Related papers: Local Interactions and Protein Folding: A Model St…
In protein folding the term plasticity refers to the number of alternative folding pathways encountered in response to free energy perturbations such as those induced by mutation. Here we explore the relation between folding plasticity and…
Spontaneous charge ordering occurring in correlated systems may be considered as a possible route to generate effective lattice structures with unconventional couplings. For this purpose we investigate the phase diagram of doped extended…
We incorporate hydrodynamic interactions (HI) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small proteins and demonstrate that HI facilitate folding. We also…
Planar/flat configurations of fixed-angle chains and trees are well studied in the context of polymer science, molecular biology, and puzzles. In this paper, we focus on a simple type of fixed-angle linkage: every edge has unit length…
We investigate the dynamics of the collapse of a single copolymer chain, when the solvent quality is suddenly quenched from good to poor. We employ Brownian dynamics simulations of a bead-spring chain model and incorporate fluctuating…
It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a…
We study the behaviour of interacting self-propelled particles, whose self-propulsion speed decreases with their local density. By combining direct simulations of the microscopic model with an analysis of the hydrodynamic equations obtained…
Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino…
In this paper we study pattern formation for a physical local/nonlocal interaction functional where the local attractive term is given by the $1$-perimeter and the nonlocal repulsive term is the Yukawa (or screened Coulomb) potential. This…
Lattice protein models, as the Hydrophobic-Polar (HP) model, are a common abstraction to enable exhaustive studies on structure, function, or evolution of proteins. A main issue is the high number of optimal structures, resulting from the…
A simple two-level model is developed and used to test the properties of effective interactions for performing nuclear structure calculations in truncated model spaces. It is shown that the effective many-body interactions sensitively…
Self-mated hydrogel contacts show extremely small friction coefficients at low loads but a distinct velocity dependence. Here we combine mesoscopic simulations and experiments to test the polymer-relaxation hypothesis for this velocity…
The two-dimensional contact process (CP) with a competitive dynamics proposed by Martins {\it et al.} [Phys. Rev. E {\bf 84}, 011125(2011)] leads to the appearance of an unusual active asymmetric phase, in which the system sublattices are…
We propose a simple model unifying two major approaches to the analysis of large multicomponent systems: interacting particle systems (IPS) and couple map lattices (CML) and show that in the weak interaction limit depending on fine…
We consider pairwise interaction energies and we investigate their minimizers among lattices with prescribed minimal vectors (length and coordination number), i.e. the one corresponding to the crystal's bonds. In particular, we show the…
In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We…
The theory of transition between $\alpha$-helix, $\beta$-sheet and random coil conformation of a protein is discussed through a simple model, that includes both short and long-range interactions. Besides the bonding parameter and helical…
Processes on different length scales affect the dynamics of chain molecules. In this work, we focus on structures on the scale of a monomer and investigate polyolefins, i.e. hydrocarbon chains with different small scale architectures. We…
Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the…
A two species interacting system motivated by the density functional theory for triblock copolymers contains long range interaction that affects the two species differently. In a two species periodic assembly of discs, the two species…