Related papers: Dynamic transition from $\alpha$-helices to $\beta…
Simulating protein-membrane interactions is an important and dynamic area of research. A proper definition of electrostatic forces on membrane surfaces is necessary for developing electromechanical models of protein-membrane interactions.…
Many elastic structures exhibit rapid shape transitions between two possible equilibrium states: umbrellas become inverted in strong wind and hopper popper toys jump when turned inside-out. This snap-through is a general motif for the…
We develop a mesoscopic model to study the plastic behavior of an amorphous material under cyclic loading. The model is depinning-like and driven by a disordered thresholds dynamics which are coupled by long-range elastic interactions. We…
We explore the non-equilibrium dissipative dynamics of a system of identical charged particles trapped on a closed helix. The particles are subject to an external force accelerating them along the underlying structure. The effective…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We present Molecular Dynamics simulations of the thermal glass transition in a dense model polymer liquid. We performed a comparative study of both constant volume and constant pressure cooling of the polymer melt. Great emphasis was laid…
We discuss the plastic behavior of an amorphous matrix reinforced by hard particles. A mesoscopic depinning-like model accounting for Eshelby elastic interactions is implemented. Only the effect of a plastic disorder is considered.…
The prototypical $\alpha\to\omega$ phase transition in zirconium is an ideal test-bed for our understanding of polymorphism under extreme loading conditions. After half a century of study, a consensus had emerged that the transition is…
Fractal patterns are observed in computational mechanics of elastic-plastic transitions in two models of linear elastic/perfectly-plastic random heterogeneous materials: (1) a composite made of locally isotropic grains with weak random…
The surface morphologies of poly(chloro-p-xylylene) films were measured using atomic force microscopy and analyzed within the frame work of the dynamic scaling theory. The evolution of polymer films grown with fixed experimental parameters…
We use computer simulations to study the microscopic dynamics of an athermal assembly of soft particles near the fluid-to-solid, jamming transition. Borrowing tools developed to study dynamic heterogeneity near glass transitions, we…
We perform large scale simulations of a two dimensional lattice model for amorphous plasticity with random local yield stresses and long-range quadrupolar elastic interactions. We show that as the external stress increases towards the…
Living cells are soft bodies of a characteristic form, but endowed with a capacity for a steady turnover of their structures. Both of these material properties, i.e. recovery of the shape after an external stress has been imposed and…
Fiber-reinforcement is a universal feature of many biological tissues. It involves the interplay between fiber stiffness, fiber orientation, and the elastic properties of the matrix, influencing pattern formation and evolution in layered…
We investigate the isotropic-to-nematic phase transition in systems of hard helical particles, using Onsager theory and Monte Carlo computer simulations. Motivation of this work resides in the ubiquity of the helical shape motif in many…
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…
Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground…
The quasi-equilibrium evolution of the helical fraction occurring in a biopolymer network (gelatin gel) under an applied stress has been investigated by observing modulation in its optical activity. Its variation with the imposed chain…
We present the results of analytic calculations and numerical simulations of the behaviour of a new class of chain molecules which we call thick polymers. The concept of the thickness of such a polymer, viewed as a tube, is encapsulated by…
The force laws governing the extension behavior of homopolypeptides are obtained from a phenomenological free energy capable of describing the helix-coil transition. Just above the melting temperature of the free chains, T*, the plot of…