All-Atom Molecular Dynamics Simulations of Poly(ethylene glycol) Networks in Water for Evaluating Negative Energetic Elasticity

被引:4
作者
Hagita, Katsumi [1 ]
Nagahara, Sota [2 ]
Murashima, Takahiro [3 ]
Sakai, Takamasa [4 ]
Sakumichi, Naoyuki [4 ]
机构
[1] Natl Def Acad, Dept Appl Phys, Yokosuka 2398686, Japan
[2] Univ Tokyo, Dept Bioengn, Tokyo 1138656, Japan
[3] Tohoku Univ, Dept Phys, Sendai 9808578, Japan
[4] Univ Tokyo, Dept Chem & Biotechnol, Tokyo 1138656, Japan
关键词
RUBBER ELASTICITY; POLYMER MELTS; RELAXATION; GELS; FOUNDATIONS; TRANSITION; FRACTURE; GROMACS; CHARMM; CHAIN;
D O I
10.1021/acs.macromol.3c01121
中图分类号
O63 [高分子化学(高聚物)];
学科分类号
070305 ; 080501 ; 081704 ;
摘要
We performed all-atom molecular dynamics simulations on poly(ethylene glycol) (PEG) hydrogels to microscopically confirm the recently discovered "negative energetic elasticity" [Y. Yoshikawa et al., Phys. Rev. X 2021, 11, 011045], which refers to a negative energetic contribution to the elastic modulus. To scrutinize the force field parameters, we evaluated the densities of aqueous solutions of linear PEG chains at varying concentrations through simulations and compared them with experimental values. We simulated a PEG network consisting of 2(3) unit cells of a diamond lattice with 60 PEG units per strand among numerous water molecules. Subsequently, we examined the temperature (T) dependence of shear stress (sigma(XY)) for each shear strain (gamma) under constant-volume conditions for a simulation duration of 360 ns. Current computational limitations lead to significant errors in sigma(XY). Thus, we employed a statistical approach considering numerous data sets (sigma(XY), gamma, T) based on the multivariate regression of the equation sigma(XY) = A gamma(T - T-E) in a narrow temperature range using fitting parameters A and T-E, where a positive T-E implies a negative energetic elasticity. The magnitude of the negative energetic elasticity (proportional to T-E) was approximately double the overall magnitude (proportional to T - T-E). We confirmed the feasibility of the obtained T-E values via a statistical error analysis. The theoretical prediction of the systematic difference between the T-E values under constant-pressure and constant-volume conditions was confirmed. Our method is effective for evaluating the negative energetic elasticity through T-E for arbitrary PEG concentrations and strand lengths.
引用
收藏
页码:8095 / 8105
页数:11
相关论文
共 14 条
  • [1] Reaching biological timescales with all-atom molecular dynamics simulations
    Zwier, Matthew C.
    Chong, Lillian T.
    CURRENT OPINION IN PHARMACOLOGY, 2010, 10 (06) : 745 - 752
  • [2] Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations
    Tamamis, Phanourios
    Morikis, Dimitrios
    Floudas, Christodoulos A.
    Archontis, Georgios
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2010, 78 (12) : 2655 - 2667
  • [3] Dynamics of Protein-RNA Interfaces Using All-Atom Molecular Dynamics Simulations
    Sabei, Afra
    Hognon, Cecilia
    Martin, Juliette
    Frezza, Elisa
    JOURNAL OF PHYSICAL CHEMISTRY B, 2024, 128 (20) : 4865 - 4886
  • [4] Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates
    Sarthak, Kumar
    Winogradoff, David
    Ge, Yingda
    Myong, Sua
    Aksimentiev, Aleksei
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2023, 19 (12) : 3721 - 3740
  • [5] Correlating structural dynamics and catalytic activity of AgAu nanoparticles with ultrafast spectroscopy and all-atom molecular dynamics simulations
    Ferbonink, G. F.
    Rodrigues, T. S.
    dos Santos, D. P.
    Camargo, P. H. C.
    Albuquerque, R. Q.
    Nome, R. A.
    FARADAY DISCUSSIONS, 2018, 208 : 269 - 286
  • [6] MkVsites: A tool for creating GROMACS virtual sites parameters to increase performance in all-atom molecular dynamics simulations
    Larsson, Per
    Kneiszl, Rosita C.
    Marklund, Erik G.
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2020, 41 (16) : 1564 - 1569
  • [7] Insights into Structure and Aggregation Behavior of Elastin-like Polypeptide Coacervates: All-Atom Molecular Dynamics Simulations
    Li, Nan K.
    Xie, Yuxin
    Yingling, Yaroslava G.
    JOURNAL OF PHYSICAL CHEMISTRY B, 2021, 125 (30) : 8627 - 8635
  • [8] Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments
    Arnittali, Maria
    Rissanou, Anastassia N.
    Amprazi, Maria
    Kokkinidis, Michael
    Harmandaris, Vagelis
    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2021, 22 (11)
  • [9] All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
    MacKerell, AD
    Banavali, NK
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2000, 21 (02) : 105 - 120
  • [10] All-atom molecular dynamics simulations of lung surfactant protein B: Structural features of SP-B promote lipid reorganization
    Khatami, Mohammad Hassan
    Saika-Voivod, Ivan
    Booth, Valerie
    BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 2016, 1858 (12): : 3082 - 3092