Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics

被引:62
|
作者
Levine, Benjamin G. [1 ,2 ]
LeBard, David N. [1 ,2 ]
DeVane, Russell [3 ]
Shinoda, Wataru [4 ]
Kohlmeyer, Axel [1 ,2 ]
Klein, Michael L. [1 ,2 ]
机构
[1] Temple Univ, Inst Computat Mol Sci, Philadelphia, PA 19122 USA
[2] Temple Univ, Dept Chem, Philadelphia, PA 19122 USA
[3] Procter & Gamble Co, Cincinnati, OH 45253 USA
[4] Natl Inst Adv Ind Sci & Technol, Tsukuba, Ibaraki, Japan
基金
美国国家科学基金会;
关键词
QUANTUM-CHEMISTRY CALCULATIONS; GRAPHICAL PROCESSING UNITS; SODIUM DODECYL-SULFATE; WATER OIL INTERFACE; COMPUTER-SIMULATIONS; PREMICELLAR AGGREGATION; MICELLE; MODEL; THERMODYNAMICS; IMPLEMENTATION;
D O I
10.1021/ct2005193
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
The computational design of advanced materials based on surfactant self-assembly without ever stepping foot in the laboratory is an important goal, but there are significant barriers to this approach, because of the limited spatial and temporal scales accessible by computer simulations. In this paper, we report our work to bridge the gap between laboratory and computational time scales by implementing the coarse-grained (CG) force field previously reported by Shinoda et al. [Shinoda, W.; DeVane, R.; Klein, M. L. Mol. Simul. 2007, 33, 27-36] into the HOOMD-Blue graphical processing unit (GPU)-accelerated molecular dynamics (MD) software package previously reported by Anderson et al. [Anderson, J. A.; Lorenz, C. D.; Travesset, A. J. Comput. Phys. 2008, 227, 5342-5359]. For a system of 25 750 particles, this implementation provides performance on a single GPU, which is superior to that of a widely used parallel MD simulation code running on an optimally sized CPU-based cluster. Using our GPU setup, we have collected 0.6 ms of MD trajectory data for aqueous solutions of 7 different nonionic polyethylene glycol (PEG) surfactants, with most of the systems studied representing similar to 1 000 000 atoms. From this data, we calculated various properties as a function of the length of the hydrophobic tails and PEG head groups. Specifically, we determined critical micelle concentrations (CMCs), which are in good agreement with experimental data, and characterized the size and shape of micelles. However, even with the microsecond trajectories employed in this study, we observed that the micelles composed of relatively hydrophobic surfactants are continuing to grow at the end of our simulations. This suggests that the final micelle size distributions of these systems are strongly dependent on initial conditions and that either longer simulations or advanced sampling techniques are needed to properly sample their equilibrium distributions. Nonetheless, the combination of coarse-grained modeling and GPU acceleration marks a significant step toward the computational prediction of the thermodynamic properties of slowly evolving surfactant systems.
引用
收藏
页码:4135 / 4145
页数:11
相关论文
共 50 条
  • [1] GPU-accelerated coarse-grained simulations of protein-protein docking with flexible linkers
    Pinska, Adrianna
    Best, Robert
    Kuttel, Michelle
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2018, 256
  • [2] GPU-Accelerated Molecular Dynamics Simulation to Study Liquid Crystal Phase Transition Using Coarse-Grained Gay-Berne Anisotropic Potential
    Chen, Wenduo
    Zhu, Youliang
    Cui, Fengchao
    Liu, Lunyang
    Sun, Zhaoyan
    Chen, Jizhong
    Li, Yunqi
    [J]. PLOS ONE, 2016, 11 (03):
  • [3] Ionomer Dispersion in Dilute Solution Studied by Coarse-Grained Molecular Dynamics
    Mabuchi, Takuya
    Tokumasu, Takashi
    [J]. 4TH INTERNATIONAL TROPICAL RENEWABLE ENERGY CONFERENCE (I-TREC 2019), 2020, 2255
  • [4] Reactive Coarse-Grained Molecular Dynamics
    Dannenhoffer-Lafage, Thomas
    Voth, Gregory A.
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2020, 16 (04) : 2541 - 2549
  • [5] Multiconfigurational Coarse-Grained Molecular Dynamics
    Sharp, Morris E.
    Vazquez, Francisco X.
    Wagner, Jacob W.
    Dannenhoffer-Lafage, Thomas
    Voth, Gregory A.
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2019, 15 (05) : 3306 - 3315
  • [6] Oligomerization of Amphipathic Peptides in a Membrane Studied by Coarse-Grained Molecular Dynamics Simulations
    Yi, Myunggi
    Zhou, Huan-Xiang
    [J]. BIOPHYSICAL JOURNAL, 2010, 98 (03) : 458A - 458A
  • [7] Polymorphic phase behavior of cardiolipin derivatives studied by coarse-grained molecular dynamics
    Dahlberg, Martin
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 2007, 111 (25): : 7194 - 7200
  • [8] Coarse-grained molecular dynamics of PEGylated assemblies
    Loverde, Sharon M.
    Shinoda, Wataru
    Discher, Dennis E.
    Klein, Michael L.
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2013, 245
  • [9] Implementation of coarse-grained models for molecular simulation on GPU architecture
    Tunbridge, Ian
    Best, Robert B.
    Kuttel, Michelle M.
    [J]. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2009, 238
  • [10] Coarse-grained protein molecular dynamics simulations
    Derreumaux, Philippe
    Mousseau, Normand
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2007, 126 (02):