Zhenli Xu
YOU?
Author Swipe
View article: Derivative-informed Graph Convolutional Autoencoder with Phase Classification for the Lifshitz-Petrich Model
Derivative-informed Graph Convolutional Autoencoder with Phase Classification for the Lifshitz-Petrich Model Open
The Lifshitz-Petrich (LP) model is a classical model for describing complex spatial patterns such as quasicrystals and multiphase structures. Solving and classifying the solutions of the LP model is challenging due to the presence of high-…
View article: Random Batch Ewald Method for Dielectrically Confined Coulomb Systems
Random Batch Ewald Method for Dielectrically Confined Coulomb Systems Open
Quasi two-dimensional Coulomb systems have drawn widespread interest. The reduced symmetry of these systems leads to complex collective behaviors, yet simultaneously poses significant challenges for particle-based simulations. In this pape…
View article: Low-dimensional compact states in 3D moiré lattices
Low-dimensional compact states in 3D moiré lattices Open
Moiré lattices formed by superimposing rotated two-dimensional (2D) periodic sublattices, such as twisted bilayer graphene, can exhibit fascinating properties not observed in their individual constituent layers. Despite extensive research …
View article: Intrinsic local Gauss's law preserving PIC method: A self-consistent field-particle update scheme for plasma simulations
Intrinsic local Gauss's law preserving PIC method: A self-consistent field-particle update scheme for plasma simulations Open
In order to perform physically faithful particle-in-cell (PIC) simulations, the Gauss's law stands as a critical requirement, since its violation often leads to catastrophic errors in long-term plasma simulations. This work proposes a nove…
View article: Weighted balanced truncation method for approximating kernel functions by exponentials
Weighted balanced truncation method for approximating kernel functions by exponentials Open
Kernel approximation with exponentials is useful in many problems with convolution quadrature and particle interactions such as integral-differential equations, molecular dynamics and machine learning. This paper proposes a weighted balanc…
View article: Machine-Learning Interatomic Potentials for Long-Range Systems
Machine-Learning Interatomic Potentials for Long-Range Systems Open
Machine-learning interatomic potentials have emerged as a revolutionary class of force-field models in molecular simulations, delivering quantum-mechanical accuracy at a fraction of the computational cost and enabling the simulation of lar…
View article: Random batch sum-of-Gaussians algorithm for molecular dynamics simulations of Yukawa systems in three dimensions
Random batch sum-of-Gaussians algorithm for molecular dynamics simulations of Yukawa systems in three dimensions Open
Yukawa systems have drawn widespread interest across various applications. In this paper, we introduce a novel random batch sum-of-Gaussians (RBSOG) algorithm for molecular dynamics simulations of 3D Yukawa systems with periodic boundary c…
View article: EGPT-PINN: Entropy-enhanced Generative Pre-Trained Physics Informed Neural Networks for parameterized nonlinear conservation laws
EGPT-PINN: Entropy-enhanced Generative Pre-Trained Physics Informed Neural Networks for parameterized nonlinear conservation laws Open
We propose an entropy-enhanced Generative Pre-Trained Physics-Informed Neural Network with a transform layer (EGPT-PINN) for solving parameterized nonlinear conservation laws. The EGPT-PINN extends the traditional physics-informed neural n…
View article: A fast spectral sum-of-Gaussians method for electrostatic summation in quasi-2D systems
A fast spectral sum-of-Gaussians method for electrostatic summation in quasi-2D systems Open
The quasi-2D electrostatic systems, characterized by periodicity in two dimensions with a free third dimension, have garnered significant interest in many fields. We apply the sum-of-Gaussians (SOG) approximation to the Laplace kernel, div…
View article: Variance-reduced random batch Langevin dynamics
Variance-reduced random batch Langevin dynamics Open
The random batch method is advantageous in accelerating force calculations in particle simulations, but it poses a challenge of removing the artificial heating effect in application to the Langevin dynamics. We develop an approach to solve…
View article: RBMD: A molecular dynamics package enabling to simulate 10 million all-atom particles in a single graphics processing unit
RBMD: A molecular dynamics package enabling to simulate 10 million all-atom particles in a single graphics processing unit Open
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of par…
View article: A note on accurate pressure calculations of Coulomb systems with periodic boundary conditions
A note on accurate pressure calculations of Coulomb systems with periodic boundary conditions Open
In this note, we address some issues concerning the accurate pressure calculation of Coulomb systems with periodic boundary conditions. First, we prove that the formulas for the excess part of the pressure with Ewald summation also reduce …
