Bo Li's Publications

Bo Li's Publications

    Published Journal Articles

    1. Bo Li, Superconvergence for higher-order triangular finite elements, Mathematica Numerica Sinica, 4(11), 413-417, 1989. Selected for republication: Chinese J. Numer. Math. Appl., 12(1), 75-79, 1990.
       
      Note: This paper is cited as "a little known but in my opinion important paper" in: L. B. Wahlbin, Superconvergence in Galerkin Finite Element Methods, volume 1605 of Lecture Notes in Mathematics, Springer, Berlin, 1995 (cf. Section 7.4. Historical remarks).
       
    2. Hongsen Chen and Bo Li, Superconvergence analysis and error expansion for the Wilson nonconforming finite element, Numer. Math., 69(2), 125-140, 1994. (Preprint in PDF)
       
    3. Petr Kloucek, Bo Li, and Mitchell Luskin, Analysis of a class of nonconforming finite elements for crystalline microstructures, Math. Comp., 65(215), 1111-1135, 1996.
       
    4. Bo Li and Mitchell Luskin, Finite element analysis of microstructure for the cubic to tetragonal transformation, SIAM J. Numer. Anal., 35(1), 376-392, 1998. (Published version in PDF - permission and copyright of SIAM.)
       
    5. Bo Li and Mitchell Luskin, Nonconforming finite element approximation of crystalline microstructure, Math. Comp., 67(223), 917-946, 1998.
       
    6. Bo Li and Michell Luskin, Approximation of a martensitic laminate with varying volume fractions, ESAIM: Math. Model. Numer. Anal., 33(1), 67-87, 1999. (Preprint in PDF)
       
    7. Bo Li and Mitchell Luskin, Theory and computation for the microstructure near the interface between twinned layers and a pure variant of martensite, Materials Sci. Eng. A, 273, 237-240, 1999. (Preprint in PDF)
       
    8. Bo Li and Zhimin Zhang, Analysis of a class of superconvergence patch recovery techniques for linear and bilinear finite elements, Numer. Methods PDE, 15(2), 151-167, 1999. (Preprint in PDF)
       
    9. Kaushik Bhattacharya, Bo Li, and Mitchell B. Luskin, The simply laminated microstructure in martensitic crystals that undergo a cubic to orthorhombic phase transformation, Arch. Rational Mech. Anal., 149(2), 123-154, 1999. (Preprint in PDF)
       
    10. Bo Li, Approximation of martensitic microstructure with general homogeneous boundary data, J. Math. Anal. Appl., 266, 451-467, 2002. (Preprint in PDF)
       
    11. Russel E. Caflisch and Bo Li, Analysis of island dynamics in epitaxial growth of thin films, Multiscale Model. Simul., 1(1), 150-171, 2003. (Published version in PDF - permission and copyright of SIAM.)
       
    12. Bo Li, Finite element analysis of a class of stress-free martensitic microstructures, Math. Comp., 72(244), 1675-1688, 2003. (Preprint in PDF)
       
    13. Xingzhou Yang, Bo Li, and Zhilin Li, The immersed interface method for elasticity problems with interfaces, Dyn. Contin. Discret Impuls. Syst. Ser. A: Math. Anal., 10(5), 783-808, 2003. (Preprint in PDF.)
       
    14. Bo Li and Jian-Guo Liu, Thin film epitaxy with or without slope selection, European J. Appl. Math., 14(6), 713-743, 2003. (Preprint in PDF)
       
    15. Bo Li, Lagrange interpolation and finite element superconvergence, Numer. Methods PDE, 20(1), 33-59, 2004. (Preprint in PDF)
       
    16. Eberhard Bänsch, Frank Hausser, Omar Lakkis, Bo Li, and Axel Voigt, Finite element method for epitaxial growth with attachment-detachment kinetics, J. Comput. Phys., 194(2), 409-434, 2004. (Preprint in PDF)
       
    17. Bo Li, Andreas Rätz, Axel Voigt, Stability of a circular epitaxial island, Physica D, 198, 231-247, 2004. (Preprint in PDF)
       
    18. Bo Li and Jian-Guo Liu, Epitaxial growth without slope selection: energetics, coarsening, and dynamic scaling, J. Nonlinear Sci., 14, 429-451, 2004. (Preprint in PDF)
       
    19. Bo Li, Variational properties of unbounded order parameters, SIAM J. Math. Anal., 38(1), 16-36, 2006. (Published version in PDF - permission and copyright of SIAM.)
       
