Related papers: How molecular knots can pass through each other
We investigate a system of two atoms in an optical lattice, performing a quantum walk by state-dependent shift operations and a coin operation acting on the internal states. The atoms interact, e.g., by cold collisions, whenever they are in…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
We study the diffusion of gas molecules through a two-dimensional network of polymers with the help of Monte Carlo simulations. The polymers are modeled as non-interacting random walks on the bonds of a two-dimensional square lattice, while…
We analyze the interaction of two conducting, charged polymer chains in solution using a minimal model for their electronic degrees of freedom. We show that a crossing of the two chains in which the polymers pass within Angstroms of each…
We analyze the free energy for translocation of a polymer from the outside of a spherical vesicle to the inside. The process is assumed to be driven by the adsorption of the polymer on the inner surface of the vesicle. We argue that in the…
Tangles of string typically become knotted, from macroscopic twine down to long-chain macromolecules such as DNA. Here we demonstrate that knotting also occurs in quantum wavefunctions, where the tangled filaments are vortices (nodal…
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…
We study the magnetic field induced singlet/triplet transition for two electrons in vertically coupled quantum dots by exact diagonalization of the Coulomb interaction. We identify the different mechanisms occurring in the transition,…
The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical…
We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose…
We use the bond fluctuation model to study the contraction process of two polymer loops with $N$ segments that are connected each to the bottom and top part of a Feringa engine. The change in the size of the molecules as well as the folding…
We model a quantum walk of identical particles that can change their exchange statistics by hopping across a domain wall in a 1D lattice. Such a "statistical boundary" is transparent to single particles and affects the dynamics only by…
Knot theory provides a powerful tool for the understanding of topological matters in biology, chemistry, and physics. Here knot theory is introduced to describe topological phases in the quantum spin system. Exactly solvable models with…
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…
When compressed, certain lattices undergo phase transitions that may allow nuclei to gain significant kinetic energy. To explore the dynamics of this phenomenon, we develop a framework to study Coulomb coupled N-body systems constrained to…
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…
It has been suggested recently that knots might exist as stable soliton solutions in a simple three-dimensional classical field theory, opening up a wide range of possible applications in physics and beyond. We have re-examined and extended…
Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
We develop a theoretical description of the topological disentanglement occurring when torus knots reach the ends of a semi-flexible polymer under tension. These include decays into simpler knots and total unknotting. The minimal number of…