Recent Publications

 

1.     J. Ying and D. Xie: A New Finite Element and Finite Difference Hybrid Method for Computing Electrostatics of Ionic Solvated Biomolecule, Journal of Computational Physics, Vol. 298, pages 636-651, 2015. [pdf]

2.     D. Xie and J. Ying: A New Box Iterative Method for a Class of Nonlinear Interface Problems with Application in Solving Poisson-Boltzmann Equation, submitted to Journal of Computational and Applied Mathematics, 2015.

3.     H. Volkmer, J. Yang, and D. Xie: Analytical Solutions of Two Nonlocal Poisson Dielectric Test Models with Spherical Solute Region Containing Multiple Point Charges, submitted, 2015.

4.     J. Ying and D. Xie: A Hybrid Solver of Size Modified Poisson-Boltzmann Equation by Domain Decomposition, Finite Element, and Finite Difference, submitted, 2015.

5.     L. R. Scott and D. Xie: Analysis of a Nonlocal Poisson-Boltzmann Equation, submitted, 2015.

6.     D. Xie and J. Li: A New Analysis of Electrostatic Free Energy Minimization and Poisson-Boltzmann Equation for Protein in Ionic Solvent, Nonlinear Analysis: Real World Applications, Vol. 21, pages 185-196, 2015. [pdf]

7.     J. Li and D. Xie: An Effective Minimization Protocol for Solving a Size-modified Poisson-Boltzmann Equation for Biomolecule in Ionic Solvent, International Journal of Numerical Analysis & Modeling, Vol. 12, No. 2, pages 286-301, 2015. [pdf]

8.     J. Li and D. Xie: A New Linear Poisson-Boltzmann Equation and Finite Element Solver by Solution Decomposition Approach, Communications in Mathematical Sciences, Vol. 13, No. 2, pages 315-325, 2015. [pdf]

9.     D. Xie and Y. Jiang: A Nonlocal Modified Poisson-Boltzmann Equation and Finite Element Solver for Computing Electrostatics of Biomolecules, submitted, 2014.

10.  D. Xie: New Solution Decomposition and Minimization Schemes for Poisson-Boltzmann Equation in Calculation of Biomolecular Electrostatics, Journal of Computational Physics, Vol. 275, pages 294-309, 2014. [pdf]

11.  Y. Jiang, J. Ying, and D. Xie: A Poisson-Boltzmann Equation Test Model for Protein in Spherical Solute Region and its Applications, Molecular Based Mathematical Biology, Vol. 2, pages 86-97, 2014. Open Access. [pdf]

12.  D. Xie, Y. Jiang, and L. R. Scott: Efficient algorithms for solving a nonlocal dielectric model for protein in ionic solvent, Vol. 35, No. 6, pages B1267-1284, SIAM Journal on Scientific Computing, 2013.  [pdf]

13.  D. Xie and H. Volkmer: A modified nonlocal continuum electrostatic model for protein in water and its analytical solutions for ionic Born models, Communications in Computational Physics, the special issue entitled  “Modeling Electrostatics in Molecular Biology”, Vol. 13, No. 1, pages 174-194, 2013. [pdf]

14.  D. Xie, Y. Jiang, P. Brune, and L. R. Scott: A fast solver for a nonlocal dielectric continuum model, SIAM Journal on Scientific Computing, Vol. 34, No. 2, B107-B126, 2012. [pdf]

15.  D. Xie: An improved approximate Newton for implicit Runge-Kutta methods, Journal of Computational and Applied Mathematics, Vol. 235, No. 17, pages 5249-5258, 2011. [pdf]

16.  D. Xie and L. R. Scott: A new boundary integral equation for molecular electrostatics with charges over whole space, BIT Numerical Mathematics, Vol. 51, No. 4, pages 1051-1071, 2011. [pdf]

17.  D. Xie and M. G. Zarrouk: Convergence analysis of truncated incomplete Hessian Newton minimization method and application in biomolecular potential energy minimization, Computational Optimization and Applications, DOI 10.1007/s1058-009-9252-7, Vol. 48, No. 2, pages 213-232, 2011. [pdf]

18.  D. Xie: A new boundary integral equation for computing biomolecular electrostatics, Proceedings of the 10th International Conference on Computational and Mathematical Methods in Science and Engineering, CMMSE 2010, Madison, 24-26 May, 2010.

