Related papers: A contact map method to capture the features of kn…
In the first part of this work a summary is provided of some recent experiments and theoretical results which are relevant in the research of systems of polymer rings in nontrivial topological conformations. Next, some advances in modeling…
The thermal properties of coarse grained knotted polymers containing two kinds of monomers $A$ and $B$ fluctuating in a solution are investigated on a simple cubic lattice using the Wang-Landau MC algorithm. These knots have a more complex…
We investigate the thermal and structural properties of knotted diblock copolymer rings using a coarse-grained lattice model in an implicit solvent. The system is studied by means of the Wang--Landau Monte Carlo algorithm, allowing us to…
In this work the thermodynamic properties of short polymer knots (up to 120 segments) defined on a simple cubic lattice are studied with the help of the Wang-Landau Monte Carlo algorithm. The sampling process is performed using pivot…
The statistical mechanics of single polymer knots is studied using Monte Carlo simulations. The polymers are considered on a cubic lattice and their conformations are randomly changed with the help of pivot transformations. After each…
The interplay between the topological and geometrical properties of a polymer ring can be clarified by establishing the entanglement trapped in any portion (arc) of the ring. The task requires to close the open arcs into a ring, and the…
The probability of two loci, separated by a certain genome length, being in contact can be inferred using the Chromosome Conformation Capture (3C) method and related Hi-C experiments. How to go from the contact map, a matrix listing the…
Counting problems, determining the number of possible states of a large system under certain constraints, play an important role in many areas of science. They naturally arise for complex disordered systems in physics and chemistry, in…
Wang-Landau sampling has been applied to investigate the thermodynamics and structural properties of a lattice hydrophobic-polar heteropolymer (the HP protein model) interacting with an attractive substrate. For simplicity, we consider a…
The topological effects on the thermal properties of several knot configurations are investigated using Monte Carlo simulations. In order to check if the topology of the knots is preserved during the thermal fluctuations we propose a method…
Monte Carlo simulations using Wang-Landau sampling are performed to study three-dimensional chains of homopolymers on a lattice. We confirm the accuracy of the method by calculating the thermodynamic properties of this system. Our results…
The mechanical properties of polymer knots under stretching in a bad or good solvent are investigated by applying a given force $F$ to a point of the knot while keeping another point fixed. The Monte Carlo sampling of the polymer…
The HP model of protein folding, where the chain exists in a free medium, is investigated using a parallel Monte Carlo scheme based upon Wang-Landau sampling. Expanding on the work of Wust and Landau by introducing a lesser known replica…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
Understanding material composition-structure-function relationships is of critical importance for the design and discovery of novel functional materials. While most such studies focus on individual materials, we conducted a global mapping…
Physical transformations are described by linear maps that are completely positive and trace preserving (CPTP). However, maps that are positive (P) but not completely positive (CP) are instrumental to derive separability/entanglement…
Contact has been well established as an important quantity to govern dilute quantum systems, in which the pairwise correlation at short distance traces a broad range of thermodynamic properties. So far, studies have been focusing on contact…
The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms leading to the…
The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter…
We study ground states of a hybrid system consisting of a polymer and an attractive nanowire by means of computer simulations. Depending on structural and energetic properties of the substrate, we find different adsorbed polymer…