Related papers: Lattice models and Monte Carlo methods for simulat…
Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform…
Self-folding origami, structures that are engineered flat to fold into targeted, three-dimensional shapes, have many potential engineering applications. Though significant effort in recent years has been devoted to designing fold patterns…
We propose a new strategy for robust high-quality self-assembly of non-trivial periodic structures out of patchy particles, and investigate it with Brownian Dynamics (BD) simulations. Its first element is the use of specific patch-patch and…
Ribbons are topological objects of biological and technological importance. Here, we study the folding of thick ribbons with hydrophobic surfaces in a bad solvent in regimes in which either the ribbon's thickness or the solvent molecule…
Origami structures are characterized by a network of folds and vertices joining unbendable plates. For applications to mechanical design and self-folding structures, it is essential to understand the interplay between the set of folds in…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
Shape-morphing finds widespread utility, from the deployment of small stents and large solar sails to actuation and propulsion in soft robotics. Origami structures provide a template for shape-morphing, but rules for designing and folding…
Due to the intrinsic complexity of the quantum many-body problem, quantum Monte Carlo algorithms and their corresponding Monte Carlo configurations can be defined in various ways. Configurations corresponding to few Feynman diagrams often…
We use simple analytic arguments and lattice-based computer simulations to study the growth of structures made from a large number of distinct component types. Components possess 'designed' interactions, chosen to stabilize an equilibrium…
A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are…
We report developments of the kinetic Monte Carlo (KMC) method with improved accuracy and increased versatility for the description of atomic diffusivity on metal surfaces. The on-lattice constraint built into our recently proposed…
We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of the individual polymers and their…
We study a harmonic triangular lattice, which relaxes in the presence of a weak, short-wavelength periodic potential. Monte Carlo simulations reveal that the elastic lattice has only short-ranged positional correlations, despite the absence…
We describe a class of growth algorithms for finding low energy states of heteropolymers. These polymers form toy models for proteins, and the hope is that similar methods will ultimately be useful for finding native states of real proteins…
We characterize the phase-space of all Helical Miura Origami. These structures are obtained by taking a partially folded Miura parallelogram as the unit cell, applying a generic helical or rod group to the cell, and characterizing all the…
We present a Monte Carlo method for the direct evaluation of the difference between the free energies of two crystal structures. The method is built on a lattice-switch transformation that maps a configuration of one structure onto a…
An alternative to Monte Carlo techniques requiring large sampling times is presented here. Ideas from a genetic algorithm are used to select the best initial states from many independent, parallel Metropolis-Hastings iterations that are run…
Periodic origami patterns made with repeating unit cells of creases and panels bend and twist in complex ways. In principle, such soft modes of deformation admit a simplified asymptotic description in the limit of a large number of cells.…
We propose the concept of autonomous self-damaging in "smart" composite materials, controlled by activation of added nanosize "damaging" capsules. Percolation-type modeling approach earlier applied to the related concept of self-healing…
Quantum Monte Carlo methods are powerful tools for studying quantum many-body systems but face difficulties in accessing excited states and in treating sign problems. We present a continuous-time path-integral Monte Carlo method for…