Neural network-assisted model of interfacial fluids with explicit coarse-grained molecular structures

被引:0
作者
Ma, Shuhao [1 ]
Li, Dechang [1 ]
Li, Xuejin [1 ]
Hu, Guoqing [1 ]
机构
[1] Zhejiang Univ, Dept Engn Mech, Hangzhou 310027, Peoples R China
基金
中国国家自然科学基金;
关键词
FORCE-FIELD; SIMULATIONS; DYNAMICS; INSIGHT;
D O I
10.1063/5.0230195
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
Interfacial fluids are ubiquitous in systems ranging from biological membranes to chemical droplets and exhibit a complex behavior due to their nonlinear, multiphase, and multicomponent nature. The development of accurate coarse-grained (CG) models for such systems poses significant challenges, as these models must effectively capture the intricate many-body interactions, both inter- and intramolecular, arising from atomic-level phenomena, and account for the diverse density distributions and fluctuations at the interface. In this study, we use advanced machine learning techniques incorporating force matching and diffusion probabilistic models to construct a robust CG model of interfacial fluids. We evaluate our model through simulations in various settings, including the water-air interface, bulk decane, and dipalmitoylphosphatidylcholine monolayer membranes. Our results show that our CG model accurately reproduces the essential many-body and interfacial properties of interfacial fluids and proves effective across different CG mapping strategies. This work not only validates the utility of our model for multiscale simulations, but also lays the groundwork for future improvements in the simulation of complex interfacial systems.
引用
收藏
页数:13
相关论文
共 91 条
[1]   Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics [J].
Arts, Marloes ;
Satorras, Victor Garcia ;
Huang, Chin-Wei ;
Zuegner, Daniel ;
Federici, Marco ;
Clementi, Cecilia ;
Noe, Frank ;
Pinsler, Robert ;
van den Berg, Rianne .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2023, 19 (18) :6151-6159
[2]   Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations [J].
Baoukina, Svetlana ;
Monticelli, Luca ;
Marrink, Siewert J. ;
Tieleman, D. Peter .
LANGMUIR, 2007, 23 (25) :12617-12623
[3]   E(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials [J].
Batzner, Simon ;
Musaelian, Albert ;
Sun, Lixin ;
Geiger, Mario ;
Mailoa, Jonathan P. ;
Kornbluth, Mordechai ;
Molinari, Nicola ;
Smidt, Tess E. ;
Kozinsky, Boris .
NATURE COMMUNICATIONS, 2022, 13 (01)
[5]   Coarse-graining errors and numerical optimization using a relative entropy framework [J].
Chaimovich, Aviel ;
Shell, M. Scott .
JOURNAL OF CHEMICAL PHYSICS, 2011, 134 (09)
[6]   Relative entropy as a universal metric for multiscale errors [J].
Chaimovich, Aviel ;
Shell, M. Scott .
PHYSICAL REVIEW E, 2010, 81 (06)
[7]   Projection of diffusions on submanifolds: Application to mean force computation [J].
Ciccotti, Giovanni ;
Lelievre, Tony ;
Vanden-Eijnden, Eric .
COMMUNICATIONS ON PURE AND APPLIED MATHEMATICS, 2008, 61 (03) :371-408
[8]   The multiscale coarse-graining method. IX. A general method for construction of three body coarse-grained force fields [J].
Das, Avisek ;
Andersen, Hans C. .
JOURNAL OF CHEMICAL PHYSICS, 2012, 136 (19)
[9]   Data-driven dynamical coarse-graining for condensed matter systems [J].
del Razo, Mauricio J. ;
Crommelin, Daan ;
Bolhuis, Peter G. .
JOURNAL OF CHEMICAL PHYSICS, 2024, 160 (02)
[10]   TorchMD: A Deep Learning Framework for Molecular Simulations [J].
Doerr, Stefan ;
Majewski, Maciej ;
Perez, Adria ;
Kramer, Andreas ;
Clementi, Cecilia ;
Noe, Frank ;
Giorgino, Toni ;
De Fabritiis, Gianni .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2021, 17 (04) :2355-2363