19.   D. Xie: An effective sparse compressed natural preconditioner by biomolecular structure, to be submitted, 2010.

20.  D. Xie and L. R. Scott: An analysis of parallel U-cycle method, Tech Report TR-2010-03, University of Chicago, April 20, 2010.

21.  D. Xie: New parallel symmetric SOR preconditioners by multi-type partitioning, Journal of Computer Mathematics, Vol. 86, No. 2, pages 287-300, 2009. [pdf]

22.  D. Xie, R. K. Dash, and D. A. Beard: An improved algorithm and its parallel implementation for solving a general blood-tissue transport and metabolism model, Journal of Computational Physics, Vol. 228, No. 20, pages 7850-7861, 2009. [pdf]

23.  X. Li, K. J. Nevels1, Z. Gryczynski, I. Gryczynski, M. Pusztai-Carey, D. Xie, and P. Butko: A molecular dynamics model of Bt toxin Cyt1A and its validation by resonance energy transfer, Biophysical Chemistry, Vol. 144, pages 53-61, 2009.

24.  D. Xie and Q. Ni: An incomplete Hessian Newton minimization method and its application in a chemical database problem, Computational Optimization and Applications, Vol. 44, No. 3, pages 467-485, 2009. [pdf]

25.  D. Xie and S. Zhou: A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation, BIT Numerical Mathematics, Vol. 47, pages 853-871, 2007. [pdf]

26.  D. Xie: New parallel symmetric SOR preconditioners by multi-type partitioning, Proceedings of the International Conference on Computational and Mathematical Methods in Science and Engineering, CMMSE 2007, Chicago, 20-23 June, 2007, pages 418-428.

27.  X. Li, K. J. Nevels, D. Xie, and P. Butko: Molecular Dynamics Simulations of the Bt Toxin Cyt1A in Solution, Proceeding of 15th Conference on Current Trends in Computational Chemistry, Jackson, Mississippi, Nov. 3-4, 2006, pages 232-234.

28.  D. Xie: A new block parallel SOR method and its analysis, SIAM J. Sci. Comput., Vol. 27, No. 5,pages 1513-1533, 2006. [pdf]

29.  J. Xie, P. Butko, and D. Xie: Molecular dynamics simulations of the cytolytic toxin Cyt1A in solution, IEEE Trans. Nanobioscience, Vol. 4, No. 3, pages 235-240, 2005. [pdf]

30.  D. Xie: Analysis of a class of parallel multigrid smoothers, BIT Numerical Mathematics, Vol. 44, pages813-828, 2004. [pdf]

31.  D. Xie: An effective sparse compressed preconditioner for large scale biomolecular simulations, Lecture Notes in Computer Science, Vol. 3314, Edited by J. Zhang etc., Springer-Verlag, pages 64-70, 2004. (Proceedings of the International Symposium on Computational and Information Sciences. Shanghai, China, December 16-18, 2004.) [pdf]

32.  D. Xie: New block parallel SOR methods by multi-type partitions, Proceedings of International Conference on Parallel Processing Workshop, Montreal, Canada, August 15-18, 2004, IEEE Computer Society Press.

