Publications
L. Lyu and H. Lei. On the generalization ability of coarse-grained molecular dynamics models for non-equilibrium processes. arXivpreprint:arXiv:2409.11519, 2024 [arXiv].
P. Ge, Z. Zhang, and H. Lei. Data-driven learning of the generalized Langevin equation with state-dependent memory. Phys. Rev. Lett. 133:077301, 2024. [link].
L. Lyu and H. Lei. Consensus-based construction of high-dimensional free energy surface. arXivpreprint:arXiv:2311.05009, 2023 [arXiv].
L. Lyu and H. Lei. Construction of coarse-grained molecular dynamics with many-body non-Markovian memory. Phys. Rev. Lett. 131:177301, 2023. [link].
Y. Zhu, H. Lei, and C. Kim. General validity of the second fluctuation-dissipation theorem in the non-equilibrium steady state: Theory and applications. Physica Scripta, 98(11):115402, 2023 [link].
W. E, H. Lei, P. Xie, and L. Zhang. Machine learning-assisted multi-scale modeling. Journal of Mathematical Physics, 64(7):071101, 2023 [link].
P. Ge, L. Zhang, and H. Lei. Machine learning assisted coarse-grained molecular dynamics modeling of meso-scale interfacial fluids. J. Chem. Phys. 158:64104, 2023 [link].
Z. She, P. Ge, and H. Lei. Data-driven construction of stochastic reduced dynamics encoded with non-Markovian features. J. Chem. Phys. 158:034102, 2023 [link].
L. Fang , P. Ge, L. Zhang, W. E, and H. Lei. DeePN2: A Deep Learning-Based non-Newtonian Hydrodynamic Model. Journal of Machine Learning 1: 114–140, 2022 [link].
Y. Zhu and H. Lei. Effective Mori-Zwanzig Equation for the Reduced-Order Modeling of Stochastic Systems. Discrete Contin Dyn Syst - S 15 (4): 959–982, 2022 [link].
H. Lei and X. Li. Petrov–Galerkin Methods for the Construction of non-Markovian Dynamics Preserving Nonlocal Statistics. J. Chem. Phys. 154 (18): 184108, 2021 [link].
H. Lei, L. Wu, and W. E. Machine Learning Based non-Newtonian Fluid Model with Molecular Fidelity. Phys. Rev. E 102: 043309, 2020 [link].
F. Grogan, H. Lei, X. Li, and N. A. Baker. Data-Driven Molecular Modeling with the Generalized Langevin Equation. J. Comput. Phys. 418: 109633–109641, 2020 [link].
P. Stinis, H. Lei, J. Li, and H. Wan. Improving Solution Accuracy and Convergence for Stochastic Physics Parameterizations with Colored Noise. Mon. Weather Rev. 148 (2): 2251–63, 2020 [link].
J. Lu, F. Liu, L. R. Leung, and H. Lei. Neutral Modes of Surface Temperature and the Optimal Ocean Thermal Forcing for Global Cooling. NPJ Clim. Atmos. Sci. 3 (1): 9, 2020 [link].
H. Lei, J. Li, P. Gao, P. Stinis, and N. A. Baker. A Data-Driven Framework for Sparsity-Enhanced Surrogates with Arbitrary Mutually Dependent Randomness. Comput. Methods Appl. Mech. Eng. 350: 199–227, 2019 [link].
Y. Wang, H. Lei, and P. Atzberger. Fluctuating Hydrodynamic Methods for Fluid-Structure Interactions in Confined Channel Geometries. Appl. Math. Mech. 39 (1): 125–152, 2018. [link].
X. Yang*, H. Lei*, P. Gao*, D. G. Thomas, D. L. Mobley, and N. A. Baker. Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations. J. Chem. Theory Comput. 14 (2): 759–767, 2018 [link].
H. Lei, X. Yang, Z. Li, and G. E. Karniadakis. Systematic Parameter Inference in Stochastic Mesoscopic Modeling. J. Comput. Phys. 330 (4): 571–593, 2017 [link].
H. Lei, N. A. Baker, and X. Li. Data-Driven Parameterization of the Generalized Langevin Equation. Proc. Natl. Acad. Sci. 113 (50): 14183–14188, 2016 [link].
X. Yang*, H. Lei*, N. A. Baker, and G. Lin. Enhancing Sparsity of Hermite Polynomial Expansions by Iterative Rotations. J. Comput. Phys. 307: 94–109, 2016 [link].
