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成果及论文

代码和软件

  1. LAMMPS-RBE: Random batch Ewald is a fast algorithm for electrostatic interactions in molecular dynamics simulations.  A brief introduction of this algorithm can be found at link. The CPU version of the package is now available for tests at the πcluster.

  2. HSMA3D and HSMA2D: Harmonic surface mapping algorithm for electrostatic interaction in MD simulations of particle systems of 3D periodicity (HSMA3D) or doubly periodic slit with dielectric interfaces along one direction (HSMA2D).
  3. HybridMD: MD package for simulating nanoparticle self-assembly. It is based on a novel hybrid ICM/moment method for fast and accurate calculation of the Poisson’s equation with closely-packed dielectric spheres and ions.
  4.  VPMR: Matlab code for SOE and SOG approximations using de la Vallée-Poussin sums – based model reduction.


部分发表论文

2022年

  1. Superscalability of the random batch Ewald method, J. Liang, P. Tan, Y. Zhao, L. Li, S. Jin, L. Hong and Z. Xu, J. Chem. Phys.,  156 (2022), 014114. arXiv: 2106.05494

  2. HSMA: An O(N) electrostatics package implemented in LAMMPS, J. Liang, J. Yuan and Z. Xu, Comput. Phys. Commun., 276(2022), 108332. arXiv: 2104.05260Code

  3. Improved random batch Ewald method in molecular dynamics simulations, J. Liang, Z. Xu and Y. Zhao, J. Phys. Chem. A, in press. arXiv: 2204:13595

  4. C. Liu, C. Wang, S. M. Wise, X. Yue, and S. Zhou, A second order accurate numerical method for the Poisson-Nernst-Planck system in the energetic variational formulation, Submitted, 2022

  5. Z. Qiao, Z. Xu, Q. Yin, and S. Zhou, An Ampère-Nernst-Planck model for dynamics of charges, Submitted, 2022

  6. Y. Qian, C. Wang, and S. Zhou, Convergence analysis on a structure-preserving numerical scheme for the Poisson-Nernst-Planck-Cahn-Hilliard system, Submitted, 2022



2021年

  1. Linear-scaling selected inversion based on hierarchical interpolative factorization for self Green’s function for modified Poisson-Boltzmann equation in two dimensions, Y. Tu, Q. Pang, H. Yang and Z. Xu, J. Comput. Phys., in press. arXiv: 2105.09200

  2. Ion transport in electrolytes of dielectric nanodevices, M. Ma, Z. Xu and L. Zhang, Phys. Rev. E, 104 (2021), 035307

  3. The theoretical model, method and applications of scattering photon burst counting based on objective scanning technique, C. Dong, Q. Wang, Z. Xu, L. Deng, T. Zhang, B. Lu, Q. Wang, and J. Ren, Anal. Chem., 93 (2021), 12556-12564

  4. Bo Wang, Zhiguo Yang, Li-Lian Wang, Shidong Jiang, On time-domain NRBC for Maxwell‘s equations and its application in electromagnetic invisibility cloaks. Journal of Scientific Computing, 86 (2), 1-34, 2021

  5. Zhiguo Yang, Li-Lian Wang, Yang Gao, A truly exact perfect absorbing layer for time-harmonic acoustic wave scattering problems. SIAM Journal of Scientific Computing, 43 (2), A1027-A1061, 2021.

  6. B. Li, Z. Zhang, and S. Zhou, The Calculus of Boundary Variations and the Dielectric Boundary Force in the Poisson--Boltzmann Theory for Molecular Solvation, To appear in J. Nonlinear Sci., 2021.

  7. S. Zhou, Y. Zhang, L. Cheng, and B. Li, Prediction of multiple dry-wet transition pathways with a mesoscale variational approach, To appear in J. Chem. Phys., 2021.

  8. An EIM-degradation free reduced basis method via over collocation and residual hyper reduction-based error estimation, Y. Chen, S. Gottlieb, L. Ji and Y. Maday, to be published at J. Comput. Phys., arXiv:2101.05902

  9. Modified Poisson-Nernst-Planck model with Coulomb and hard-sphere correlations, M. Ma, Z. Xu and L. Zhang, to be published at SIAM J. Appl. Math.. arXiv: 2002.07489

  10. A random batch Ewald method for particle systems with Coulomb interactions, S. Jin, L. Li, Z. Xu and Y. Zhao, to be published at SIAM J. Sci. Comput.. arXiv: 2010.01559

  11. A kernel-independent sum-of-Gaussians method by de la Vallée-Poussin sums, J. Liang, Z. Gao and Z. Xu, to be published at Adv. Appl. Math. Mech.. arXiv: 2010.05192, Code

  12. L1-based reduced over-collocation and hyper reduction for steady state and time-dependent nonlinear equations, Y. Chen, L. Ji, A. Narayan and Z. Xu, J. Sci. Comput. 87(2021), 10. arXiv: 2009.04812

  13. A high-accurate fast Poisson solver based on harmonic surface mapping algorithm, J. Liang, P. Liu and Z. Xu, Commun. Comput. Phys., 30 (2021), 210-226.

  14. C. Liu, C. Wang, S. M. Wise, X. Yue, and S. Zhou, A positivity-preserving, energy stable and convergent numerical scheme for the Poisson--Nernst--Planck system, Math. Comput. , In Press, 2021.

  15. Y. Qian, C. Wang, and S. Zhou, A Positive and Energy Stable Numerical Scheme for the Poisson--Nernst--Planck--Cahn--Hilliard Equations with Steric Interactions, J. Comput. Phys. , 426, 109908, 2021.