33.  D. Xie: Visualization of large chemical databases with application to drug design, one chapter of Numerical Linear Algebra and Optimization, edited by Y. Yuan, Science Press (Beijing/New York), pages 81-97, 2003. [pdf]

34.  D. Xie, S. B. Singh, E. M. Fluder, and T. Schlick: Principal component analysis combined with truncated-Newton minimization for dimensionality reduction of chemical databases, Mathematical Programming, Vol. 95, No. 1, pages 161-185, 2003. [pdf]

35.  D. Xie and T. Schlick: A more lenient stopping rule for line search algorithms, Optimization Methods and Software, Vol. 17, No. 4, pages 683-700, 2002. [pdf]

36.  D. Xie, L. R. Scott, and T. Schlick: Analysis of the SHAKE-SOR algorithm for constrained molecular dynamics simulations, Methods and Applications of Analysis, Vol. 7, No. 3, page 577-590, 2000. [pdf]

37.  D. Xie and T. Schlick: Visualization of chemical databases using the singular value decompositionand truncated-Newton minimization, Optimization in Computational Chemistry and Molecular Biology: Local and Global Approaches, C. A. Floudas and P. M. Pardalos, Editors, Nonconvex Optimization and Its Applications, Kluwer Academic Publishers, Vol. 40, pages 267-286, 2000.

38.  D. Xie, A. Tropsha, and T. Schlick: An efficient projection protocol for chemical databases: the singular value decomposition combined with truncated-Newton minimization, Journal of Chemical Information and Computer Sciences, Vol. 40, pages 167-177, 2000. [pdf]

39.  L. R. Scott and D. Xie: Parallel Linear Stationary Iterative Methods, Parallel Solution of Partial Differential Equations, P. Bjorstad and M. Luskin, Editors, IMA Volumes in Mathematics and Its Applications, Springer-Verlag, Vol. 120, pages 31-55, 2000. [pdf]

40.  D. Xie and T. Schlick: Efficient implementation of the truncated-Newton algorithm for large-scale chemistry applications, SIAM J. Opt., Vol. 10, pages 132-154, 1999. [pdf]

41.  D. Xie and L. Adams: New Parallel SOR Method by Domain Partitioning, SIAM J. on Scientific Computing, Vol. 20, No. 6, pages 2261-2281, 1999. [pdf]

42.  D. Xie and T. Schlick: Remark on Algorithm 702---The Updated Truncated Newton Minimization Package, ACM Trans. on Math. Software, Vol. 25, No. 1, pages 108-122, 1999. [pdf]

43.  D. Xie, New nonlinear multigrid analysis, Proceedings of 1995 Copper Mountain Conference on Multigrid Methods, NASA Conference Publication 3339, 1996. [pdf]

44.  D. Xie, New parallel iterative methods, new nonlinear multigrid analysis, and application in computational chemistry, Research report UH/MD 208, Ph.D. thesis, University of Houston, 1995.

45.  B. Bagheri, A. Ilin, J. A. McCammon, L. R. Scott, and D. Xie: Parallel algorithms for biomolecular modeling, Proceedings of the Workshop on Algorithms for Macromolecular Modeling, pages 77-82, Lawrence, KA, September 1994.

46.  L. R. Scott, B. Bagheri, A. Ilin, and D. Xie: Parallel solution of elliptic boundary value problems, Proceedings of the Third International Workshop on Computational Electronics, Portland, OR, May 1994. Added to ScientificCommons in 2008.

47.  D. Xie, The convergence of the non-linear multigrid methods for solving a kind of finite element equation, J. Comp. Math., 1, 1993, (in Chinese). [pdf]

48.  D. Xie, On the essential assumptions of multigrid convergence proofs, J. Comp. Math., Supplementary Issue, pages 158-164, 1992, (in Chinese).

49.  D. Xie, On the essential assumption and convergence estimation of multigrid analysis, J. Hunan University, 17, pages 103-112, 1990, (in Chinese).

50.  D. Xie, A new multigrid iteration for solving interface problems with small media ratio, Comm. Appl. Math. Comput., 1, pages 47-57, 1987, (in Chinese).

51.  D. Xie, Analysis of the multigrid iterative algorithms, J. Hunan University, 13, pages 231-237, 1986 (in Chinese).

 

Last modified April 1, 2015