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Wenxiao Pan

Publications and source records attributed to Wenxiao Pan.

18 recordsLinked to original sources

SPLIT-PINN: Separable Probability Learning Technique via Physics-Informed Neural Networks for High-Dimensional Probabilistic Modeling

We present a probabilistic modeling framework for incorporating small-scale spatial heterogeneity into macroscopic descriptions of material behavior for polycrystalline metallic materials. Spatially heterogeneous material state fields are represented using probability density functions (PDFs), providing a principled statistical description of microstructural variability and state evolution across different computational polycrystalline realizations. The framework is built on the inverse identification of a probabilistic transport model, formulated as a Liouville equation with an unknown drift term. To enable accurate, stable, and interpretable inference of this drift field in high-dimensional, transport-dominated settings, we develop a Separable Probability Learning Technique via Physics-Informed Neural Networks (SPLIT-PINN). This method incorporates a marginal-correction drift decomposition, orthogonality constraints, and residual-based adaptive training to enhance well-posedness, numerical stability, and physical consistency without imposing restrictive parametric assumptions. Using SPLIT-PINN, the drift field governing the temporal evolution of joint state PDFs is inferred directly from data. After benchmark validation, the framework is applied to physical computational datasets describing the evolution of polycrystalline microstructural states, including von Mises stress, dislocation density, and equivalent plastic strain rate. The learned Liouville model, trained on a single dataset, is subsequently used in forward predictions of the temporal evolution of joint and marginal PDFs for multiple unseen polycrystal realizations. Quantitative comparisons with reference PDFs demonstrate that the proposed framework yields accurate and robust probabilistic predictions and generalizes effectively across datasets.

cond-mat.mtrl-sci

Error Estimates for the Arnoldi Approximation of a Matrix Square Root

The Arnoldi process provides an efficient framework for approximating functions of a matrix applied to a vector, i.e., of the form $f(M)\bm{b}$, by repeated matrix-vector multiplications. In this paper, we derive error estimates for approximating the action of a matrix square root using the Arnoldi process, where the integral representation of the error is reformulated in terms of the error for solving the linear system $M\bm{x}=\bm{b}$. The results extend the error analysis of the Lanczos method for Hermitian matrices in [Chen et al., SIAM J. Matrix Anal. Appl., 2022] to non-Hermitian cases and provide an improved bound for the Hermitian case. Furthermore, in practical settings, the matrix may only be available via approximate or structured representations. Motivated by this, we extend the analysis and establish a generalized error bound for perturbed matrices. The numerical results on matrices with different structures demonstrate that our theoretical analysis yields a reliable upper bound. Finally, simulations on large-scale matrices arising in particulate suspensions, represented in hierarchical matrix form, validate the effectiveness and practicality of the approach.

math.NA

Towards Quantum Accelerated Large-scale Topology Optimization

We present a new method that efficiently solves TO problems and provides a practical pathway to leverage quantum computing to exploit potential quantum advantages. This work targets on large-scale, multi-material TO challenges for three-dimensional (3D) continuum structures, beyond what have been addressed in prior studies. Central to this new method is the modified Dantzig-Wolfe (MDW) decomposition, which effectively mitigates the escalating computational cost associated with using classical Mixed-Integer Linear Programming (MILP) solvers to solve the master problems involved in TO, by decomposing the MILP into local and global sub-problems. Evaluated on 3D bridge designs, our classical implementation achieves comparable solution quality to state-of-the-art TO methods while reducing computation time by orders of magnitude. It also maintains low runtimes even in extreme cases where classical MILP solvers fail to converge, such as designs involving over 50 million variables. The computationally intensive local sub-problems, which are essentially Binary Integer Programming (BIP) problems, can potentially be accelerated by quantum computing via their equivalent Quadratic Unconstrained Binary Optimization (QUBO) formulations. Enabled by the MDW decomposition, the resulting QUBO formulation requires only sparse qubit connectivity and incurs a QUBO construction cost that scales linearly with problem size, potentially accelerating BIP sub-problem solutions by an additional order of magnitude. All observed and estimated speedups become increasingly significant with larger problem sizes and when moving from single-material to multi-material designs. This suggests that this new method, along with quantum computing, will play an increasingly valuable role in addressing the scale and complexity of real-world TO applications.

physics.comp-ph

$\mathcal{H}$-HIGNN: A Scalable Graph Neural Network Framework with Hierarchical Matrix Acceleration for Simulation of Large-Scale Particulate Suspensions

