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Applied Mathematics and Mechanics (English Edition) ›› 2018, Vol. 39 ›› Issue (1): 3-20.doi: https://doi.org/10.1007/s10483-018-2252-6

• 论文 • 上一篇    下一篇

Modeling biomembranes and red blood cells by coarse-grained particle methods

H. LI1, H. Y. CHANG1, J. YANG2, L. LU1, Y. H. TANG1, G. LYKOTRAFITIS3   

  1. 1. Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, U. S. A;
    2. Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, U. S. A;
    3. Department of Mechanical Engineering, University of Connecticut, Storrs, Connecticut 06269, U. S. A
  • 收稿日期:2017-07-04 修回日期:2017-09-13 出版日期:2018-01-01 发布日期:2018-01-01
  • 通讯作者: H. LI E-mail:he_li@brown.edu
  • 基金资助:

    Project supported by the National Institutes of Health of U. S. A. (No. U01HL114476) and the National Science Foundation of U. S. A. (Nos. CMMI-1235025 and PHY-1205910)

Modeling biomembranes and red blood cells by coarse-grained particle methods

H. LI1, H. Y. CHANG1, J. YANG2, L. LU1, Y. H. TANG1, G. LYKOTRAFITIS3   

  1. 1. Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, U. S. A;
    2. Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, U. S. A;
    3. Department of Mechanical Engineering, University of Connecticut, Storrs, Connecticut 06269, U. S. A
  • Received:2017-07-04 Revised:2017-09-13 Online:2018-01-01 Published:2018-01-01
  • Contact: H. LI E-mail:he_li@brown.edu
  • Supported by:

    Project supported by the National Institutes of Health of U. S. A. (No. U01HL114476) and the National Science Foundation of U. S. A. (Nos. CMMI-1235025 and PHY-1205910)

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摘要：

In this work, the previously developed coarse-grained (CG) particle models for biomembranes and red blood cells (RBCs) are reviewed, and the advantages of the CG particle methods over the continuum and atomistic simulations for modeling biological phenomena are discussed. CG particle models can largely increase the length scale and time scale of atomistic simulations by eliminating the fast degrees of freedom while preserving the mesoscopic structures and properties of the simulated system. Moreover, CG particle models can be used to capture the microstructural alternations in diseased RBCs and simulate the topological changes of biomembranes and RBCs, which are the major challenges to the typical continuum representations of membranes and RBCs. The power and versatility of CG particle methods are demonstrated through simulating the dynamical processes involving significant topological changes, e.g., lipid self-assembly vesicle fusion and membrane budding.

关键词: forming process, numerical simulation, non-incremental algorithm, time-space function, red blood cell membrane, lipid bilayer, membrane fusion, coarse-grained molecular dynamics

Abstract:

In this work, the previously developed coarse-grained (CG) particle models for biomembranes and red blood cells (RBCs) are reviewed, and the advantages of the CG particle methods over the continuum and atomistic simulations for modeling biological phenomena are discussed. CG particle models can largely increase the length scale and time scale of atomistic simulations by eliminating the fast degrees of freedom while preserving the mesoscopic structures and properties of the simulated system. Moreover, CG particle models can be used to capture the microstructural alternations in diseased RBCs and simulate the topological changes of biomembranes and RBCs, which are the major challenges to the typical continuum representations of membranes and RBCs. The power and versatility of CG particle methods are demonstrated through simulating the dynamical processes involving significant topological changes, e.g., lipid self-assembly vesicle fusion and membrane budding.

Key words: forming process, numerical simulation, non-incremental algorithm, time-space function, lipid bilayer, red blood cell membrane, membrane fusion, coarse-grained molecular dynamics

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