Related papers: Linking in domain-swapped protein dimers
The pinning-depinning phase transitions of interfaces for two classes of discrete elastic-string models are investigated numerically. In the (1+1)-dimensions, we revisit these two elastic-string models with slight modification to growth…
The information regarding the structure of a single protein is encoded in the network of interacting amino acids. Considering each protein as a weighted and unweighted network of amino acids we have analyzed a total of forty nine protein…
Active polymers possess numerous unique properties that are quite different from those observed in the system of small active molecule due to the intricate interplay between their activity and topological constraints. This study focuses on…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…
The viscous flow of polymer chains in dense melts is dominated by topological constraints whenever the single chain contour length, N, becomes larger than the characteristic scale Ne, defining comprehensively the macroscopic rheological…
We study the interplay between entropy and topological constraints for a polymer chain in which sliding rings (slip-links) enforce pair contacts between monomers. These slip-links divide a closed ring polymer into a number of sub-loops…
Below about 150 K, the spin arrangement in the chain arrays of Sr14Cu24O41 is shown to develop in two dimensions (2D). Both the correlations and the dispersion of the observed elementary excitations agree well with a model of interacting…
Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications…
The dynamics of a single chain tethered to an interface and in contact with a cross-linked network is examined numerically. When the network is put in contact with the tethered chain, the chain moves with dynamics that are highly…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
We study a blend of two kinds of homopolymers with tendency for segragation. Cross-links between the chains of different kinds do not allow macrophase separation. Instead microphase structure appears. Starting from a microscopic model we…
Several processes in the cell, such as gene regulation, start when key proteins recognise and bind to short DNA sequences. However, as these sequences can be hundreds of million times shorter than the genome, they are hard to find by simple…
Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and…
The entanglement between spin-1/2 interstitial Heisenberg dimers in the mixed spin-(1,1/2) Ising-XXZ double sawtooth ladder is investigated at low temperature. Here, we consider a cyclic four-spin exchange interaction in square plaquette of…
We discuss the appropriate techniques for modelling the geometry of open ended elastic polymer molecules. The molecule is assumed to have fixed endpoints on a boundary surface. In particular we discuss the concept of the winding number, a…
Weakly coupled Ising chains provide a condensed-matter realization of confinement. In these systems, kinks and antikinks bind into mesons due to an attractive interaction potential that increases linearly with the distance between the…
Protein interactions are important in a broad range of biological processes. Traditionally, computational methods have been developed to automatically predict protein interface from hand-crafted features. Recent approaches employ deep…
We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost…
For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling $G$ between twisting and bending, known to arise from…