Related papers: Compact phases of polymers with hydrogen bonding
We study the thermodynamic behavior of a model protein with 54 amino acids that is designed to form a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid, and has the…
The intrinsic property of proteins to form structural motifs such as alpha-helices and beta-sheets leads to a complex phase behavior in which proteins can assemble into various types of aggregates including crystals, liquidlike phases of…
Motivated by recent experimental studies of hydrogen-bonded molecular conductors $\kappa$-$X_3$(Cat-EDT-TTF)$_2$ [$X$=H, D], interplays of protons and correlated electrons, and their effects on magnetic, dielectric, and optical properties,…
Lattice mismatch can substantially impact the spatial organization of heterogeneous materials. We examine a simple model for lattice-mismatched solids over a broad range of temperature and composition, revealing both uniform and spatially…
We report a preliminary numerical study by kinetic Monte Carlo simulation of the dynamics of phase separation following a quench from high to low temperature in a system with a single, conserved, scalar order parameter (a kinetic Ising…
We present an enhanced off-lattice kinetic Monte Carlo (OLKMC) model, based on a new method for tolerant classification of atomistic local-environments that is invariant under Euclidean-transformations and permutations of atoms. Our method…
We propose a hybrid Molecular Dynamics/Multi-particle Collision Dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte-Carlo scheme to deal with single monomer addition…
For a model deca-alanine peptide the cavity (ideal hydrophobic) contribution to hydration favors the helix state in the coil-to-helix transition and the paired helix bundle in the assembly of two helices. The energetic contributions of…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
We investigate the phase diagram of a one-dimensional model of hardcore bosons or spinless fermions with tunable nearest-neighbor interactions. By introducing alternating repulsive and attractive interactions on consecutive bonds, we show…
Wang-Landau sampling has been applied to investigate the thermodynamics and structural properties of a lattice hydrophobic-polar heteropolymer (the HP protein model) interacting with an attractive substrate. For simplicity, we consider a…
Investigating thermodynamic properties of liquid-solid transitions of flexible homopolymers with elastic bonds by means of multicanonical Monte Carlo simulations, we find crystalline conformations that resemble ground-state structures of…
It is observed that low-lying transitions of an interstitial hydrogen adatom on a metallic lattice correspond classically to dipoles oscillating at frequencies where band electrons typically have a low electromagnetic absorption. Such…
The hydrophobic-polar (HP) model represents proteins as binary strings embedded in lattices, with fold quality measured by an energy score. We prove that the optimal fold energy is not monotonic under concatenation for several standard…
We study the phase behaviour of a binary mixture of colloidal hard spheres and freely-jointed chains of beads using Monte Carlo simulations. Recently Panagiotopoulos and coworkers predicted [Nat. Commun. 5, 4472 (2014)] that the hexagonal…
Hydrogen is key in reducing greenhouse gas emissions in materials production. At the same time, it significantly affects mechanical properties, often causing unwanted embrittlement. However, rather than solely addressing these…
We analyze the hard-core Bose-Hubbard model with both the three-body and nearest neighbor repulsions on the triangular lattice. The phase diagram is achieved by means of the semi-classical approximation and the quantum Monte Carlo…
We use numerical simulations to study the phase behavior of a system of purely repulsive soft dumbbells as a function of size ratio of the two components and their relative degree of deformability. We find a plethora of different phases…
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 report an extensive numerical study of a charged colloidal system with competing short-range depletion attraction and long-range electrostatic repulsion. By analizing the cluster properties, we identify two distinct regions in the phase…