Chao Yang

Phone:	(510)486-6424
Fax:	(510)486-5812
e-mail:	cyang@lbl.gov

Three-dimensional Image Reconstruction for Cryo-Electron Microscopy
Large-scale Eigenvalue Calculation with Applications in Electromagetics
Large-scale Normal Coordinate Analysis for Molecular Vibrations
Scalable Parallel Software for Interior Eigenvalue Calculation

Recent Publication:

• Accelerating Full Configuration Interaction Calculations for Nuclear Structure with P. Sternberg, P. Maris, E. Ng, M. Sosonkina, H. V. Le and J. Vary , LBNL Report-591E , accepted by Supercomputing 2008, 2008

• V. Donde, V. Lopez, B. Lesieutre, A. Pinar, C. Yang and J. Meza. Severe multiple contingency screening in electric power systems. IEEE Trans. on Power Systems , vol. 23, no. 2, pp. 406--417, 2008.

• KSSOLV: a MATLAB Toolbox for Solving the Kohn-Sham Equations with B. Lee, J. Meza and L. W. Wang , LBNL Report 63624 , submitted, 2007.

• On the Convergence of the Self-consistent Field Iteration for a Class of Nonlinear Eigenvalue Problems with W. Gao and J. Meza LBNL Report 63037 , 2007.

• An Implementation and Evaluation of the AMLS Method for Sparse Eigenvalue Problems with W. Gao, X. S. Li and Z. Bai LBNL Report 57438 , accepted ACM Transactions on Mathematical Software , 2007.

• A Trust Region Direct Constrained Minimization Algorithm for the Kohn-Sham Equation with J. C. Meza and L. Wang, LBNL Report 59841 , SIAM Journal of Scientific Computing , vol 29, pp 1854-1875, 2007.

• SPARX: a new environment for Cryo-EM imaging processing M. Hohn, G. Tang, G. Goodyear, P. R. Baldwin, Z. Huang, P. A. Penczek, C. Yang, R. M. Glaeser, P. D. Adams, S. J. Ludtke. Journal of Struct. Biology , vol. 157, pages 47-55, 2007.

• The Parallelization of SPIDER on Distributed-memory Computer using MPI with P. A. Penczek, A. Leith, F. J. Asturias, R. M. Glaeser and J. Frank, Journal of Struct. Biology , vol. 157, pages 240-249, 2007.

• From Self-consistency to SOAR: Solving nonlinear eigenvalue problems with Z. Bai , SIAM News , April, 2006.

• P. A. Penczek, C. Yang, J. Frank and C. M. T. Spahn, Estimation of variance in single-particle reconstruction using the bootstrap technique , Journal of Structural Biology , vol. 154, pages 168-183, 2006

• A Constrained Optimization Algorithm for Total Energy Minimization in Electronic Structure Calculation with J. C. Meza and L. Wang. Journal of Computational Physics , vol 217, pages 709-721, 2006.

• Solving Large-scale eigenvalue problems in SciDAC applications LBNL Report 58339 , Journal of Physics, Conference Series, vol. 16, SciDAC 2005, pages 425-434, 2005.

• Algebraic Sub-structuring for Electromagnetic Applications with W. Gao, Z. Bai, X. S. Li, L. Lee, P. Husbands and E. G. Ng Proceedings for the Para'04 Workshop on State-of-the-art in Scientific Computing, editor Jack Dongarra, Kaj Madsen, and Jerzy Wasniewski, Lecture Notes in Computer Science, vol. 3732, pages 364-373 , 2005.

• Unified 3-D structure and projection orientation refinement using Quasi-newton algorithm with E. G. Ng and P. A. Penczek J. Structure Biology , vol 149, pages 53-64, 2005.

• An Algebraic Sub-structuring Algorithm for Large-scale Eigenvalue Calculation with W. G. Gao, Z. Bai, X. Li, L. Lee, P. Husbands and E. G. Ng. LBNL Tech Report, No. 55050, SIAM J. Sci. Comp., vol. 27, no. 3, pages 873-892, 2005.