We present a fast and scalable framework, leveraging graph neural networks (GNNs) and hierarchical matrix ($\mathcal{H}$-matrix) techniques, for simulating large-scale particulate suspensions, which have broader impacts across science and engineering. The framework draws on the Hydrodynamic Interaction Graph Neural Network (HIGNN) that employs GNNs to model the mobility tensor governing particle motion under hydrodynamic interactions (HIs) and external forces. HIGNN offers several advantages: it effectively captures both short- and long-range HIs and their many-body nature; it realizes a substantial speedup over traditional methodologies, by requiring only a forward pass through its neural networks at each time step; it provides explainability beyond black-box neural network models, through direct correspondence between graph connectivity and physical interactions; and it demonstrates transferability across different systems, irrespective of particles' number, concentration, configuration, or external forces. While HIGNN provides significant speedup, the quadratic scaling of its overall prediction cost (with respect to the total number of particles), due to intrinsically slow-decaying two-body HIs, limits its scalability. To achieve superior efficiency across all scales, in the present work we integrate $\mathcal{H}$-matrix techniques into HIGNN, reducing the prediction cost scaling to quasi-linear. Through comprehensive evaluations, we validate $\mathcal{H}$-HIGNN's accuracy, and demonstrate its quasi-linear scalability and superior computational efficiency. It requires only minimal computing resources; for example, a single mid-range GPU is sufficient for a system containing 10 million particles. Finally, we demonstrate $\mathcal{H}$-HIGNN's ability to efficiently simulate practically relevant large-scale suspensions of both particles and flexible filaments.

physics.comp-ph

Discrete Variable Topology Optimization Using Multi-Cut Formulation and Adaptive Trust Regions

We present a new framework for solving general topology optimization (TO) problems that find an optimal material distribution within a design space to maximize the performance of a structure while satisfying design constraints. These problems involve state variables that nonlinearly depend on the design variables, with objective functions that can be convex or non-convex, and may include multiple candidate materials. The framework is designed to greatly enhance computational efficiency, primarily by diminishing optimization iteration counts and thereby reducing the solving of associated state-equilibrium partial differential equations (PDEs). It maintains binary design variables and addresses the large-scale mixed integer nonlinear programming (MINLP) problem that arises from discretizing the design space and PDEs. The core of this framework is the integration of the generalized Benders' decomposition and adaptive trust regions. The trust-region radius adapts based on a merit function. To mitigate ill-conditioning due to extreme parameter values, we further introduce a parameter relaxation scheme where two parameters are relaxed in stages at different paces. Numerical tests validate the framework's superior performance, including minimum compliance and compliant mechanism problems in single-material and multi-material designs. We compare our results with those of other methods and demonstrate significant reductions in optimization iterations by about one order of magnitude, while maintaining comparable optimal objective function values. As the design variables and constraints increase, the framework maintains consistent solution quality and efficiency, underscoring its good scalability. We anticipate this framework will be especially advantageous for TO applications involving substantial design variables and constraints and requiring significant computational resources for PDE solving.

math.NA

Nanoscale Imaging of Phonons and Reconfiguration in Topologically-Engineered, Self-Assembled Nanoparticle Lattice

Topologically-engineered mechanical frames are important model constructs for architecture, machine mechanisms, and metamaterials. Despite significant advances in macroscopically fashioned frames, realization and phonon imaging of nanoframes have remained challenging. Here we extend for the first time the principles of topologically-engineered mechanical frames to lattices self-assembled from nanoparticles. Liquid-phase transmission electron microscopy images the vibrations of nanoparticles in self-assembled Maxwell and hexagonal lattices at the nanometer resolution, measuring a series of otherwise inaccessible properties such as phonon spectra and nonlinear lattice deformation paths. These properties are experimentally modulated by ionic strength, captured by our discrete mechanical model considering the complexity of nanoscale interactions and thermal fluctuations. The experiment-theory integration bridges mechanical metamaterials and colloidal self-assembly, opening new opportunities to manufacture phononic devices with solution processibility, transformability, light weight, and emergent functions, at underexplored length, frequency, and energy scales.

