shock velocity stable but also suppresses the normal target normal sheath acceleration. The effects of target composition are also examined, where a similar collective velocity of all ion species is demonstrated. The results also give some reference to future experiments of producing energetic heavy ions.展开更多
基金Supported by the National Natural Science Foundation of China under Grant Nos 31200545,11274206 and 11574184
文摘We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11374209,11374210,and 11774227)the Major State Basic Research Development Program of China(Grant No.2015CB859700)
文摘By using three-dimensional particle-in-cell simulations, externally injected electron beam acceleration and radiation in donut-like wake fields driven by a Laguerre-Gaussian pulse are investigated. Studies show that in the acceleration process the total charge and azimuthal momenta of electrons can be stably maintained at a distance of a few hundreds of micrometers. Electrons experience low-frequency spiral rotation and high-frequency betatron oscillation, which leads to a synchrotron-like radiation. The radiation spectrum is mainly determined by the betatron motion of electrons. The far field distribution of radiation intensity shows axial symmetry due to the uniform transverse injection and spiral rotation of electrons. Our studies suggest a new way to simultaneously generate hollow electron beam and radiation source from a compact laser plasma accelerator.
基金Project supported by the Shanghai Natural Special Foundation for Outstanding Young Teachers in University,China(Grant No.yyy10043)
文摘The shock wave acceleration of ions driven by laser-heated thermal pressure is studied through one-dimensional particle-in-cell simulation and analysis. The generation of high-energy mono-energetic protons in recent experiments （D. Haberberger et al., 2012 Nat. Phys. 8 95） is attributed to the use of exponentially decaying density profile of the plasma target. It does not only keep the shock velocity stable but also suppresses the normal target normal sheath acceleration. The effects of target composition are also examined, where a similar collective velocity of all ion species is demonstrated. The results also give some reference to future experiments of producing energetic heavy ions.
