Related papers: Cooperative melting in double-stranded peptide cha…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
A molecular dynamics study of a two dimensional system of particles interacting through a Lennard-Jones pairwise potential is performed at fixed temperature and vanishing external pressure. As the temperature is increased, a solid-to-liquid…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
We study analytically the intricate phase behavior of cross-linked $AB$ diblock copolymer melts, which can undergo two main phase transitions due to quenched random constraints: Gelation, i.e., spatially random localization of polymers…
Using Brownian dynamics simulation, we study the orientational order in melting transition of colloidal systems with $'$soft$'$ Yukawa potential. The bond-orientational order parameter $\Phi_{6}$ and the bond-orientational order function…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
We study melting in a two-dimensional system of classical particles with Gaussian-core interactions in disordered environments. The pure system validates the conventional two-step melting with a hexatic phase intervening between the solid…
We discuss a possibility to control a heat conductivity in simple one-dimensional models of dielectrics by means of external mechanical loads. To illustrate such possibilities we consider first a well-studied chain with degenerate…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Sublattice melting is the loss of order of one lattice component in binary or ternary ionic crystals upon increase in temperature. A related transition has been predicted in colloidal crystals. To understand the nature of this transition,…
In the present paper, using a molecular dynamics simulation, we study a nature of melting of a two-dimensional ($2D$) system of classical particles interacting through a purely repulsive isotropic core-softened potential which is used for…
The dynamics of polymer melts at the crossover between unentagled and entangled regimes is formalized here through an extension of the Cooperative Dynamics Generalized Langevin Equation (CDGLE) (\textit{J. Chem. Phys.} 110,7574 (1999)), by…
We introduce a simple geometric model for a double-stranded and double-helical polymer. We study the statistical mechanics of such polymers using both analytical techniques and simulation. Our model has a single energy-scale which…
We investigate the kinetics of a polymer collapse due to the formation of irreversible crosslinks between its monomers. Using the contact probability $P(s)$ as a scale-dependent order parameter depending on the chemical distance $s$, our…
We study the interplay between an isostructural critical point and dislocation mediated two-dimensional melting, using a combination of Landau and continuum elasticity theory. If dislocations are excluded, coupling to the elastic degrees of…
In dimensions 3 or larger, it is a classical fact that the directed polymer model has two phases: Brownian behavior at high temperature, and non-Brownian behavior at low temperature. We consider the response of the polymer to an external…
Mechanically induced folding of passive cross-linkers is a fundamental biological phenomenon. A typical example is a conformational change in myosin II responsible for the power-stroke in skeletal muscles. In this paper we present an…
We investigate the characteristics of two dimensional melting in simple atomic systems via isobaric-isothermal ($NPT$) and isochoric-isothermal ($NVT$) molecular dynamics simulations with special focus on the effect of the range of the…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…