View article: TGPT-PINN: Nonlinear model reduction with transformed GPT-PINNs
TGPT-PINN: Nonlinear model reduction with transformed GPT-PINNs Open
We introduce the Transformed Generative Pre-Trained Physics-Informed Neural Networks (TGPT-PINN) for accomplishing nonlinear model order reduction (MOR) of transport-dominated partial differential equations in an MOR-integrating PINNs fram…
View article: Fast Algorithm for Quasi-2D Coulomb Systems
Fast Algorithm for Quasi-2D Coulomb Systems Open
Quasi-2D Coulomb systems are of fundamental importance and have attracted much attention in many areas nowadays. Their reduced symmetry gives rise to interesting collective behaviors, but also brings great challenges for particle-based sim…
View article: Energy Stable Scheme for Random Batch Molecular Dynamics
Energy Stable Scheme for Random Batch Molecular Dynamics Open
The computational bottleneck of molecular dynamics is the pairwise additive long-range interactions between particles. The random batch Ewald (RBE) method provides a highly efficient and superscalable solver for long-range interactions, bu…
View article: Local Structure-Preserving Relaxation Method for Charged Systems on Unstructured Meshes
Local Structure-Preserving Relaxation Method for Charged Systems on Unstructured Meshes Open
This work considers charged systems described by the modified Poisson--Nernst--Planck (PNP) equations, which incorporate ionic steric effects and the Born solvation energy for dielectric inhomogeneity. Solving the steady-state modified PNP…
View article: Hierarchical Interpolative Factorization for Self Green's Function in 3D Modified Poisson-Boltzmann Equations
Hierarchical Interpolative Factorization for Self Green's Function in 3D Modified Poisson-Boltzmann Equations Open
The modified Poisson-Boltzmann (MPB) equations are often used to describe equilibrium particle distribution of ionic systems. In this paper, we propose a fast algorithm to solve MPB equations with the self Green's function as the self ener…
View article: An asymptotic-preserving and energy-conserving particle-in-cell method for Vlasov–Maxwell equations
An asymptotic-preserving and energy-conserving particle-in-cell method for Vlasov–Maxwell equations Open
In this paper, we develop an asymptotic-preserving and energy-conserving (APEC) Particle-In-Cell (PIC) algorithm for the Vlasov–Maxwell system. This algorithm not only guarantees that the asymptotic limiting of the discrete scheme is a con…
View article: How Thermal Effect Regulates Cyclic Voltammetry of Supercapacitors
How Thermal Effect Regulates Cyclic Voltammetry of Supercapacitors Open
Cyclic voltammetry (CV) is a powerful technique for characterizing electrochemical properties of electrochemical devices. During charging-discharging cycles, thermal effect has profound impact on its performance, but existing theoretical m…
View article: Error estimate of the u-series method for molecular dynamics simulations
Error estimate of the u-series method for molecular dynamics simulations Open
This paper provides an error estimate for the u-series method of the Coulomb interaction in molecular dynamics simulations. We show that the number of truncated Gaussians $M$ in the u-series and the base of interpolation nodes $b$ in the b…
View article: A Maxwell–Ampère Nernst–Planck Framework for Modeling Charge Dynamics
A Maxwell–Ampère Nernst–Planck Framework for Modeling Charge Dynamics Open
Understanding the properties of charge dynamics is crucial to many practical applications, such as electrochemical energy devices and transmembrane ion channels. This work proposes a Maxwell–Ampère Nernst–Planck (MANP) framework for the de…
View article: Dual-Mode Biosensor for Simultaneous and Rapid Detection of Live and Whole Salmonella typhimurium Based on Bioluminescence and Fluorescence Detection
Dual-Mode Biosensor for Simultaneous and Rapid Detection of Live and Whole Salmonella typhimurium Based on Bioluminescence and Fluorescence Detection Open
Both live and dead Salmonella typhimurium (S.T) are harmful to human health, but there are differences in pathological mechanism, dosage, and security. It is crucial to develop a rapid and simultaneous assay to distinguish and quantify liv…
View article: A microfluidic chip-based multivalent DNA walker amplification biosensor for the simultaneous detection of multiple food-borne pathogens
A microfluidic chip-based multivalent DNA walker amplification biosensor for the simultaneous detection of multiple food-borne pathogens Open
A multivalent DNA walker amplification biosensor combined with the microfluidic chip for simultaneously and sensitively detecting V.P, S.T, and S.A bacteria.
View article: Improved Random Batch Ewald Method in Molecular Dynamics Simulations
Improved Random Batch Ewald Method in Molecular Dynamics Simulations Open
The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano/microscale. The method shows great potential to solve the computational bottleneck of long-range inter…