    20. Bo Li, High-order surface relaxation vs. the Ehrlich-Schwoebel effect, Nonlinearity, 19(11), 2581-2603, 2006. (Preprint in PDF)
       
    21. 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. PubMed PMID: 17764265. (Preprint in PDF)
       
    22. 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.)
       
    23. 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. PubMed PMID: 18275182. (Preprint in PDF)
       
    24. 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)
       
    25. 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. PubMed: PMC2680306. (Preprint in PDF)
       
    26. 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.)
       
      Note: See: Bo Li, Erratum: "Minimization of Electrostatic Free Energy and the Poisson-Boltzmann Equation for Molecular Solvation with Implicit Solvent" [SIAM J. Math. Anal., Vol. 40, No. 6, pp. 2536-2566, 2009], SIAM J. Math. Anal., 43, 2776-2777, 2011. (Published version in PDF - permission and copyright of SIAM.)
       
    27. Bo Li, Continuum electrostatics for ionic solutions with non-uniform ionic sizes, Nonlinearity, 22, 811-833, 2009. published version in PDF 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."
       
      Note: This article was selected to be part of Nonlinearity's collection of the most downloaded articles of 2009. From the publisher: "The articles selected represent the most frequently downloaded during 2009 and feature extremely high quality research."
       
    28. 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. PubMed: PMC2771049. (Preprint in PDF)
       
    29. Piotr Setny, Zhongming Wang, Li-Tien Cheng, Bo Li, J. Andrew McCammon, and Joachim Dzubiella, Dewetting-controlled binding of ligands to hydrophobic pockets, Phys. Rev. Lett., 103, 187801, 2009. PubMed: PMC2832595. (Preprint in PDF)
       
    30. Bo Li, Benzhuo Lu, Zhongming Wang, and J. Andrew McCammon, Solutions to a reduced Poisson-Nernst-Planck system and determination of reaction rates, Physica A, 389, 1329-1345, 2010. PubMed: PMC2835320. (Preprint in PDF)
       
    31. Li-Tien Cheng, Bo Li, and Zhongming Wang, Level-Set minimization of potential controlled Hadwiger valuations for molecular solvation, J. Comput. Phys., 229, 8497-8510, 2010. PubMed: PMC3273873. (Preprint in PDF)
       
    32. Bo Li and John Shopple, An interface-fitted finite element level set method with application to solidification and solvation, Commun. Comput. Phys., 10, 32-56, 2011. PubMed: PMC3778506. (Preprint in PDF)
       
    33. Hsiao-Bing Cheng, Li-Tien Cheng, and Bo Li, Yukawa-field approximation of electrostatic free energy and dielectric boundary force, Nonlinearity, 24, 3215-3236, 2011. PubMed: PMC3709021. (Preprint in PDF)
       
    34. Shenggao Zhou, Zhongming Wang, and Bo Li, Mean-field description of ionic size effects with non-uniform ionic sizes: A numerical approach, Phys. Rev. E, 84, 021901, 2011. PubMed: PMC3727298. (Preprint in PDF)
       
    35. Bo Li, Xiaoliang Cheng, and Zhengfang Zhang, Dielectric boundary force in molecular solvation with the Poisson-Boltzmann free energy: A shape derivative approach, SIAM J. Applied Math., 71, 2093-2111, 2011. PubMed: PMC3778505. (Published version in PDF - permission and copyright of SIAM.)
       
