Related papers: Discrete breathers in protein secondary structure
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…
Protein representation and potential function are essential ingredients for studying proteins folding and protein prediction. We introduce a novel geometric representation of contact interactions using the edge simplices from alpha shape of…
The random-field spin-1/2 XXZ chains, and the corresponding Anderson insulators of spinless fermions with density-density interaction, have been intensively studied in the context of many-body localization. However, we recently argued [B.…
The two-dimensional Active Brownian Particles system is meant to be composed of hard disks, that show excluded volume interactions, usually simulated via molecular dynamics using pure repulsive potentials. We show that the softness of the…
In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
We describe a chain of unidirectionally coupled adaptive excitable elements slowly driven by a stochastic process from one end and open at the other end, as a minimal toy model of unresolved irreducible uncertainty in a system performing…
We study anharmonic localization in a periodic five atom chain with quadratic-quartic spring potential. We use discrete symmetries to eliminate the degeneracies of the harmonic chain and easily find periodic orbits. We apply linear…
We prove nonexistence of breathers (spatially localized and time-periodic oscillations) for a class of Fermi-Pasta-Ulam lattices representing an uncompressed chain of beads interacting via Hertz's contact forces. We then consider the…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker proteins in the cytoskeleton. The presence of…
Experiments measuring contact formation between a probe and quencher in disordered chains provide information on the fundamental dynamical timescales relevant to protein folding, but their interpretation usually relies on simplified…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
We investigate protein-protein interactions in solution by small-angle X-ray scattering (SAXS) and theoretical modeling. The structure factor for solutions of bovine pancreatic trypsin inhibitor (BPTI), myoglobin (Mb), and intestinal fatty…
Surfaces and structures capable of multiple stable configurations have attracted growing interest for on-demand shape morphing. In this work, we consider an elastic compliant plate coupled to a two-dimensional foundation comprising an array…
The $\alpha$ and $\beta$ subunits comprising the hexameric assembly of F1-ATPase share a high degree of structural identity, though low primary identity. Each subunit binds nucleotide in similar pockets, yet only $\beta$ subunits are…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…