Related papers: Lattice models and Monte Carlo methods for simulat…
Thick origami structures are considered here as assemblies of polygonal panels hinged to each other along their edges according to a corresponding origami crease pattern. The determination of the internal actions caused by external loads in…
This paper presents two novel ensemble domain decomposition methods for fast-solving the Stokes-Darcy coupled models with random hydraulic conductivity and body force. To address such random systems, we employ the Monte Carlo (MC) method to…
Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are…
Accelerated algorithms for simulating the morphological evolution of strained heteroeptiaxy based on a ball and spring lattice model in three dimensions are explained. We derive exact Green's function formalisms for boundary values in the…
It was recently proposed that neural networks could be used to approximate many-dimensional probability distributions that appear e.g. in lattice field theories or statistical mechanics. Subsequently they can be used as variational…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
A lattice model is used to estimate the self-diffusivity of entangled cyclic and linear polymers in blends of varying compositions. To interpret simulation results, we suggest a minimal model based on the physical idea that constraints…
The full design of relevant systems for quantum applications, ranging from quantum simulation to sensing, is presented using a combination of atomistic methods. A prototypical system features a two-dimensional ordered distribution of spins…
Two-component submonolayer growth on triangular lattice is qualitatively studied by kinetic Monte Carlo techniques. The hopping barrier governing surface diffusion of the atoms is estimated with an improved formula and using realistic pair…
Both biological and artificial self-assembly processes can take place by a range of different schemes, from the successive addition of identical building blocks, to hierarchical sequences of intermediates, all the way to the fully…
We present here the systematic development of quantitative lattice simulations of dense polymers through a novel computational technique that allows for an efficient accounting of the chain conformations. Our approach is based on the…
Inverse methods of statistical mechanics have facilitated the discovery of pair potentials that stabilize a wide variety of targeted lattices at zero temperature. However, such methods are complicated by the need to compare, within the…
Electrical conductivity of DNA has been a controversial topic since it was first proposed in 1962. Disparities in the experimental results can often be explained by differences of the ambient or experimental conditions. We report the…
We present a nonequilibrium strong-coupling approach to inhomogeneous systems of ultracold atoms in optical lattices. We demonstrate its application to the Mott-insulating phase of a two-dimensional Fermi-Hubbard model in the presence of a…
We report on a molecular simulation method which captures the self-assembly of cationic lipid-DNA (CL-DNA) gene delivery complexes. Computational efficiency required for large length- and time-scale simulations is achieved through a…
Nanoparticles of plasmonic metals have significantly to the development of spectroscopic techniques, enabling strong confinement of electromagnetic fields at the nanoscale and corresponding signal amplification. However, to date, plasmonic…
The self-assembly of complex structures from engineered subunits is a major goal of nanotechnology, but controlling their size becomes increasingly difficult in larger assemblies. Existing strategies present significant challenges, among…
High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from…
Motivated by the way Japanese tatami mats are placed on the floor, we consider domino tilings with a constraint and estimate the number of such tilings of plane regions. We map the system onto a monomer-dimer model with a novel local…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…