    36. Zhongming Wang, Jianwei Che, Li-Tien Cheng, Joachim Dzubiella, Bo Li, and J. Andrew McCammon, Level-set variational implicit-solvent modeling of biomolecules with the Coulomb-field approximation, J. Chem. Theory Comput., 8, 386-397, 2012. PubMed: PMC3278970. (Preprint in PDF)
       
    37. Jiayi Wen, Shenggao Zhou, Zhenli Xu, and Bo Li, Competitive adsorption and ordered packing of counterions near highly charged surfaces: From mean-field theory to Monte Carlo simulations, Phys. Rev. E, 85, 041406, 2012. PubMed: PMC3725615. (Preprint in PDF)
       
    38. Bo Li and Yanxiang Zhao, Variational implicit solvation with solute molecular mechanics: From diffuse-interface to sharp-interface models, SIAM J. Applied Math., 73(1), 1-23, 2013. PubMed: PMC3778507. (Published version in PDF - permission and copyright of SIAM.)
       
    39. Li-Tien Cheng, Bo Li, Michael White, and Shenggao Zhou, Motion of a cylindrical dielectric boundary, SIAM J. Applied Math., 73(1), 594-616, 2013. PubMed: PMC3718573. (Published version in PDF - permission and copyright of SIAM.)
       
    40. Zuojun Guo, Bo Li, Joachim Dzubiella, Li-Tien Cheng, J. Andrew McCammon, and Jianwei Che, Evaluation of hydration free energy by level-set variational implicit-solvent model with Coulomb-field approximation, J. Chem. Theory Comput., 9, 1778-1787, 2013. PubMed: PMC3596957. (Preprint in PDF)
       
    41. Yanxiang Zhao, Yuen-Yick Kwan, Jianwei Che, Bo Li, and J. Andrew McCammon, Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation, J. Chem. Phys., 139, 024111, 2013. PubMed: PMC3724799. (Preprint in PDF)
       
      Note: Press Release by the journal: What Water Looks Like to DNA - New Computational Method Described in "The Journal of Chemical Physics" Allows Researchers to Predict how Biological Molecules Interact with Water. Read more at AIP Publishing and EurekAlert.
       
      Note: This paper was also selected to be included in JCP Editor's Choice for 2013. Click here for articles in the collection. (Freely available until the end of 2014.)
       
    42. Shenggao Zhou, Kathleen E. Rogers, Cesar Augusto F. de Oliveira, Riccardo Baron, Li-Tien Cheng, Joachim Dzubiella, Bo Li, and J. Andrew McCammon, Variational implicit-solvent modeling of host-guest binding: A case study on Cucurbit[7]uril, J. Chem. Theory Comput., 9, 4195-4204, 2013. PubMed: PMC3770055. (Preprint in PDF)
       
    43. Bo Li, Pei Liu, Zhenli Xu, and Shenggao Zhou, Ionic size effects: generalized Boltzmann distributions, counterion stratification, and modified Debye length, Nonlinearity, 26, 2899-2922, 2013. PubMed: PMC3899944. (Preprint in PDF)
       
      Note: This paper is included in Nonlinearity Highlights of 2013. See the journal Certificate signed by the joint Editors-in-Chief.
       
    44. Brian A. Camley, Yanxiang Zhao, Bo Li, Herbert Levine, and Wouter-Jan Rappel, Periodic migration in a physical model of cells on micropatterns, Phys. Rev. Lett., 111, 158102, 2013. PubMed: PMC3855234. (Preprint in PDF)
       
    45. Zuojun Guo, Bo Li, Joachim Dzubiella, Li-Tien Cheng, J. Andrew McCammon, and Jianwei Che, Heterogeneous hydration of p53/MDM2 complex, J. Chem. Theory Comput., 10(3), 1302-1313, 2014. PubMed: PMC3958133.
       
    46. Shenggao Zhou, Li-Tien Cheng, Joachim Dzubiella, Bo Li, and J. Andrew McCammon, Variational implicit solvation with Poisson-Boltzmann theory, J. Chem. Theory Comput., 10, 1454-1467, 2014. PubMed: PMC3985794. (Preprint in PDF)
       
    47. Brian A. Camley, Yunsong Zhang, Yanxiang Zhao, Bo Li, Eshel Ben-Jacob, Herbert Levine, and Wouter-Jan Rappel, Polarity mechanisms like contact inhibition of locomotion regulate persistent rotational motion of mammalian cells on micropatterns, Proc. Natl Acad. Sci. USA, 111 (41) 14770-14775, 2014. PubMed: PMC4205601.
       