cond-mat.mtrl-sci

Quantum Topology Optimization via Quantum Annealing

We present a quantum annealing-based solution method for topology optimization (TO). In particular, we consider TO in a more general setting, i.e., applied to structures of continuum domains where designs are represented as distributed functions, referred to as continuum TO problems. According to the problem's properties and structure, we formulate appropriate sub-problems that can be solved on an annealing-based quantum computer. The methodology established can effectively tackle continuum TO problems formulated as mixed-integer nonlinear programs. To maintain the resulting sub-problems small enough to be solved on quantum computers currently accessible with small numbers of quits and limited connectivity, we further develop a splitting approach that splits the problem into two parts: the first part can be efficiently solved on classical computers, and the second part with a reduced number of variables is solved on a quantum computer. By such, a practical continuum TO problem of varying scales can be handled on the D-Wave quantum annealer. More specifically, we concern the minimum compliance, a canonical TO problem that seeks an optimal distribution of materials to minimize the compliance with desired material usage. The superior performance of the developed methodology is assessed and compared with the state-of-the-art heuristic classical methods, in terms of both solution quality and computational efficiency. The present work hence provides a promising new avenue of applying quantum computing to practical designs of topology for various applications.

math.NA

Fast Simulation of Particulate Suspensions Enabled by Graph Neural Network

Predicting the dynamic behaviors of particles in suspension subject to hydrodynamic interaction (HI) and external drive can be critical for many applications. By harvesting advanced deep learning techniques, the present work introduces a new framework, hydrodynamic interaction graph neural network (HIGNN), for inferring and predicting the particles' dynamics in Stokes suspensions. It overcomes the limitations of traditional approaches in computational efficiency, accuracy, and/or transferability. In particular, by uniting the data structure represented by a graph and the neural networks with learnable parameters, the HIGNN constructs surrogate modeling for the mobility tensor of particles which is the key to predicting the dynamics of particles subject to HI and external forces. To account for the many-body nature of HI, we generalize the state-of-the-art GNN by introducing higher-order connectivity into the graph and the corresponding convolutional operation. For training the HIGNN, we only need the data for a small number of particles in the domain of interest, and hence the training cost can be maintained low. Once constructed, the HIGNN permits fast predictions of the particles' velocities and is transferable to suspensions of different numbers/concentrations of particles in the same domain and to any external forcing. It has the ability to accurately capture both the long-range HI and short-range lubrication effects. We demonstrate the accuracy, efficiency, and transferability of the proposed HIGNN framework in a variety of systems. The requirement on computing resource is minimum: most simulations only require a desktop with one GPU; the simulations for a large suspension of 100,000 particles call for up to 6 GPUs.

cs.LG

A Multigrid Preconditioner for Spatially Adaptive High-order Meshless Method on Fluid-solid Interaction Problems

We present a monolithic geometric multigrid preconditioner for solving fluid-solid interaction problems in Stokes limit. The problems are discretized by a spatially adaptive high-order meshless method, the generalized moving least squares (GMLS) with adaptive $h$-refinement. In Stokes limit, solid kinematics can be dominated by the singularities governing the lubrication effects. Resolving those singularities with adaptive $h$-refinement can lead to an ill-conditioned linear system of equations. For constructing the interpolation and restriction operators - the key ingredients of the multigrid preconditioner, we utilize the geometric information of hierarchical sets of GMLS nodes generated in adaptive $h$-refinement. We build decoupled smoothers through physics-based splitting and then combine them via a multiplicative overlapping Schwarz approach. Through numerical examples with the inclusion of different numbers and shapes of solid bodies, we demonstrate the performance and assess the scalability of the designed preconditioner. As the total degrees of freedom and the number of solid bodies $N_s$ increase, the proposed monolithic geometric multigrid preconditioner can ensure convergence and good scalability when using the Krylov iterative method for solving the linear systems of equations generated from the spatially adaptive GMLS discretization. More specifically, for a fixed number of solid bodies, as the discretization resolution is incrementally refined, the number of iterations of the linear solver can be maintained at the same level, indicating nearly linear scalability of our preconditioner with respect to the total degrees of freedom. When $N_s$ increases, the number of iterations is nearly proportional to $\sqrt{N_s}$, implying the sublinear optimality with respect to the number of solid bodies.

