相关论文: Conserved Linking in Single- and Double-Stranded P…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
The freely rotating chain is one of the classic discrete models of a polymer in dilute solution. It consists of a broken line of N straight segments of fixed length such that the angle between adjacent segments is constant and the N-1…
Single three dimensional polymers confined to a slab, i.e. to the region between two parallel plane walls, are studied by Monte Carlo simulations. They are described by $N$-step walks on a simple cubic lattice confined to the region $1 \le…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
We test the standard model for the length contraction of a bundle of strings under twist, and find deviation that is significantly greater than typically appreciated and that has a different nature at medium and large twist angles. By…
The hydrophobic-polar (HP) model represents proteins as binary strings embedded in lattices, with fold quality measured by an energy score. We prove that the optimal fold energy is not monotonic under concatenation for several standard…
We study a model of two polymers confined to a slit with sticky walls. More precisely, we find and analyse the exact solution of two directed friendly walks in such a geometry on the square lattice. We compare the infinite slit limit, in…
We study the behavior of self avoiding polymers in a background of vertically aligned rods that are either frozen into random positions or free to move horizontally. We find that in both cases the polymer chains are highly elongated, with…
Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple-histogram method, the conformational free energy, F, of the polymers was measured as a function of…
We present the benchmark of the polynomial expansion Monte Carlo method to a Kondo lattice model with classical localized spins on a geometrically frustrated lattice. The method enables to reduce the calculation amount by using the…
Two-dimensional monodisperse linear polymer chains are known to adopt for sufficiently large chain lengths $N$ and surface fractions $\phi$ compact configurations with fractal perimeters. We show here by means of Monte Carlo simulations of…
The denaturation transition of circular DNA is studied within a Poland-Scheraga type approach, generalized to account for the fact that the total linking number (LK), which measures the number of windings of one strand around the other, is…
We have studied polyacene within the Hubbard model to explore the effect of electron correlations on the Peierls' instability in a system marginally away from one-dimension. We employ the projector quantum Monte Carlo method to obtain…
We present an analysis for the ring closure probability of semiflexible polymers within the pure bend Worm Like Chain (WLC) model. The ring closure probability predicted from our analysis can be tested against fluorescent actin cyclization…
Recent measurements of the force versus extension curves in stretched single stranded DNA, under conditions where the hydrogen bonding between complementary bases is inhibited, provide a new handle for the study of self-avoiding effects in…
Experiments using nanofluidic devices have proven effective in characterizing the physical properties of polymers confined to small cavities. Two recent studies using such methods examined the organization and dynamics of two DNA molecules…
We present a study of site and bond percolation on periodic lattices with (on average) fewer than three nearest neighbors per site. We have studied this issue in two contexts: By simulating oxides with a mixture of 2-coordinated and…
The statistical mechanics of a ribbon polymer made up of two semiflexible chains is studied using both analytical techniques and simulation. The system is found to have a crossover transition at some finite temperature, from a type of short…
Polymer chains immersed in different solvent molecules exhibit diverse properties due to multiple spatiotemporal scales and complex interactions. Using molecular dynamics simulations, we study the conformational and static properties of…
We investigate a model of chaperone-assisted polymer translocation through a nanopore in a membrane. Translocation is driven by irreversible random sequential absorption of chaperone proteins that bind to the polymer on one side of the…