152 citations · 411 across the 16 of their papers we have counts for
16 papers
Construction of coarse-grained molecular dynamics with many-body non-Markovian memory
Liyao Lyu, Huan Lei
We introduce a machine-learning-based coarse-grained molecular dynamics (CGMD) model that faithfully retains the many-body nature of the inter-molecular dissipative interactions. U…
Machine learning assisted coarse-grained molecular dynamics modeling of meso-scale interfacial fluids
Pei Ge, Linfeng Zhang, Huan Lei
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and conti…
Data-driven construction of stochastic reduced dynamics encoded with non-Markovian features
Zhiyuan She, Pei Ge, Huan Lei
One important problem in constructing the reduced dynamics of molecular systems is the accurate modeling of the non-Markovian behavior arising from the dynamics of unresolved varia…
Generalized second fluctuation-dissipation theorem in the nonequilibrium steady state: Theory and applications
Yuanran Zhu, Huan Lei, Changho Kim
In this paper, we derive a generalized second fluctuation-dissipation theorem (FDT) for stochastic dynamical systems in the steady state. The established theory is built upon the M…
Effective Mori-Zwanzig equation for the reduced-order modeling of stochastic systems
Yuanran Zhu, Huan Lei
Built upon the hypoelliptic analysis of the effective Mori-Zwanzig (EMZ) equation for observables of stochastic dynamical systems, we show that the obtained semigroup estimates for…
Machine learning based non-Newtonian fluid model with molecular fidelity
Huan Lei, Lei Wu, Weinan E
We introduce a machine-learning-based framework for constructing continuum non-Newtonian fluid dynamics model directly from a micro-scale description. Dumbbell polymer solutions ar…
Data-driven molecular modeling with the generalized Langevin equation
Francesca Grogan, Huan Lei, Xiantao Li +1
The complexity of molecular dynamics simulations necessitates dimension reduction and coarse-graining techniques to enable tractable computation. The generalized Langevin equation…
Improving solution accuracy and convergence for stochastic physics parameterizations with colored noise
Panos Stinis, Huan Lei, Jing Li +1
Stochastic parameterizations are used in numerical weather prediction and climate modeling to help capture the uncertainty in the simulations and improve their statistical properti…
A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness
Huan Lei, Jing Li, Peiyuan Gao +2
The challenge of quantifying uncertainty propagation in real-world systems is rooted in the high-dimensionality of the stochastic input and the frequent lack of explicit knowledge…
A General Framework for Enhancing Sparsity of Generalized Polynomial Chaos Expansions
Xiu Yang, Xiaoliang Wan, Lin Lin +1
Compressive sensing has become a powerful addition to uncertainty quantification when only limited data is available. In this paper we provide a general framework to enhance the sp…
Atomic radius and charge parameter uncertainty in biomolecular solvation energy calculations
Xiu Yang, Huan Lei, Peiyuan Gao +3
Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determine…
Systematic parameter inference in stochastic mesoscopic modeling
Huan Lei, Xiu Yang, Zhen Li +1
We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by diss…
Data-driven parameterization of the generalized Langevin equation
Huan Lei, Nathan Baker, Xiantao Li
We present a data-driven approach to determine the memory kernel and random noise in generalized Langevin equations. To facilitate practical implementations, we parameterize the ke…
Smoothed Dissipative Particle Dynamics model for mesoscopic multiphase flows in the presence of thermal fluctuations
Huan Lei, Nathan A. Baker, Lei Wu +3
Thermal fluctuations cause perturbations of fluid-fluid interfaces and highly nonlinear hydrodynamics in multiphase flows. In this work, we develop a novel multiphase smoothed diss…
Enhancing Sparsity of Hermite Polynomial Expansions by Iterative Rotations
Xiu Yang, Huan Lei, Nathan A. Baker +1
Compressive sensing has become a powerful addition to uncertainty quantification in recent years. This paper identifies new bases for random variables through linear mappings such…
Quantifying the influence of conformational uncertainty in biomolecular solvation
Huan Lei, Xiu Yang, Bin Zheng +2
Biomolecules exhibit conformational fluctuations near equilibrium states, inducing uncertainty in various biological properties in a dynamic way. We have developed a general method…