Related papers: Backbone and Sidechain Ordering in a small Protein
We study the interplay between the stripe order and the superconducting order in a strongly coupled striped superconductor using gauge/gravity duality. In particular, we study the effects of inhomogeneity introduced by the stripe order on…
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
Lateral microsegregation in a monolayer of a binary mixture of particles or macromolecules is studied by MD simulations in a generic model with the interacting potentials inspired by effective interactions in biological or soft-matter…
The protein dynamical transition is investigated as a function of protein structure using terahertz time domain spectroscopy (THz-TDS). Measurements performed for native state and denatured hen egg white lysozyme (HEWL) show that protein…
The formation of protein patterns inside cells is generically described by reaction-diffusion models. The study of such systems goes back to Turing, who showed how patterns can emerge from a homogenous steady state when two reactive…
Effect of distribution of stickers along the backbone on structural properties in associating polymer solutions is studied using self-consistent field lattice model. Only two inhomogeneous morphologies, i.e., microfluctuation homogenous…
We present exact numerical results for the effects of thermal fluctuations on the experimentally relevant thermodynamic and spectral properties of Peierls chains. To this end, a combination of classical Monte Carlo sampling and exact…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Homogeneous nucleation of a new phase near a second, continuous, transition, is considered. The continuous transition is in the metastable region associated with the first-order phase transition, one of whose coexisting phases is…
Order parameter fluctuations (the largest cluster size distribution) are studied within a three-dimensional bond percolation model on small lattices. Cumulant ratios measuring the fluctuations exhibit distinct features near the percolation…
Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
Availability of high-resolution crystal structures of ribosomal subunits of different species opens a route to investigate about molecular interactions between its constituents and stabilization strategy. Structural analysis of the small…
Using small angle neutron scattering, we conducted a detailed structural study of poly(3-alkylthiophenes) dispersed in deuterated dicholorbenzene. The focus was placed on addressing the influence of spatial arrangement of constituent atoms…
Competing and intertwined orders including inhomogeneous patterns of spin and charge are observed in many correlated electron materials, such as high-temperature superconductors. Introducing a new development of the constrained-path…
Self-assembly of particles with short-range attraction and long-range repulsion (SALR) interactions on a flat and on a spherical surface is compared. Molecular dynamics (MD) simulations are performed for the two systems having the same area…
Focusing on a small set of proteins that i) fold in a concerted, all-or-none fashion and ii) do not contain knots or slipknots, we show that the Gauss linking integral, the torsion and the number of sequence-distant contacts provide…
Phase transitions of first and second order can easily be distinguished in small systems in the microcanonical ensemble. Configurations of phase coexistence, which are suppressed in the canonical formulation, carry important information…
We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible…
The ordering of weakly coupled random antiferromagnetic $S=1/2$ chains, as relevant for recent experimentally investigated spin chain materials, is considered theoretically. The one-dimensional isotropic Heisenberg model with random…