H. Lei, N. A. Baker, L. Wu, G. K. Schenter, C. J. Mundy, and A. M. Tartakovsky. Smoothed Dissipative Particle Dynamics Model for Mesoscopic Multiphase Flows in the Presence of Thermal Fluctuations. Phys. Rev. E 94: 023304, 2016 [link].
K. Lykov, X. Li, H. Lei, I. V. Pivkin, and G. E. Karniadakis. Inflow/Outflow Boundary Conditions for Particle-Based Blood Flow Simulations: Application to Arterial Bifurcations and Trees. PLoS Comput. Biol. 11 (8): e1004410, 2015 [link].
H. Lei, X. Yang, B. Zheng, G. Lin, and N. A. Baker. Constructing Surrogate Models of Complex Systems with Enhanced Sparsity: Quantifying the Influence of Conformational Uncertainty in Biomolecular Solvation. SIAM Multiscale Model. Simul. 13 (4): 1327–1353, 2015 [link].
H. Lei, C. J. Mundy, G. K. Schenter, and N. K. Voulgarakis. 2015. Modeling Nanoscale Hydrodynamics by Smoothed Dissipative Particle Dynamics. J. Chem. Phys. 142 (19): 194504, 2015 [link].
X. Li, E. Du, H. Lei, Y. Tang, M. Dao, S. Suresh, and G. E. Karniadakis. Patient-Specific Blood Rheology in Sickle-Cell Anaemia. Interface Focus 6 (1): 20150065, 2015 [link].
X. Li, Z. Peng, H. Lei, M. Dao, and G. E. Karniadakis. Probing Red Blood Cell Mechanics, Rheology and Dynamics with a Two-Component Multi-Scale Model. Phil. Trans. R. Soc. A 372 (2021): 20130389, 2014 [link].
Z. Li, Y. Tang, H. Lei, B. Caswell, and G. E. Karniadakis. Energy-Conserving Dissipative Particle Dynamics with Temperature-Dependent Properties. J. Comput. Phys. 265: 113–27, 2014 [link].
H. Lei and G. E. Karniadakis. Probing Vasoocclusion Phenomena in Sickle Cell Anemia via Mesoscopic Simulations. Proc. Natl. Acad. Sci. 110 (28): 11326–30, 2013 [link].
H. Lei, D. A. Fedosov, B. Caswell, and G. E. Karniadakis. Blood Flow in Small Tubes: Quantifying the Transition to the Non-Continuum Regime. J. Fluid Mech. 722: 214–39, 2013 [link].
H. Lei and G. E. Karniadakis. Predicting the Morphology of Sickle Red Blood Cells Using Coarse-Grained Models of Intracellualr Aligned Hemoglobin Polymers. Soft Matter 8: 4507–16, 2012 [link].
H. Lei and G. E. Karnidakis. Quantifying the Rheological and Hemodynamic Characteristics of Sickle Cell Anemia. Biophys. J. 102: 185–194, 2012 [link].
L. Grinberg, M. Deng, H. Lei, J. A. Insley, and G. E. Karniadakis. Multiscale Simulations of Blood Flow: From a Platelet to an Artery. Proc. of Conference of the Extreme Science and Engineering Discovery 33: 1–7, 2012 [link].
D. A. Fedosov, H. Lei, B. Caswell, S. Suresh, and G. E. Karniadakis. Multiscale Modeling of Red Blood Cell Mechanics and Blood Flow in Malaria. PLoS Comput. Biol. 7 (12): e1002270, 2011 [link].
H. Lei, D. A. Fedosov, and G. E. Karniadakis. Time-Dependent and Outflow Boundary Conditions for Dissipative Particle Dynamics. J. Comput. Phys. 230 (10): 3765–3779, 2011 [link].
H. Lei, B. Caswell, and G. E. Karniadakis. Direct Construction of Mesoscopic Models from Microscopic Simulations. Phys. Rev. E 81: 026704, 2010 [link].
Book Chapters
H. Lei and G. E. Karniadakis. Multiscale Modeling of Sickle Cell Anemia. In A. Quarteroni, editor, Modeling the Heart and the Circulatory System, 119–156. Springer, 2015 [link].
X. Li and H. Lei. Multiscale Modeling of Sickle Cell Anemia. In W. Andreoni and S. Yip, editors, Handbook of Materials Modeling: Applications: Current and Emerging Materials 1–18. Springer, 2018 [link].