Related papers: Temperature- and Force-Induced beta-Sheet Unfoldin…
We study numerically a lattice model of semiflexible homopolymers with nearest neighbor attraction and energetic preference for straight joints between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched Rosenbluth…
We solve a two dimensional model for polymer chain folding in the presence of mechanical pulling force ($f$) exactly using equilibrium statistical mechanics. Using analytically derived expression for the partition function we determine the…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
Using a combination of the replica-exchange Monte Carlo algorithm and the multicanonical method, we investigate the influence of bending stiffness on the conformational phases of a bead-stick homopolymer model and present the pseudo-phase…
At large parallel magnetic field $B_\parallel$, the ground state of bilayer quantum Hall system forms uniform soliton lattice phase. The soliton lattice will melt due to the proliferation of unbound dislocations at certain finite…
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…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
In this paper we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix-random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory…
The melting transitions of a colloidal lattice confined to a two-dimensional ($2D$) periodic substrate of square symmetry are studied using Monte Carlo simulations. When the strengths of interparticle and particle-substrate interactions are…
The $\beta$-relaxation associated with the sub-glass transition temperature ($T_{\text{g},\beta}$) is attributed to fast, localised molecular motions which can occur below the primary glass transition temperature ($T_{g\alpha}$). Despite…
We consider the fracture of a free-standing two-dimensional (2D) elastic-brittle network to be used as protective coating subject to constant tensile stress applied on its rim. Using a Molecular Dynamics simulation with Langevin thermostat,…
The glass transition of supercooled fluids is a particular challenge for computer simulation, because the (longest) relaxation times increase by about 15 decades upon approaching the transition temperature T_g. Brute-force molecular…
In a system of interacting thin rigid rods of equal length $2 \ell$ on a two-dimensional grid of lattice spacing $a$, we show that there are multiple phase transitions as the coupling strength $\kappa=\ell/a$ and the temperature are varied.…
Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different…
Microgels are often discussed as well-suited model system for soft colloids. In contrast to rigid spheres, the microgel volume and, coupled to this, the volume fraction in dispersion can be manipulated by external stimuli. This behavior is…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
We introduce a polymer model where the transition from swollen to compact configurations is due to interactions between the monomers and the solvent. These interactions are the origin of the effective attractive interactions between…
The unfolding of a polymer below the $\theta$ point when pulled by an external force is studied both in d=2 on the lattice and in $d=3$ off lattice. A ground state analysis of finite length chains shows that the globule unfolds via multiple…
Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…