Related papers: Lattice models and Monte Carlo methods for simulat…
We present a method for direct hybrid Monte Carlo simulation of graphene on the hexagonal lattice. We compare the results of the simulation with exact results for a unit hexagonal cell system, where the Hamiltonian can be solved…
We propose a novel approach called Self-Learning Hybrid Monte Carlo (SLHMC) which is a general method to make use of machine learning potentials to accelerate the statistical sampling of first-principles density-functional-theory (DFT)…
We formulate statistical-mechanical inverse methods in order to determine optimized interparticle interactions that spontaneously produce target many-particle configurations. Motivated by advances that give experimentalists greater and…
An off-lattice Monte Carlo algorithm for solutions of equilibrium polymers (EP) is proposed. At low and moderate densities this is shown to reproduce faithfully the (static) properties found recently for flexible linear EP using a lattice…
Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA -- subject to the earlier found unusual, frustrated…
We investigate the salt-dependent current modulation of bundled DNA nanostructures in a nanopore. To this end, we developed four simulation models for a 2x2 origami structure with increasing level of detail: from the mean-field level to an…
In this work we introduce a worldline based fermion Monte Carlo algorithm for studying few body quantum mechanics of self-interacting fermions in the Hamiltonian lattice formulation. Our motivation to construct the method comes from our…
Topological mechanical metamaterials have been widely explored for their boundary states, which can be robustly isolated or transported in a controlled manner. However, such systems often require pre-configured design or complex active…
Non-Euclidean origami is a promising technique for designing multistable deployable structures folded from nonplanar developable surfaces. The impossibility of flat foldability inherent to non-Euclidean origami results in two disconnected…
We demonstrate the use of a new algorithm called the Flat Histogram sampling algorithm for the simulation of lattice polymer systems. Thermodynamics properties, such as average energy or entropy and other physical quantities such as…
Branched junction molecule assembly of DNA nanostructures, pioneered by Seeman's laboratory in the 1980s, has become increasingly sophisticated, as have the assembly targets. A critical design step is finding minimal sets of branched…
Experiments have reached a monumental capacity for designing and synthesizing microscopic particles for self-assembly, making it possible to precisely control particle concentrations, shapes, and interactions. However, more physical insight…
Monte Carlo (MC) simulations are extensively used for various purposes in modern high-energy physics (HEP) experiments. Precision measurements of established Standard Model processes or searches for new physics often require the collection…
The harmonic Frenkel-Kontorova model is used to illustrate with an exactly solvable example a general technique of mapping a coherently strained epitaxial system with continuous atomic displacements onto a lattice gas model (LGM) with only…
We reformulate the O(N) sigma model as a loop model whose configurations are the all-order strong coupling graphs of the original model. The loop configurations are represented by a pointer list in the computer and a Monte Carlo update…
Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA…
Origami metamaterials typically consist of folded sheets with periodic patterns, conferring them with remarkable mechanical properties. In the context of Continuum Mechanics, the majority of existing predictive methods are mechanism analogs…
This work presents a novel lattice-based methodology for incorporating multidimensional constraints into continuous decision variables within a genetic algorithm (GA) framework. The proposed approach consolidates established transcription…
The ground state of the bipartite $t$-$J$ model must satisfy a specific sign structure, based on which the single-hole and two-hole ground state $Ans\ddot{a}tze$ on honeycomb lattice are constructed and studied by a variational Monte Carlo…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…