    48. Timonthy Banham, Bo Li, and Yanxiang Zhao, Pattern formation by phase-field relaxation of bending energy with fixed surface area and volume, Phys. Rev. E, 90, 033308, 2014. PubMed: PMC4288938. (Preprint in PDF)
       
    49. Nuo Wang, Shenggao Zhou, Peter Kekenes-Huskey, Bo Li, and J. Andrew McCammon, Poisson-Boltzmann vs. size-modified Poisson-Boltzmann electrostatics applied to lipid bilayers, J. Phys. Chem. B, 118 (51), 14827-14832, 2014. PubMed: PMC4280115.
       
    50. Maryann E. Hohn, Bo Li, and Weihua Yang, Analysis of coupled reaction-diffusion equations for RNA interactions, J. Math. Anal. Appl., 425, 212-233, 2015. PubMed: PMC4296743. (Preprint in PDF)
       
    51. Zuojun Guo, Bo Li, Shenggao Zhou, Li-Tien Cheng, J. Andrew McCammon, and Jianwei Che, Identification of protein-ligand binding sites by the level-set variational implicit solvent approach, J. Chem. Theory Comput., 11, 753--765, 2015. PubMed: PMC4410907.
       
    52. Bo Li, Hui Sun, and Shenggao Zhou, Stability of a cylindrical solute-solvent interface: Effect of geometry, electrostatics, and hydrodynamics, SIAM J. Applied Math., 75(3), 907-928, 2015. PubMed: PMC4752181. (Published version in PDF - permission and copyright of SIAM.)
       
    53. Shenggao Zhou, Li-Tien Cheng, Hui Sun, Jianwei Che, Joachim Dzubiella, Bo Li, and J. Andrew McCammon, LS-VISM: A software package for analysis of biomolecular solvation, J. Comput. Chem., 36 (14), 1047-1059, 2015. PubMed: PMC4412808.
       
      Note: A figure of computational result from this article was selected by the journal as a cover image.
       
    54. Bo Li and Yuan Liu, Diffused solute-solvent interface with Poisson-Boltzmann electrostatics: Free-energy variation and sharp-interface limit, SIAM J. Applied Math, 75(5), 2072-2092, 2015. PubMed: PMC4752183. (Published version in PDF - permission and copyright of SIAM.)
       
    55. Hui Sun, Jiayi Wen, Yanxiang Zhao, Bo Li, and J. Andrew McCammon, A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics, J. Chem. Phys., 143, 243110, 2015. PubMed: PMC4605633.
       
    56. Bo Li, Jiayi Wen, and Shenggao Zhou, Mean-field theory and computation of electrostatics with ionic concentration dependent dielectrics, Commun. Math. Sci., 14(1), 249-271, 2016. PubMed: PMC4752182. (Preprint in PDF)
       
    57. Hui Sun, Shenggao Zhou, David K. Moore, Li-Tien Cheng, and Bo Li, Numerical treatment of Stokes solvent flow and solute-solvent interfacial dynamics for nonpolar molecules, J. Sci. Comput., 67(2), 705-723, 2016. PubMed: PMC4922513.
       
    58. Gary A. Huber, Yinglong Miao, Shenggao Zhou, Bo Li and J. Andrew McCammon, Hybrid finite element and Brownian dynamics method for charged particles, J. Chem. Phys. 144, 164107, 2016. PubMed: PMC4851620.
       
    59. Shenggao Zhou, Hui Sun, Li-Tien Cheng, Joachim Dzubiella, Bo Li, and J. Andrew McCammon, Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations, J. Chem. Phys., 145, 054114, 2016. PubMed: PMC4975753.
       
    60. Xiaofei Guan, Manman Ma, Zecheng Gan, Zhenli Xu, and Bo Li, Hybrid Monte Carlo and continuum modeling of electrolyte with concentration-induced dielectric variations, Phys. Rev. E, 94, 053312, 2016.
       
