Related papers: Smoluchowski aggregation-fragmentation equations: …
In this paper, we demonstrate that in many NP-complete variants of the stable matching problem, such as the Stable Hypergraph Matching problem, the Stable Multicommodity Flow problem, and the College Admission problem with common quotas, a…
Numerical solution of the chemical master equation for stochastic reaction networks typically suffers from the state space explosion problem due to the curse of dimensionality and from stiffness due to multiple time scales. The dimension of…
Spectral clustering is a novel clustering method which can detect complex shapes of data clusters. However, it requires the eigen decomposition of the graph Laplacian matrix, which is proportion to $O(n^3)$ and thus is not suitable for…
In this paper we present a fast algorithm for the numerical solution of systems of reaction-diffusion equations, $\partial_t u + a \cdot \nabla u = \Delta u + F (x, t, u)$, $x \in \Omega \subset \mathbf{R}^3$, $t > 0$. Here, $u$ is a…
Direct factorization methods for the solution of large, sparse linear systems that arise from PDE discretizations are robust, but typically show poor time and memory scalability for large systems. In this paper, we describe an efficient…
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…
Astrochemical simulations are a powerful tool for revealing chemical evolution in the interstellar medium. Astrochemical calculations require efficient processing of large matrices for the chemical networks. The large chemical reaction…
Spectral clustering is one of the most popular clustering methods. However, the high computational cost due to the involved eigen-decomposition procedure can immediately hinder its applications in large-scale tasks. In this paper we use…
This work presents a novel stabilization strategy for the Galerkin formulation of the incompressible Navier-Stokes equations, developed to achieve high accuracy while ensuring convergence and compatibility with high-order elements on…
We propose a simple and efficient clustering method for high-dimensional data with a large number of clusters. Our algorithm achieves high-performance by evaluating distances of datapoints with a subset of the cluster centres. Our…
We propose a zero-order optimization method for sequential min-max problems based on two populations of interacting particles. The systems are coupled so that one population aims to solve the inner maximization problem, while the other aims…
We study a multigrid method for solving large linear systems of equations with tensor product structure. Such systems are obtained from stochastic finite element discretization of stochastic partial differential equations such as the…
This paper presents an efficient approach to image segmentation that approximates the piecewise-smooth (PS) functional in [12] with explicit solutions. By rendering some rational constraints on the initial conditions and the final solutions…
We study numerical methods for dissipative particle dynamics (DPD), which is a system of stochastic differential equations and a popular stochastic momentum-conserving thermostat for simulating complex hydrodynamic behavior at mesoscales.…
We study the positive stationary solutions of a standard finite-difference discretization of the semilinear heat equation with nonlinear Neumann boundary conditions. We prove that, if \emph{the absorption is small enough}, compared with the…
The key problem of statistical physics standing over one hundred years is how to exactly calculate the partition function (or free energy) of many-body interaction systems, which severely hinders application of the theory for realistic…
We present two accelerated numerical algorithms for single-component and binary Gross-Pitaevskii (GP) equations coupled with microwaves (electromagnetic fields) in steady state. One is based on a normalized gradient flow formulation, called…
A new approach to the steady state detection in the uniformization method of solving continuous time Markov chains is introduced. The method is particularly useful in solving inhomogenous CTMC's in multiple steps, where the desired error…
Using molecular dynamics simulations, the kinetics of bundle formation for stiff polyelectrolytes such as actin is studied in the solution of multivalent salt. The dominant kinetic mode of aggregation is found to be the case of one end of…
Kernel based methods provide a way to reconstruct potentially high-dimensional functions from meshfree samples, i.e., sampling points and corresponding target values. A crucial ingredient for this to be successful is the distribution of the…