Related papers: Temperature- and Force-Induced beta-Sheet Unfoldin…
We investigate a lattice model of polymers where the nearest-neighbour monomer-monomer interaction strengths differ according to whether the local configurations have so-called ``hydrogen-like'' formations or not. If the interaction…
As a prototype of systems bearing a localization-delocalization transition, the strand-separation (melting) process in a double-stranded biopolymer is studied by a mapping to a quantum-mechanical problem with short-ranged potentials. Both…
The associative interaction, such as hydrogen bonding, can bring about versatile functionalities to polymer systems, which has been investigated by tremendous researches, but the fundamental understanding on association process is still…
We report results of molecular-dynamics simulations of a model polymer melt consisting of short non-entangled chains in the supercooled state above the critical temperature of mode-coupling theory (MCT). To analyse the dynamics of the…
Dynamics of a polymer chain in solution gets significantly affected by the temperature and the frictional forces arising due to solvent viscosity. Here, using an explicit solvent framework for polymer simulation with the liberty to tune the…
Whereas the first part of this paper dealt with the relaxation in the beta-regime, this part investigates the final (alpha) relaxation of a simulated polymer melt consisting of short non-entangled chains above the critical temperature Tc of…
Three-dimensional shell-like structures can be obtained spontaneously at the microscale from the self-folding of 2D templates of rigid panels. At least for simple structures, the motion of each panel is consistent with a Brownian process…
The overall solid-to-solid phase transformation kinetics under non-isothermal conditions has been modeled by means of a differential equation method. The method requires provisions for expressions of the fraction of the transformed phase in…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
We numerically studied magnetic reconnection in a high $\beta$ hydrogen-helium plasma at different altitudes from the photosphere to the upper chromosphere. The time dependent ionization degrees were included to get more realistic…
Molecular dynamics simulations have been employed to study the formation of a physical (thermoreversible) gel by amphiphilic A-B-A triblock copolymers in aqueous solution. In order to mimic the structure of hydrogel-forming polypeptides…
Recent advances in Generalized Ensemble simulations and microcanonical analysis allowed the investigation of structural transitions in polymer models over a broad range of local bending and torsion strengths. It is reasonable to argue that…
Controlled mechanical loading was applied to Ti-15Mo alloy during annealing at 550 $^\circ$C. Massive formation of the $\omega_{\textrm{iso}}$ phase from the parent $\beta$-phase occurred during annealing at 550 $^\circ$C without external…
In our common experience, crumpling a sheet requires external compressive force and leads to a random network of folds. However, thin sheets have been theoretically predicted to spontaneously transition from a flat to a crumpled state…
We present results from extensive Monte Carlo simulations of polymer models where each lattice site can be visited by up to $K$ monomers and no restriction is imposed on the number of bonds on each lattice edge. These \textit{multiple…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
We present fully atomistic Molecular Dynamics simulation results on a main-chain polymer, 1,4-Polybutadiene, in the merging region of the $\alpha$- and $beta$-relaxations. A real space analysis reveals the occurrence of localized motions…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
By means of molecular-dynamics simulations, temperature driven diffusionless structural phase transitions in equi- and nearly equiatomic ordered nickel-titanium alloys were investigated. For this purpose, a model potential from the…
The self-assembly of proteins into $\beta$-sheet-rich amyloid fibrils has been observed to occur with sigmoidal kinetics, indicating that the system initially is trapped in a metastable state. Here, we use a minimal lattice-based model to…