Related papers: Local Interactions and Protein Folding: A Model St…
Nano- to micro-sized particles with differently charged surface areas exhibit complex interaction patterns, characterized by both opposite-charge attraction and like-charge repulsion. While several successful models have been proposed in…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
We use a combination of unsupervised clustering and sparsity-promoting inference algorithms to learn locally dominant force balances that explain macroscopic pattern formation in self-organized active particle systems. The self-organized…
In this work the observational constraints on interaction coupling parameter between dynamical dark energy and cold dark matter were obtained using CMB, BAO and SN Ia data. The dark energy in considered models is dynamical and evolution of…
In the present work the steady-state crack propagation in a chain of oscillators with non-local interactions is considered. The interactions are modeled as linear springs while the crack is presented by the absence of extra springs. The…
The dynamics of flexible polymer molecules are often assumed to be governed by hydrodynamics of the solvent. However there is considerable evidence that internal dissipation of a polymer contributes as well. Here we investigate the dynamics…
A non-linear Penner type interaction is introduced and studied in the random matrix model of homo-RNA. The asymptotics in length of the partition function is discussed for small and large $N$ (size of matrix). The interaction doubles the…
The equations for strands of rigid charge configurations interacting nonlocally are formulated on the special Euclidean group, SE(3), which naturally generates helical conformations. Helical stationary shapes are found by minimizing the…
We study the dynamics of one--dimensional discrete models of one--component active medium built up of spatially inhomogeneous chains of diffusively coupled piecewise linear maps. The nonhomogeneities (``defects'') are treated in terms of…
The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are…
Few-layer graphene systems come in various stacking orders. Considering tight-binding models for electrons on stacked honeycomb layers, this gives rise to a variety of low-energy band structures near the charge neutrality point. Depending…
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
The self-consistent field (SCF) theory of dense polymer liquids assumes that short-range correlations are almost independent of how monomers are connected into polymers. Some limits of this idea are explored in the context of a perturbation…
Monte Carlo simulations show that long-range interactions play a major role in determining the folding rates of 48-mer three-dimensional lattice polymers modelled by the Go potential. For three target structures with different native…
We introduce a particle-based framework inspired by smoothed particle hydrodynamics (SPH) to simulate the dynamics of a continuous field of coupled phase oscillators. This methodology discretizes the spatial domain into particles and…
The density of states contains all informations on energetic quantities of a statistical system, such as the mean energy, free energy, entropy, and specific heat. As a specific application, we consider in this work a simple lattice model…
We present a nonlocal formulation of contact mechanics that accounts for the interplay of deformations due to multiple contact forces acting on a single particle. The analytical formulation considers the effects of nonlocal mesoscopic…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations,…