Related papers: Excluded Volume in Protein Sidechain Packing
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
The study on the relationship between the spheres and voids in packing system suggests that the edge effect at the interface between the container and the particles is an important factor lowering the packing ratio. To pack spheres in a…
The dynamics of one-dimensional quantum many-body systems is often numerically simulated with matrix-product states (MPSs). The computational complexity of MPS methods is known to be related to the growth of entropies of reduced density…
We study structural properties of a ring polymeric melt confined in a film in comparison to a linear counterpart using molecular dynamics simulations. Local structure orderings of ring and linear polymers in the vicinity of the surface are…
We investigate the excluded volume effects in good solvents for the isolated comb polymers having $\nu_{0}=1/4$. In particular, we investigate the change of the size exponent, $\nu$, defined by $\langle s_{N}^{2}\rangle\propto N^{2\nu}$,…
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…
An empirical investigation of the interaction of sample size and discretization - in this case the entropy-based method CAIM (Class-Attribute Interdependence Maximization) - was undertaken to evaluate the impact and potential bias…
Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the…
We study Renyi and von Neumann entanglement entropies in the ground state of the one dimensional quarter-filled Hubbard model with periodic boundary conditions. We show that they exhibit an unexpected dependence on system size: for L=4 mod…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
Lattice-field calculations are performed on a Gaussian polymer chain confined to move within the region defined by two fused spheres. The results of the calculations are in accord with recent experimental measurements and computer…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
The work addresses the analogy between trivial knotting and excluded volume in looped polymer chains of moderate length, $N<N_0$, where the effects of knotting are small. A simple expression for the swelling seen in trivially knotted loops…
We study spherical completeness of ball spaces and its stability under expansions. We introduce the notion of an ultra-diameter, mimicking diameters in ultrametric spaces. We prove some positive results on preservation of spherical…
The classical bond-fluctuation model (BFM) is an efficient lattice Monte Carlo algorithm for coarse-grained polymer chains where each monomer occupies exclusively a certain number of lattice sites. In this paper we propose a generalization…
Numerous processes across both the physical and biological sciences are driven by diffusion. Partial differential equations (PDEs) are a popular tool for modelling such phenomena deterministically, but it is often necessary to use…
We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and…
The molecular dynamics simulations were used to obtain the radius of gyration of real ring polymer chains with different topological structures consisting of 360 monomers. We focus on the entropic force which is exerted by a dilute solution…
The stochastic entropy generated during the evolution of a system interacting with an environment may be separated into three components, but only two of these have a non-negative mean. The third component of entropy production is…