    61. Brian A. Camley, Yanxiang Zhao, Bo Li, Herbert Levine, and Wouter-Jan Rappel, Crawling and turning in a minimal reaction-diffusion cell motility model: Coupling cell shape and biochemistry, Phys. Rev. E, 95, 012401, 2017.
       
      Note: This article was selected by the journal as "Editor's suggestion".
       
    62. Clarisse G. Ricci, Bo Li, Li-Tieng Cheng, Joachim Dzubiella, and J. Andrew McCammon, 'Martinizing' the variational implicit solvent method (VISM): Solvation free energy for coarse-grained proteins, J. Phys. Chem. B, 121, 6538-6548 2017.
       
    63. Shibin Dai, Bo Li, and Jianfeng Lu, Convergence of phase-field free energy and boundary force for molecular solvation, Arch. Rational Mech. Anal., 227(1), 105-147, 2018. (Preprint in PDF)
       
    64. Clarisse G. Ricci, Bo Li, Li-Tien Cheng, Joachim Dzubiella, and J. Andrew McCammon, Tailoring the variational implicit solvent method for new challenges: Biomolecular recognition and assembly, Front. Mol. Biosci., 5:13, 2018. (Open access at journal website)

    Articles Accepted for Publication

    1. Yanxiang Zhao, Yanping Ma, Hui Sun, Bo Li, and Qiang Du, A new phase-field approach to variational implicit solvation of charged molecules with the Coulomb-field approximation, Commun. Math. Sci., 2018. (Preprint in PDF)
       

    Articles Submitted for Publication

    1. Hui Sun, Shenggao Zhou, Li-Tien Cheng, and Bo Li, Numerical methods for solvent Stokes flow and solute-solvent interfacial dynamics of charged molecules, J. Comput. Phys., 2017 (submitted).
       
    2. Benjamin Ciotti and Bo Li, Legendre transforms of electrostatic free-energy functionals, SIAM J. Applied Math., 2018 (submitted).

    Miscellaneous: Technical Reports, Translations, Thesis, and Lecture Notes

    1. Bo Li, A convergence analysis of the Wilson nonconforming finite element (in Chinese), First Chinese national conference on numerical solutions of PDEs, Shanghai, China, 1987. Collected in the book Superconvergence Theory of Finite Element Methods by Qiding Zhu and Qun Lin, Hunan Science Press, 1989. English translation, 1995.
       
    2. Bo Li, English translation of Kang Feng's article: Difference Schemes Based on Variational Principle, in Collected Works of Kang Feng, 1994.
       
    3. Bo Li, Analysis and computation of martensitic microstructure, Ph.D. Thesis, University of Minnesota, 1996.
       
    4. Bo Li, Weak Convergence Methods for Variational Problems Modeling Crystalline Solids, Lecture notes for a graduate seminar course, UCLA, Spring, 1998.
       
    5. Bo Li, Continuum Models and Analysis for Epitaxial Growth of Thin Films, Lecture notes for an advanced graduate course, University of Maryland, College Park, Fall, 2003.
       
    6. Bo Li, Weak Convergence Methods for Energy Minimization, Lecture notes for Math 241B: Function Analysis, University of California, San Diego, Winter, 2007,
       
    7. Bo Li, Lecture Notes on Numerical Analysis, University of California, San Diego, Spring, 2009.
       
    8. Bo Li, Topics on Mathematics and Biochemistry-Biophysics, Lecture Notes for Math 277B: Topics in Mathematics and Biochemistry-Biophysics, UCSD, Spring 2011.
       
    9. Bo Li, Lecture Notes for Math 210ABC: Mathematical Methods for Physical Sciences and Engieering, UCSD, 2013 - 2014.
       
    10. Bo Li, Continuum Electrostatics, Variational Implicit Solvation, and Diffuse Interface for Cell Motion, Lecture Series, Winter School: Modeling, Simulation and Analysis of Biology and Physiology Mathematics Division, Taiwn National Center for Theoretical Sciences, Taipei, Taiwan, December 18, 2015 - January 8, 2016. Lecture notes: Outline, Lecture 1, Lecture 2, Lecture 3, Lecture 4.
Last updated by Bo Li on April 8, 2018. © Bo Li, 2002-2018.