  16. C. Duan, W. Chen, C. Liu, X. Yue, and S. Zhou, Structure-Preserving Numerical Methods for Nonlinear Fokker--Planck Equations with Nonlocal Interactions by an Energetic Variational Approach, SIAM J. Sci. Comput. , 43(1), B82-B107, 2021.

2020年

  1. Harmonic surface mapping algorithm for molecular dynamics simulations of particle systems with planar dielectric interfaces, J. Liang, J. Yuan, E. Luijten and Z. Xu, J. Chem. Phys., 152 (2020), 134109.

  2. A random-batch Monte Carlo method for many-body systems with singular kernels, L. Li, Z. Xu and Y. Zhao, SIAM J. Sci. Comput., 42 (2020), A1486–A1509. arXiv: 2003.06554

  3. Effects of kinetic dielectric decrement on ion diffusion and capacitance in electrochemical systems, L. Qing, J. Lei, T. Zhao, G. Qiu, M. Ma, Z. Xu and S. Zhao, Langmuir, 36 (2020), 4055-4064.

  4. J. Ding, H. Sun, and S. Zhou, Hysteresis and Linear Stability Analysis on Multiple Steady-State Solutions to the Poisson--Nernst--Planck equations with Steric Interactions: A Numerical Approach, Phys. Rev. E , 102, 053301, 2020.

  5. J. Ding, Z. Wang, and S. Zhou, Structure-Preserving and Efficient Numerical Methods for Ion Transport, J. Comput. Phys. , 418, 109597, 2020.

  6.  Yanxia Qian, Zhiguo Yang, Suchuan Dong,  gPAV-based unconditionally energy-stable schemes for the Cahn-Hilliard equation: stability and error analysis. Computer Methods in Applied Mechanical Engineering,Vol.372,113444,2020.                                              

  7. Fukeng Huang, Jie Shen, Zhiguo Yang (corr), A highly efficient and accurate new scalar auxiliary variable approach for gradient flows. SIAM Journal of Scientific Computing, Vol. 42(4), A2514-A2536, 2020.

  8. Lianlei Lin, Naxian Ni, Zhiguo Yang, Suchuan Dong, An energy-stable scheme for incompressible Navier-Stokes equations with periodically updated coefficient matrix. Journal of Computational Physics, Vol. 418, 109624 , 2020.

  9. Zhiguo Yang, Suchuan Dong, A roadmap for discretely energy-stable schemes for dissipative systems based on a generalized auxiliary variable with guaranteed positivity. Journal of Computational Physics, Vol. 404, 109-121, 2020.

2019年

  1. Efficient dynamic simulations of charged dielectric colloids through a novel hybrid method, Z. Gan, Z. Wang, S. Jiang, Z. Xu and E. Luijten, J. Chem. Phys., 151, 024112 (2019). This paper has been selected the 2019 Editors’ Choice Collection.

  2. A reduced basis method for the nonlinear Poisson-Boltzmann equation, L. Ji, Y. Chen and Z. Xu, Adv. Appl. Math. Mech., 11 (2019), pp. 1200-1218. arXiv: 1808.09392

  3. S. Zhou, R. G. Weiss, L. Cheng, J. Dzubiella, J. A. McCammon, and B. Li, Variational implicit-solvent predictions of the dry-wet transition pathways for ligand-receptor binding and unbinding kinetics, Proc. Natl Acad. Sci. USA (PNAS) , 116(30), 14989-14994, 2019.

  4. J. Ding, Z. Wang, and S. Zhou, Positivity Preserving Finite Difference Methods for Poisson–Nernst–Planck Equations with Steric Interactions: Application to Slit-Shaped Nanopore Conductance, J. Comput. Phys. , 397, 108864, 2019.

  5. X. Ji and S. Zhou, Variational Approach to Concentration Dependent Dielectrics with the Bruggeman Model: Theory and Numerics, Commun. Math. Sci. , 17(7), 1949-1974, 2019.

  6. Y. Qian, Z. Wang, and S. Zhou, A conservative, free energy dissipating, and positivity preserving finite difference scheme for multi-dimensional nonlocal Fokker–Planck equation, J. Comput. Phys., 386, 22-36, 2019.

  7. J. Ding, C. Wang, and S. Zhou, Optimal rate convergence analysis of a second order numerical scheme for the Poisson--Nernst--Planck system, Numer. Math.: Theory, Methods and Appl. , 12, 607-626, 2019.

  8. Zhiguo Yang, Suchuan Dong, An unconditionaly energy-stable scheme based on an implicit energy variable for incompressible two-phase flows of different densities involving only precomputable coefficient matrices. Journal of Computational Physics, Vol. 393,  229--257, 2019.

  9. Lianlei Lin, Zhiguo Yang, Suchuan Dong, Numerical approximation of incompressible Navier-Stokes equations based on an auxiliary energy variable. Journal of Computational Physics, Vol. 388, 1--22, 2019.

  10. Naxian Ni, Zhiguo Yang, Suchuan Dong, Energy-stable boundary conditions based on a quadratic form: applications to outflow/open-boundary problems in incompressible flows. Journal of Computational Physics, Vol. 391, 179--215, 2019.

  11. Zhiguo Yang, Lianlei Lin, Suchuan Dong, A family of second-order energy-stable schemes for Cahn–Hilliard type equations.  Journal of Computational Physics, Vol. 383, 24--54, 2019.