math.NA

Data-driven Coarse-grained Modeling of Non-equilibrium Systems

Modeling a high-dimensional Hamiltonian system in reduced dimensions with respect to coarse-grained (CG) variables can greatly reduce computational cost and enable efficient bottom-up prediction of main features of the system for many applications. However, it usually experiences significantly altered dynamics due to loss of degrees of freedom upon coarse-graining. To establish CG models that can faithfully preserve dynamics, previous efforts mainly focused on equilibrium systems. In contrast, various soft matter systems are known out of equilibrium. Therefore, the present work concerns non-equilibrium systems and enables accurate and efficient CG modeling that preserves non-equilibrium dynamics and is generally applicable to any non-equilibrium process and any observable of interest. To this end, the dynamic equation of a CG variable is built in the form of the non-stationary generalized Langevin equation (nsGLE) to account for the dependence of non-equilibrium processes on the initial conditions, where the two-time memory kernel is determined from the data of the two-time auto-correlation function of the non-equilibrium trajectory-averaged observable of interest. By embedding the non-stationary non-Markovian process in an extended stochastic framework, an explicit form of the non-stationary random noise in the nsGLE is introduced, and the cost is significantly reduced for solving the nsGLE to predict the non-equilibrium dynamics of the CG variable. To prove and exploit the equivalence of the nsGLE and extended dynamics, the memory kernel is parameterized in a two-time exponential expansion. A data-driven hybrid optimization process is proposed for the parameterization, a non-convex and high-dimensional optimization problem.

cs.CE

Transfer Learning of Memory Kernels in Coarse-grained Modeling

The present work concerns the transferability of coarse-grained (CG) modeling in reproducing the dynamic properties of the reference atomistic systems across a range of parameters. In particular, we focus on implicit-solvent CG modeling of polymer solutions. The CG model is based on the generalized Langevin equation, where the memory kernel plays the critical role in determining the dynamics in all time scales. Thus, we propose methods for transfer learning of memory kernels. The key ingredient of our methods is Gaussian process regression. By integration with the model order reduction via proper orthogonal decomposition and the active learning technique, the transfer learning can be practically efficient and requires minimum training data. Through two example polymer solution systems, we demonstrate the accuracy and efficiency of the proposed transfer learning methods in the construction of transferable memory kernels. The transferability allows for out-of-sample predictions, even in the extrapolated domain of parameters. Built on the transferable memory kernels, the CG models can reproduce the dynamic properties of polymers in all time scales at different thermodynamic conditions (such as temperature and solvent viscosity) and for different systems with varying concentrations and lengths of polymers.

cs.CE

Data-driven nonintrusive reduced order modeling for dynamical systems with moving boundaries using Gaussian process regression

We present a data-driven nonintrusive model order reduction method for dynamical systems with moving boundaries. The proposed method draws on the proper orthogonal decomposition, Gaussian process regression, and moving least squares interpolation. It combines several attributes that are not simultaneously satisfied in the existing model order reduction methods for dynamical systems with moving boundaries. Specifically, the method requires only snapshot data of state variables at discrete time instances and the parameters that characterize the boundaries, but not further knowledge of the full-order model and the underlying governing equations. The dynamical systems can be generally nonlinear. The movements of boundaries are not limited to prescribed or periodic motions but can be free motions. In addition, we numerically investigate the ability of the reduced order model constructed by the proposed method to forecast the full-order solutions for future times beyond the range of snapshot data. The error analysis for the proposed reduced order modeling and the criteria to determine the furthest forecast time are also provided. Through numerical experiments, we assess the accuracy and efficiency of the proposed method in several benchmark problems. The snapshot data used to construct and validate the reduced order model are from analytical/numerical solutions and experimental measurements.

cs.CE

A spatially adaptive high-order meshless method for fluid-structure interactions

We present a scheme implementing an a posteriori refinement strategy in the context of a high-order meshless method for problems involving point singularities and fluid-solid interfaces. The generalized moving least squares (GMLS) discretization used in this work has been previously demonstrated to provide high-order compatible discretization of the Stokes and Darcy problems, offering a high-fidelity simulation tool for problems with moving boundaries. The meshless nature of the discretization is particularly attractive for adaptive h-refinement, especially when resolving the near-field aspects of variables and point singularities governing lubrication effects in fluid-structure interactions. We demonstrate that the resulting spatially adaptive GMLS method is able to achieve optimal convergence in the presence of singularities for both the div-grad and Stokes problems. Further, we present a series of simulations for flows of colloid suspensions, in which the refinement strategy efficiently achieved highly accurate solutions, particularly for colloids with complex geometries.

physics.comp-ph

Discrete-element model for the interaction between ocean waves and sea ice

We present a discrete element method (DEM) model to simulate the mechanical behavior of sea ice in response to ocean waves. The interaction of ocean waves and sea ice can potentially lead to the fracture and fragmentation of sea ice depending on the wave amplitude and period. The fracture behavior of sea ice is explicitly modeled by a DEM method, where sea ice is modeled by densely packed spherical particles with finite size. These particles are bonded together at their contact points through mechanical bonds that can sustain both tensile and compressive forces and moments. Fracturing can be naturally represented by the sequential breaking of mechanical bonds. For a given amplitude and period of incident ocean wave, the model provides information for the spatial distribution and time evolution of stress and micro-fractures and the fragment size distribution. We demonstrate that the fraction of broken bonds, , increases with increasing wave amplitude. In contrast, the ice fragment size l decreases with increasing amplitude. This information is important for the understanding of breakup of individual ice floes and floe fragment size.

