People

Faculty

• Li-Tien Cheng (Math, UCSD)
• Bo Li (Math and CTBP, UCSD)

Postdocs

• Zhongming Wang (Math and Biochem, UCSD)

Graduate Students

• Alex Bilik (Math, UCSD)
• John Shopple (Math, UCSD)

Undergraduate Students

• April Prak (Math, UCSD)
• Raul Serrano (Biochemistry and Math, UCSD)
• Yang Xie (MAE, UCSD)

Collaborators

• John Che (Senior scientist, Genomics Institute of Novartis Research Foundation)
• Joachim Dzubiella (Emmy-Noether fellow, Biophysics, Tech. Univ. Munich)
• McCammon's group (Chemistry and Biochemistry, and CTBP, UCSD)

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, Ricci flow, probability and 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.
3. Singularities in geometrically based molecualr surface evolution: level-set computation and analysis.
4. Analytical and numerical investigation of Tolman curvature correction of surface tension for systems of small scale.
5. Analysis and improvement of the Generalized Born model in the framework of variational implicit solvent description.
6. Analysis of diffusion of ions and substrates in a molecular system.
7. Multiscale modeling and simulation of the molecular mechnics of solute atoms and the solute-solvent interface dynamics.
8. Fluid density functional theory and numerical calculations for the solvation of biomolecules.

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.
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
5. Bo Li, Minimization of electrostatic free energy and the Poisson-Boltzmann equation for molecular solvation with implicit solvent, 2008 (submitted).
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, submitted for publications, 2008. (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.

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 NSF Center of Theoretical and Biological Physics (CTBP) at UCSD.

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