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Lattice model of directed self avoiding walk has been solved analytically to investigate adsorption desorption phase transition behaviour of a semiflexible sequential copolymer chain on a two dimensional impenetrable surface perpendicular…
A polycrystalline graphene consists of perfect domains tilted at angle {\alpha} to each other and separated by the grain boundaries (GB). These nearly one-dimensional regions consist in turn of elementary topological defects, 5-pentagons…
Recently, the prospects for amorphous phases of graphene (a-G) have been explored computationally. Initial models were flat, and contained odd-member rings, while maintaining three-fold coordination and sp2 bonding. Upon relaxation,…
We analyse the conformational behaviour of a linear semiflexible homo-polymer chain confined by two geometrical constraints under a good solvent condition in two dimensions. The constraints are stair shaped impenetrable surfaces. The…
The interaction between graphene and copper (111) surface have been investigated using the molecular dynamics simulations. We have shown that it is possible to fit Lennard-Jones potential leading to the correct values of the binding energy…
Since the discovery of high-temperature superconductivity in the thin-film FeSe/SrTiO$_3$ system, iron selenide and its derivates have been intensively scrutinized. Using ab initio density functional theory calculations we review the…
We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that 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…
Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical predictions, we find that the folding time grows as a power…
We show that a constriction-type Josephson junction realized by an epitactic thin film of a d-wave superconductor with an appropriate boundary geometry exhibits intrinsic phase differences between 0 and pi depending on geometric parameters…
During the melting transition of dimyristoyl phosphatidylglycerol (DMPG), the order of the lipid chains and the three-dimensional, vesicular structural arrangement change simultaneously. These changes result in peculiar heat capacity…
Twist-grain-boundary phases in smectics are the geometrical analogs of the Abrikosov flux lattice in superconductors. At large twist angles, the nonlinear elasticity is important in evaluating their energetics. We analytically construct the…
We investigate the interplay between post-translational folding and escape of two small single-domain proteins at the ribosomal exit tunnel by using Langevin dynamics with coarse-grained models. It is shown that at temperatures lower or…
Interfaces have long been known to be the key to many mechanical and electric properties. To nickel base superalloys which have perfect creep and fatigue properties and have been widely used as materials of turbine blades, interfaces…
We study the potential and the charge distribution across the interface of a plasma and a dielectric wall. For this purpose, the charge bound to the wall is modelled as a quasi-stationary electron surface layer which satisfies Poisson's…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight…
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…
We analyse the nature of the confinement of an infinitely long (and finite) linear semiflexible homo-polymer chain confined in between two geometrical constraints (A&B) under good solvent condition in two dimensions. The constraints are…
Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape.…
The thermodynamic behavior and structural properties of hydrophobic-polar (HP) lattice proteins interacting with attractive surfaces are studied by means of Wang-Landau sampling. Three benchmark HP sequences (48mer, 67mer, and 103mer) are…