Related papers: A contact map method to capture the features of kn…
Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture…
We show that Wang-Landau sampling, combined with suitable Monte Carlo trial moves, provides a powerful method for both the ground state search and the determination of the density of states for the hydrophobic-polar (HP) protein model and…
Given a finite collection of two-dimensional tile types, the field of study concerned with covering the plane with tiles of these types exclusively has a long history, having enjoyed great prominence in the last six to seven decades. Much…
The conformational behavior of a coarse-grained finite polymer chain near an attractive spherical surface was investigated by means of multicanonical Monte Carlo computer simulations. In a detailed analysis of canonical equilibrium data…
This paper visualizes a knot reduction algorithm
Many standard structural quantities, such as order parameters and correlation functions, exist for common condensed matter systems, such as spherical and rod-like particles. However, these structural quantities are often insufficient for…
We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined into nano-channels and under periodic compression. We…
Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The…
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…
The conformational statistics of ring polymers in melts or dense solutions is strongly affected by their quenched microscopic topological state. The effect is particularly strong for untangled (i.e. non-concatenated and unknotted) rings,…
The three-dimensional organization of chromatin, on the length scale of a few genes, is crucial in determining the functional state - accessibility and the amount of gene expression - of the chromatin. Recent advances in chromosome…
We study a strongly attractive system of a few spin-1/2 fermions confined in a one-dimensional harmonic trap, interacting via two-body contact potential. Performing exact diagonalization of the Hamiltonian we analyze the ground state and…
A numerical algorithm for studying strongly correlated electron systems is proposed. The groundstate wavefunction is projected out after numerical renormalization procedure in the path integral formalism. The wavefunction is expressed from…
We present a high-accuracy procedure for electronic structure calculations of strongly correlated materials. To address limitations in current electronic structure methods, we employ density functional theory in combination with the…
The material eroded from the surface of plasma facing components is redeposited partly close to high heat flux areas. At these locations, the deposit is heated by the plasma and the deposition pattern evolves depending on the operation…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
Network theory provides various tools for investigating the structural or functional topology of many complex systems found in nature, technology and society. Nevertheless, it has recently been realised that a considerable number of systems…
The Replica Exchange Wang-Landau Method is used to estimate the energy landscape of a polymer composed of a simple hydrophobic and polar sequence using the HP protein model. Calculations of state transitions between the energy levels of the…
Super-moir\'e materials represent a novel playground to engineer states of matter beyond the possibilities of conventional moir\'e materials. However, from the computational point of view, understanding correlated matter in these systems…
The tube model is a central concept in polymer physics, and allows to reduce the complex many-filament problem of an entangled polymer solution to a single filament description. We investigate the probability distribution function of…