Related papers: Local Interactions and Protein Folding: A Model St…
By means of contact-density chain-growth simulations, we investigate a simple lattice model of a flexible polymer interacting with an attractive substrate. The contact density is a function of the numbers of monomer-substrate and…
Single molecule probes are widely used to characterize dynamic heterogeneity in glass forming liquids, but interpreting probe dynamics remains challenging because the measured response depends on how the probe couples to its host…
We seek to understand the interplay between amino acid sequence and local structure in proteins. Are some amino acids unique in their ability to fit harmoniously into certain local structures? What is the role of sequence in sculpting the…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
This paper investigates the structure-property relations of thin-walled lattices under dynamic longitudinal compression, characterized by their cross-sections and heights. These relations elucidate the interactions of different geometric…
Responsive particles, such as biomacromolecules or hydrogels, display a broad and polymodal distribution of conformations and have thus the ability to change their properties (e.g, size, shape, charge density, etc.) substantially in…
We study localization driven solely by interparticle interactions in moir\'e lattice systems without intrinsic disorder or externally imposed quasiperiodic potentials. We consider a one-dimensional bilayer with incommensurate lattice…
Almost all the polymer crystals have several polymorphic modifications. Their structure and existence conditions, as well as transitions between them are not understood even in the case of the 'model' polymer polyethylene (PE). For analysis…
An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive because they enable efficient search of…
We analyze diffusion of small particles in a solid polymeric medium taking into account a short range particle-polymer interaction. The system is modeled by a particle diffusion on a ternary lattice where the sites occupied by polymer…
The emergence of scanning probe and electron beam imaging techniques have allowed quantitative studies of atomic structure and minute details of electronic and vibrational structure on the level of individual atomic units. These microscopic…
We extend recent studies of the minimal energy packings of short flexible polymers with hard-core-like repulsions and short-range attractions to include bond-angle interactions with the aim of describing the collapsed conformations of…
One- to three-dimensional hypercubic lattices half-filled with localized particles interacting via the long-range Coulomb potential are investigated numerically. The temperature dependences of specific heat, mean staggered occupation, and…
We combine small angle scattering experiments and simulations to investigate the internal structure and interactions of composite Poly(N-isopropylacrylamide)-Poly(ethylene glycol) (PNIPAM-PEG) microgels. At low temperatures the…
We investigate the local and global optimality of the triangular, square, simple cubic, face-centred-cubic (FCC), body-centred-cubic (BCC) lattices and the hexagonal-close-packing (HCP) structure for a potential energy per point generated…
Dynamics of two particles with short range repulsive or attractive interaction is studied numerically in the Harper model. It is shown that interaction leads to appearance of localized states and pure-point spectrum component in the case…
We study the impact of classical short-range nonlinear interactions on transport in lattices with no dispersion. The single particle band structure of these lattices contains flat bands only, and cages non-interacting particles into compact…
The present paper is devoted to the study of a simple model of interacting electrons in a random background. In a large interval $\Lambda$, we consider $n$ one dimensional particles whose evolution is driven by the Luttinger-Sy model, i.e.,…
The statistical mechanics of single polymer knots is studied using Monte Carlo simulations. The polymers are considered on a cubic lattice and their conformations are randomly changed with the help of pivot transformations. After each…
The amorphous solids can be theoretically modeled by anharmonic disordered lattices. However, most of theoretical studies on thermal conductivity in anharmonic disordered lattices only focus on the potentials of hard-type (HT)…