• Matrix-free Constructions of Circulant and Block Circulant Preconditioners with E. G. Ng and P. A. Penczek, Numerical Linear Algebra with Applications, Vol. 11, pages 773-793, 2004.

• Vibrational Normal Modes of Polymer Nanoparticle Dimers Using the Time Averaged Normal Coordinate Analysis Method with B. C. Hathorn, B. G. Sumpter, D. W. Noid and R. E. Tuzun J. of Physical Chemistry , vol 106, No. 40, pp 9174-9180, 2002.

• Normal coordinate analysis for polymer systems: capabilities and new opportunities , with R. E. Tuzun, D. W. Noid, B. G. Sumpter. Macromolecular Theory and Simulations 11, pp 711-728, 2002.

• Large-scale Normal Coordinate Analysis on Distributed Memory Parallel Systems with P. Raghavan, L. Arrowood, D. W. Noid, B. G. Sumpter, and R. E. Tuzun, International Journal on High Performance Computing Applications , vol 16. No. 4, pp. 409-424, 2002.

• An Efficient Algorithm for Calculating the Heat Capacity of a Large-scale Molecular System with D. W. Noid, B. G. Sumpter, D. C. Sorensen and R. E. Tuzun, Macromolecular Theory and Simulations , 10, 756-761, 2001

• Large-scale Normal Coordinate Analysis for Molecular Structures with B. W. Peyton, D. W. Noid, B. G. Sumpter and R. E. Tuzun, SIAM J. Sci. Comp. , vol 23, no. 2, 563-582, 2001.

• Analysis of Eigenvalues and Eigenvectors of Polymer Particles: Random Normal Modes with D. W. Noid, K. Fukui, B. G. Sumpter and R. E. Tuzun, vol. 11, 191-196, Computational and Theoratical Polymer Sciences , 2001.

• Computing the Density of States for Large-scale Polymer Systems with D. W. Noid, K. Fukui, B. G. Sumpter and R. E. Tuzun. Macromolecular Theory and Simulations , vol. 9, 428-432, 2000

• Multi-level Methods for Large-scale Eigenvalue Calculation , with W. F. Lawkins, ORNL Technical Report TM-2000/43, 2000.

• Spectral Analysis for Macromolecular System: Chain Length Effects in Polymer Particles , with D. W. Noid, K. Fukui, B. G. Sumpter and R. E. Tuzun. Journal of Polymer Science: Part B , vol. 38, 1812-1823, 2000.

• Large-scale Normal Coordinate Analysis of Macromolecular Systems: Thermal Properties of Polymer Particles and Crystals with D. W. Noid, K. Fukui, B. G. Sumpter and R. E. Tuzun. J. Physical Chemistry B., 104, 526-531, 2000.

• Time Averaged Normal Coordinate Analysis of Polymer Particles and Crystals with D. W. Noid, K. Fukui, B. G. Sumpter and R. E. Tuzun. Chem. Phys. Lett. 316, 285-296, 2000.

• Factorization-free Methods for Interior Eigenvalue Calculation . Iterative Methods in Scientific Computation IV, IMACS Series in Computational and Applied Mathematics , Vol 5, pp. 325-339, 1999

• Convergence Analysis of an Inexact Truncated RQ-Iteration ETNA, 7(4) pp. 40-55, 1998

• Accelerating the Arnoldi Iteration: Theory and Practice Ph.D Thesis, Department of Computational and Applied Mathematics, Rice University, Houston, Jan. 1998.

• A Truncated RQ-iteration for Large Scale Eigenvalue Calculations with D. C. Sorensen. SIAM Journal on Matrix Analysis and Applications , vol. 19, No. 4, 1998.

• ARPACK User's Guide -- Solution of Large-scale Eigenvalue Problems with Implicitly Restarted Arnoldi Methods with R.B. Lehoucq and D. C. Sorensen. SIAM series in software, environments and tools, SIAM 1998. ISBN 0-89871-407-9.

Research Interests:

Numerical Analysis
High Performance Computing
Mathematical Software