Research Summary (November 2009)

Current Research

• Mathematics and Biochemistry-Biophysics - Research Initiative. (people, research description, publications, presentations, funding, etc.)
  Informal Seminars on Mathematics and Biochemistry-Biophysics
• Computational modeling and numerical analysis of solvation of molecules, PI, NSF grant DMS-0811259, 7/1/2008 - 6/30/2011.
• Senior Scientist of the Center for Theoretical Biological Physics (CTBP), an NSF Physics Frontiers Center located at UC San Diego, NSF PHY-0822283, 7/1/2008 - 6/30/2013.
• Multiscale design of advanced materials based on hybrid ab initio and quasicontinuum methods, Co-PI, DOE grant DE-FG02-05ER25707, 8/15/2005 - 8/14/2009.
• Book project: Weak Convergence Methods for Variational Models of Crystalline Solids, Springer-Verlag, 2009.

Recent Publications

• Li-Tien Cheng, Joachim Dzubiella, J. Andrew McCammon, and Bo Li, Application of the level-set method to the implicit solvation of nonpolar molecules, J. Chem. Phys., 127, 084503, 2007. (Preprint)
        Note: This article was selected for republication in The Virtual J. of Nanoscale Sci. & Tech., Volume 16, Issue 10, 2007.
• Yan Gong, Bo Li, and Zhilin Li, Immersed-interface finite-element method for elliptic interface problems with non-homogeneous jump conditions, SIAM J. Numer. Anal., 46(1), 472-495, 2008. (Reprint - permission and copyright of SIAM)
• Jianwei Che, Joachim Dzubiella, Bo Li, and J. Andrew McCammon, Electrostatic free energy and its variations in implicit solvent models, J. Phys. Chem. B, 112(10), 3058-3069, 2008. (Preprint)
• Bo Li, John Lowengrub, Andreas Ratz, and Axel Voigt, Geometric evolution laws for thin crystalline films: modeling and numerics, Commun. Comput. Phys., 6(3), 433-482, 2009. (Preprint)
• Li-Tien Cheng, Yang Xie, Joachim Dzubiella, J. Andrew McCammon, Jianwei Che, and Bo Li, Coupling the level-set method with molecular mechanics for variational implicit solvation of nonpolar molecules, J. Chem. Theory Comput., 5(2), 257-266, 2009. (Preprint)
• Bo Li, Minimization of electrostatic free energy and the Poisson-Boltzmann equation for molecular solvation with implicit solvent, SIAM J. Math. Anal., 40, 2536-2566, 2009. (Reprint - permission and copyright of SIAM)
• Bo Li, Continuum electrostatics for ionic solutions with nonuniform ionic sizes, Nonlinearity, 22, 811-833, 2009. (Preprint, published version at the journal website.)
        Note: This article was selected for inclusion in IOP (Institute of Physics) Select. Subject: Applied Mathematics and Mathematical Physics. From the IOP website: IOP select comprises ``articles chosen by our Editors for their novelty, significance and potential impact on future research", and ``reflects both the breadth and international significance of papers published in our prestigious peer reviewed journals."
• Li-Tien Cheng, Zhongming Wang, Piotr Setny, Joachim Dzubiella, Bo Li, and J. Andrew McCammon, Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach, J. Chem. Phys., 131, 144102, 2009. (Preprint)
        Note: This article was selected for republication in The Virtual J. of Biological Physics Research, Volume 18, Issue 8, 2009.
• Piotr Setny, Zhongming Wang, Li-Tien Cheng, Bo Li, J. Andrew McCammon, and Joachim Dzubliella, Dewetting-controlled binding of ligands to hydrophobic pockets, Phys. Rev. Lett., 103, 187801, 2009. (Preprint)
        Note: This article was selected for republication in The Virtual J. of Biological Physics Research, Volume 18, Issue 9, 2009.
• Bo Li, Zhongming Wang, Benzhuo Lu, and J. Andrew McCammon, Solutions to a reduced Poisson-Nernst-Planck system and determination of reaction rates, Physica A, 2009 (submitted). (Preprint)

Recent Presentations

• Bo Li, Surface Relaxation vs. the Ehrlich-Schwoebel Effect in Thin-film Growth, Workshop: Nonequilibrium Interface Dynamics: Theory and Simulation from Atomistic to Continuum Scales, University of Maryland, April 23-27, 2007.
• Bo Li, Coupling the Level-Set Method with Variational Implicit Solvent Modeling of Molecular Solvation. Variations of this talk were given in Summer School: Coarse-Grained Physical Modeling of Biological Systems: Advanced Theory and Methods, August 11-15, 2008, and Seminar, October 10, 2008, Center for Theoretical Biological Physics, UC San Diego, and in the IMA workshop: Solvation, December 8-12, 2008.
• Bo Li, The Poisson-Boltzmann Theory of Continuum Electrostatics with Application to Variational Solvation of Molecules. Variations of this talk were given in Informal Seminar on Mathematics and Biochemistry-Biophysics, UC San Diego, February 3, 2009, and International Workshop on Selected Topics in Mathematical and Numerical Aspects of Materials and Biological Sciences, Zhejiang University, Hangzhou, China, September 11, 2009.
• Bo Li and Zhongming Wang, Solutions to a Model Poisson-Nernst-Planck System and the Determination of Reaction Rates, International Workshop on Selected Topics in Mathematical and Numerical Aspects of Materials and Biological Sciences, Zhejiang University, Hangzhou, China, September 11, 2009.
• Bo Li, Level-Set Variational Solvation Coupling Solute Molecular Mechanics with Continuum Solvent, International Workshop on Continuum Modeling of Biomolecules, Institute of Computational Mathematics and Scientific/Engineering Computing, Chinese Academy of Sciences, Beijing, China, September 14-16, 2009.
• Bo Li, Continuum Electrostatics for Ionic Solutions with Nonuniform Ionic Sizes, Seminar of Institute of Computational Mathematics and Scientific/Engineering Computing, Chinese Academy of Sciences, Beijing, China, September 18, 2009.

Recent Conferences, Workshops, and Summer Schools

• Summer School: Coarse-Grained Physical Modeling of Biological Systems, the NSF Center for Theoretical Biological Physics, UC San Diego, August 11-15, 2008.
• Workshop on Solvation, Institute for Mathematics and Its Applications, Universty of Minnesota, December 8-12, 2008.
• Molecular Simulation & Structure Prediction using CHARMM & the MMTSB Tool Set,, Summer School, Center for Theoretical Biological Physics, UC San Diego, August 4-7, 2009.
• International Workshop on Selected Topics in Mathematical and Numerical Aspects of Materials and Biological Sciences, Department of Mathematics, Zhejiang University, Hangzhou, China, September 11, 2009.
• International Workshop on Continuum Modeling of Biomolecules, Institute of Computational Mathematics and Scientific/Engineering Computing, Chinese Academy of Sciences, Beijing, China, September 14-16, 2009.
• Workshop: Interface Problems in Fluids and Materials, Center of Mathematical Modeling and Scientific Computing (CMMSC), National Chiao Tung University, Taiwan, December 18-20, 2009.

Seminars and Colloquia

• 2009-2010 Department of Mathematics Colloquium
• Informal Seminars on Mathematics and Biochemistry-Biophysics
• Center for Theoretical Biological Physics seminars

Teaching in Fall quarter 2009

• Math 210A: Mathematical Methods in Physical Sciences and Engineering, Fall quarter, 2009

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