Math and Biochem-Biophysics Research Webpage - Bo Li

Mathematics and Biochemistry-Biophysics

RESEARCH INITIATIVE

People

Faculty

Postdocs
  • Zhongming Wang (Math and Biochem, UCSD)

Graduate Students
  • Allison Cuttler (Math, UCSD)
  • Maryann Hohn (Math, UCSD)
  • John Shopple (Math, UCSD)

Undergraduate Students
  • Diego Onuchic (Math, UCSD)
  • Raul Serrano (Math and Biochemistry, UCSD)

Collaborators
  • Jianwei Che (Genomics Institute of Novartis Research Foundation)
  • Joachim Dzubiella (Biophysics, Tech. Univ. Munich)
  • Benzhuo Lu (Institute of Computational Mathematics, Chinese Academy of Sciences)
  • Piotr Setny (Biophysics, University of Warsaw, Poland)
  • McCammon's group (Chemistry and Biochemistry, and CTBP, UCSD)
  • Yang Xie (Mechanical Engineering, Georgia Tech)

Research Interests

  • Biochemistry and biophysics: solvation, implicit solvent modeling, electrostatics, hydrophobic interactions, free energy landscapes and approximations, molecular forces, diffusion, protein folding, molecular recognition, ion transport, memberane structure and functions, single molecular systems, fluctuations in molecular systems, etc.

  • Mathematics: nonlinear PDE, the calculus of variations, nonlinear dynamical systems, geometrical measure theory, differential geometry, stochastic systems, numerical PDE, models and numerical methods for interface motion, the level-set method, fluid density functional approach, multiscale methods, etc.

Current Projects

  1. Level-set variational implicit solvent modeling, simulation, and analysis of the solvation of biomolecules with appilcations to molecular recognition and protein folding.
  2. Analysis and improvement of mean-field models of electrostatics in solvation systems. Size-modified Poisson-Boltzmann theory. Analysis and improvement of Generalized Born models.
  3. Singularities in geometrically based molecualr surface evolution: Hadwiger surfaces, level-set computation and analysis.
  4. Diffusion of ions and substrates in a molecular system. Wasserstein metric theory.
  5. Fluid density functional theory and numerical calculations for the solvation of biomolecules.
  6. Multiscale modeling and simulation of the molecular mechnics of solute atoms and the solute-solvent interface dynamics.

Recent Publications

  1. 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. Selected for Virtual J. of Nanoscale Sci. & Tech., Volume 16, Issue 10, 2007.
  2. Li-Tien Cheng, Efficient level set methods for constructing wavefronts in three spatial dimensions, J. Comp. Phys., 2007 (accepted).
  3. 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. (Published version in PDF - permission and copyright of SIAM.)
  4. 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 in PDF, published version in PDF at the journal website.)
  5. Bo Li, John Lowengrub, Andreas Ratz, and Axel Voigt, Geometric evolution laws for thin crystalline films: modeling and numerics, Review Article, Commun. Comput. Phys., 6(3), 433-482, 2009. (Preprint in PDF, published version in PDF at the journal website.)
  6. 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 in PDF, published version in PDF at the journal website.)
  7. 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. (Published version in PDF - permission and copyright of SIAM.)
  8. Bo Li, Continuum electrostatics for ionic solutions with nonuniform ionic sizes, Nonlinearity, 22, 811-833, 2009. Selected for inclusion in IOP Select - collected articles from the Institute of Physics. Subject: Applied Mathematics and Mathematical Physics. (Preprint in PDF, published version in PDF at the journal website.)
  9. Bo Li, Zhongming Wang, Benzhuo Lu, and J. Andrew McCammon, Solutions to a reduced Poisson-Nernst-Planck system and determination of reaction rates, 2009 (submitted). (Preprint in PDF.)
  10. P. Setny, Z. Wang, L.-T. Cheng, B. Li, J. A. McCammon, and J. Dzubliella, Dewetting-controlled binding of ligands to hydrophobic pockets, 2009 (submitted). (Preprint in PDF.)

Recent Presentations

  1. Bo Li, A Level-Set Variational Implicit Solvent Approach for Nonpolar Molecules. Talks given in Chinese Academy of Sciences, Summer 2006, the Second SIAM Conference on Computational Science and Engineering, Spring, 2007, and Zhejiang University, China, Summer 2007.
  2. Li-Tien Cheng, ICIAM, Zurich, 2007.
  3. Yang Xie, Modeling Non-Polar Molecules in Implicit Solvent Using the Level-Set Approach, Informal Seminar on Mathematics and Biochemistry-Biophysics, Department of Mathematics, UCSD, Summer 2007.
  4. John Shopple, Level Set Method in a Finite Element Setting, UCSD Computational and Applied Mathematics Seminar, November 6, 2007.
  5. Alex Bilik, Diffuse-interface modeling and simulation of solvation of nonpolar molecules, Informal Seminar on Mathematics and Biochemistry-Biophysics, Department of Mathematics, UCSD, November 27, 2007.
  6. Joachim Dzubiella, Variational Theory of Solvation, Summer School on Coarse-Grained Physical Modeling of Biological Systems, Center for Theoretical Biological Physics, UCSD, 2008.
  7. Bo Li, Coupling the level-set method with the variational implicit solvent modeling of molecular solvation, Summer School on Coarse-Grained Physical Modeling of Biological Systems, Center for Theoretical Biological Physics, UCSD, 2008.
  8. Bo Li, Coupling the level-set method with variational implicit-solvent models for molecular solvation, Center for Theoretical Biological Physics, UCSD, October 10, 2008.
  9. Bo Li, Coupling the level-set method with variational implicit-solvent models for molecular solvation,, IMA workshop: Solvation, December 8-12, 2009.
  10. Piotr Setny, Hydrophobic effects in vicinity of concave nanoscopic objects, Informal Seminar on Mathematics and Biochemistry-Biophysics, Department of Mathematics, UCSD, January 19, 2009.
  11. Zhongming Wang, A level-set variational implicit-solvent approach to hydrophobic interactions, Informal Seminar on Mathematics and Biochemistry-Biophysics, Department of Mathematics, UCSD, January 27, 2009.
  12. Bo Li, The Poisson-Boltzmann Theory of Continuum Electrostatics with Application to Variational Solvation of Molecules. Informal Seminars on Mathematics and Biochemistry-Biophysics, UCSD, February 3, 2009.
  13. Zhongming Wang, A Bloch Band Based Level Set Method for Computing The Semiclassical Limit of Schrodinger Equations,, Kinetic Description of Multiscale Phenomena, Kinetic Young Researchers Workshop, CSCAMM, Univ. of Maryland, March 3-5, 2009.

Informal Seminars on Mathematics and Biochemistry-Biophysics

2:00 pm - 3:00 pm, Tuesdays, AP&M 5829.

Founding

Our research has been partially supported by the NSF (DMS-0451466, DMS-0511766, and DMS-0811259) and DOE (DE-FG02-05ER25707), a Sloan Fellowship, and the Center of Theoretical and Biological Physics (CTBP) at UCSD through the NSF grant NSF PHY-0822283.

Links

UCSD Math, Phys, Chem-Biochem, MAE, Biosciences, CTBP
Salk, TSRI, GNF, Burnham, McCammon seminars, Onuchic-Wolynes semianrs
AMS, SIAM, APS, AIP, ACS, NSF, DOE, NIH, IMA, IPAM, Science, Nature

Last updated by Bo Li on January 14, 2009. © Bo Li, 2007-2009.