physics.comp-ph

A Consistent Spatially Adaptive Smoothed Particle Hydrodynamics Method for Fluid-Structure Interactions

A new consistent, spatially adaptive, smoothed particle hydrodynamics (SPH) method for Fluid-Structure Interactions (FSI) is presented. The method combines several attributes that have not been simultaneously satisfied by other SPH methods. Specifically, it is second-order convergent; it allows for resolutions spatially adapted with moving (translating and rotating) boundaries of arbitrary geometries; and, it accelerates the FSI solution as the adaptive approach leads to fewer degrees of freedom without sacrificing accuracy. The key ingredients in the method are a consistent discretization of differential operators, a \textit{posteriori} error estimator/distance-based criterion of adaptivity, and a particle-shifting technique. The method is applied in simulating six different flows or FSI problems. The new method's convergence, accuracy, and efficiency attributes are assessed by comparing the results it produces with analytical, finite element, and consistent SPH uniform high-resolution solutions as well as experimental data.

physics.flu-dyn

A Consistent Multi-Resolution Smoothed Particle Hydrodynamics Method

We seek to accelerate and increase the size of simulations for fluid-structure interactions (FSI) by using multiple resolutions in the spatial discretization of the equations governing the time evolution of systems displaying two-way fluid-solid coupling. To this end, we propose a multi-resolution smoothed particle hydrodynamics (SPH) approach in which subdomains of different resolutions are directly coupled without any overlap region. The second-order consistent discretization of spatial differential operators is employed to ensure the accuracy of the proposed method. As SPH particles advect with the flow, a dynamic SPH particle refinement/coarsening is employed via splitting/merging to maintain a predefined multi-resolution configuration. Particle regularity is enforced via a particle-shifting technique to ensure accuracy and stability of the Lagrangian particle-based method embraced. The convergence, accuracy, and efficiency attributes of the new method are assessed by simulating four different flows. In this process, the numerical results are compared to the analytical, finite element, and consistent SPH single-resolution solutions. We anticipate that the proposed multi-resolution method will enlarge the class of SPH-tractable FSI applications.

physics.flu-dyn

Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smooth particle hydrodynamics

Background. The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors. We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. Results. The numerical method is first verified in simple systems and then applied to the calculation of ligand binding to an acetylcholinesterase monomer. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) boundary condition, is considered on the reactive boundaries. This new boundary condition treatment allows for the analysis of enzymes with "imperfect" reaction rates. Rates for inhibitor binding to mAChE are calculated at various ionic strengths and compared with experiment and other numerical methods. We find that imposition of the Robin BC improves agreement between calculated and experimental reaction rates. Conclusions. Although this initial application focuses on a single monomer system, our new method provides a framework to explore broader applications of SPH in larger-scale biomolecular complexes by taking advantage of its Lagrangian particle-based nature.

q-bio.BM

Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion

The currently existing theory of fluorescence correlation spectroscopy(FCS) is based on the linear fluctuation theory originally developed by Einstein, Onsager, Lax, and others as a phenomenological approach to equilibrium fluctuations in bulk solutions. For mesoscopic reaction-diffusion systems with nonlinear chemical reactions among a small number of molecules, a situation often encountered in single-cell biochemistry, it is expected that FCS time correlation functions of a reaction-diffusion system can deviate from the classic results of Elson and Magde. We first discuss this nonlinear effect for reaction systems without diffusion. For nonlinear stochastic reaction-diffusion systems here are no closed solutions; therefore, stochastic Monte-Carlo simulations are carried out. We show that the deviation is small for a simple bimolecular reaction; the most significant deviations occur when the number of molecules is small and of the same order. Our results show that current linear FCS theory could be adequate for measurements on biological systems that contain many other sources of uncertainties. At the same time it provides a framework for future measurements of nonlinear, fluctuating chemical reactions with high-precision FCS. Extending Delbrück-Gillespie's theory for stochastic nonlinear reactions with rapidly stirring to reaction-diffusion systems provides a mesoscopic model for chemical and biochemical reactions at nanometric and mesoscopic level such as a single biological cell.

physics.bio-ph