Coarse Stability and Bifurcation Analysis Using Stochastic Simulators: Kinetic Monte Carlo Examples
arXiv:nlin/0111038 · doi:10.1063/1.1476929
Abstract
We implement a computer-assisted approach that, under appropriate conditions, allows the bifurcation analysis of the coarse dynamic behavior of microscopic simulators without requiring the explicit derivation of closed macroscopic equations for this behavior. The approach is inspired by the so-called time-step per based numerical bifurcation theory. We illustrate the approach through the computation of both stable and unstable coarsely invariant states for Kinetic Monte Carlo models of three simple surface reaction schemes. We quantify the linearized stability of these coarsely invariant states, perform pseudo-arclength continuation, detect coarse limit point and coarse Hopf bifurcations and construct two-parameter bifurcation diagrams.
26 pages, 5 figures
Cited by in corpus (37)
- Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations
- Compressive Sampling of Polynomial Chaos Expansions: Convergence Analysis and Sampling Strategies
- Coherence Motivated Sampling and Convergence Analysis of Least-Squares Polynomial Chaos Regression
- Coarse Brownian Dynamics for Nematic Liquid Crystals: Bifurcation Diagrams via Stochastic Simulation
- Coarse-Grained Kinetic Computations for Rare Events: Application to Micelle Formation
- Coarse Projective kMC Integration: Forward/Reverse Initial and Boundary Value Problems
- Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation
- Constructing coarse-scale bifurcation diagrams from spatio-temporal observations of microscopic simulations: A parsimonious machine learning approach
- Microscopic/stochastic timesteppers and coarse control: a kinetic Monte Carlo example
- Basis Adaptive Sample Efficient Polynomial Chaos (BASE-PC)
- Coarse Bifurcation Diagrams via Microscopic Simulators: A State-Feedback Control-Based Approach
- A comparative study of two stochastic mode reduction methods
- Coarse Grained Computations for a Micellar System
- Deterministic continutation of stochastic metastable equilibria via Lyapunov equations and ellipsoids
- Fitting Effective Diffusion Models to Data Associated with a "Glassy Potential": Estimation, Classical Inference Procedures and Some Heuristics
- Equation-Free Multiscale Computational Analysis of Individual-Based Epidemic Dynamics on Networks
- Adaptive Detection of Instabilities: An Experimental Feasibility Study
- Efficient calculation of phase coexistence and phase diagrams: application to a binary phase-field crystal model
- Going with the Flow: a Lagrangian approach to self-similar dynamics and its consequences
- Equation-Free Multiscale Computations in Social Networks: from Agent-based Modelling to Coarse-grained Stability and Bifurcation Analysis
- Multiscale analysis of re-entrant production lines: An equation-free approach
- Multiscale Computations on Neural Networks: From the Individual Neuron Interactions to the Macroscopic-Level Analysis
- Equation-free optimal switching policies for bistable reacting systems using coarse time-steppers
- Adaptive stochastic continuation with a modified lifting procedure applied to complex systems
- Convergence of equation-free methods in the case of finite time scale separation with application to deterministic and stochastic systems
- Equation-free, multiscale computation for unsteady random diffusion
- A Numerical Method for the Parametrization of Stable and Unstable Manifolds of Microscopic Simulators
- Uncertainty Quantification for Atomistic Reaction Models: An Equation-Free Stochastic Simulation Algorithm Example
- Optimal switching policies using coarse timesteppers
- The gap-tooth scheme for homogenization problems
- Patch dynamics with buffers for homogenization problems
- System Level Numerical Analysis of a Monte Carlo Simulation of the E. Coli Chemotaxis
- A Systems-Based Approach to Multiscale Computation: Equation-Free Detection of Coarse-Grained Bifurcations
- Coarse-Grained Analysis of Microscopic Neuronal Simulators on Networks: Bifurcation and Rare-events computations
- Detection of coarse-grained unstable states of microscopic/stochastic systems: a timestepper-based iterative protocol
- Towards an efficient multiscale modeling of low-dimensional reactive systems: study of numerical closure procedures
- A Compressive Sampling Approach To Adaptive Multi-Resolution Approximation of Differential Equations With Random Inputs