Related papers: Lattice models and Monte Carlo methods for simulat…
Coordinating functional parts to operate in concert is essential for machinery. In gear trains, meshed gears are compactly interlocked, working together to impose rotation or translation. In photosynthetic systems, a variety of biological…
In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger…
Quantum Monte-Carlo simulations of hybrid quantum-classical models such as the double exchange Hamiltonian require calculating the density of states of the quantum degrees of freedom at every step. Unfortunately, the computational…
For much of the last three decades Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, $J$, or J factor, for DNA models having sequence-dependent bends or inhomogeneous…
We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction $0.5$. In order to reduce the local density fluctuations, we test a…
We generalize the Hamiltonian Monte Carlo algorithm with a stack of neural network layers and evaluate its ability to sample from different topologies in a two dimensional lattice gauge theory. We demonstrate that our model is able to…
Biology is full of intricate molecular structures whose geometries are inextricably linked to their function. Many of these structures exhibit varying curvature, such as the helical structure of the bacterial flagellum, which is critical…
We introduce an off-lattice model with continuous particle distances and pair-potential interactions which allows for the efficient simulation of strained heteroepitaxial growth by means of kinetic Monte Carlo (KMC) simulations. We discuss…
The interaction between light and matter can be controlled efficiently by structuring materials at a length scale shorter than the wavelength of interest. With the goal to build optical devices that operate at the nanoscale, plasmonics has…
We develop a direct diagrammatic Monte Carlo framework for the Renyi entanglement entropy of interacting lattice fermions. The method starts from the fermionic graded-swap representation of Z_n[A]=Tr_A\rho_A^n, which converts the entropy…
The use of origami in engineering has significantly expanded in recent years, spanning deployable structures across scales, folding robotics, and mechanical metamaterials. However, finding foldable paths can be a formidable task as the…
Critical slowing down, where autocorrelation grows rapidly near the continuum limit due to Hybrid Monte Carlo (HMC) moving through configuration space inefficiently, still challenges lattice gauge theory simulations. Combining neural field…
Monte Carlo (MC) simulations of lattice models are a widely used way to compute thermodynamic properties of substitutional alloys. A limitation to their more widespread use is the difficulty of driving a MC simulation in order to obtain the…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable quasicrystals even at very narrow patch widths, provided…
Most binary superlattices created using DNA functionalization or other approaches rely on particle size differences to achieve compositional order and structural diversity. Here we study two-dimensional (2D) assembly of DNA-functionalized…
Controlling the size and shape of assembled structures is a fundamental challenge in self-assembly, and is highly relevant in material design and biology. Here, we show that specific, but promiscuous, short-range binding interactions make…
The silicification of DNA origami structures increases their mechanical and thermal stability and provides chemical protection. So far, it is unclear how silicification affects the internal structure of the DNA origami and whether the whole…
We present in detail two variants of the lattice Monte Carlo method aimed at tackling systems in external trapping potentials: a uniform-lattice approach with hard-wall boundary conditions, and a non-uniform Gauss-Hermite lattice approach.…
The Watson-Crick complementary properties of DNA make DNA a useful tool for the self-assembly of various target complexes. Concepts from graph theory can be used to model the self-assembling process in which the vertices of the graph…