Simulating sticky particles: A Monte Carlo method to sample a stratification
arXiv:1912.10176 · doi:10.1063/5.0019550
Abstract
Many problems in materials science and biology involve particles interacting with strong, short-ranged bonds, that can break and form on experimental timescales. Treating such bonds as constraints can significantly speed up sampling their equilibrium distribution, and there are several methods to sample probability distributions subject to fixed constraints. We introduce a Monte Carlo method to handle the case when constraints can break and form. More generally, the method samples a probability distribution on a stratification: a collection of manifolds of different dimensions, where the lower-dimensional manifolds lie on the boundaries of the higher-dimensional manifolds. We show several applications of the method in polymer physics, self-assembly of colloids, and volume calculation in high dimensions.
References in corpus (21)
- Extended corresponding-states behavior for particles with variable range attractions
- Collective Langevin Dynamics of Flexible Cytoskeletal Fibers
- Coarse-graining DNA for simulations of DNA nanotechnology
- Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles
- Phase diagram of the adhesive hard sphere fluid
- Rejection-free Geometric Cluster Algorithm for Complex Fluids
- Geodesic Monte Carlo on Embedded Manifolds
- Turning Statistical Physics Models Into Materials Design Engines
- A geometrical approach to computing free energy landscapes from short-ranged potentials
- Two-Dimensional Clusters of Colloidal Spheres: Ground States, Excited States, and Structural Rearrangements
- Enumerating rigid sphere packings
- Analytic solutions for Baxter's model of sticky hard sphere fluids within closures different from the Percus_Yevick approximation
- Majorization for Changes in Angles Between Subspaces, Ritz Values, and Graph Laplacian Spectra
- The Information Capacity of Specific Interactions
- Sticky Brownian Motion and its Numerical Solution
- Efficient sampling of reversible cross-linking polymers: Self-assembly of single-chain polymeric nanoparticles
- Linear Dimensions of Adsorbed Semiflexible Polymers: What can be learned about their persistence length?
- Free energy of singular sticky-sphere clusters
- A new configurational bias scheme for sampling supramolecular structures
- Simulated Tempering Method in the Infinite Switch Limit with Adaptive Weight Learning
- From canyons to valleys: Numerically continuing sticky hard sphere clusters to the landscapes of smoother potentials