Related papers: Dynamic transition from $\alpha$-helices to $\beta…
We demonstrate that plastic deformation in solids is associated with a dynamic transition that is reminiscent to the transition from a superconducting to a mixed phase in Type II superconductors. We report analytic calculations, extensive…
Thin bilayers made of elastic sheets with different strain recoveries can be used for dynamic shape morphing through ambient stimuli, such as temperature, mass diffusion, and light. As a fundamentally different approach to designing…
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…
Colloidal magnetic particles embedded in an elastic polymer matrix constitute a smart material called ferrogel. It responds to an applied external magnetic field by changes in elastic properties, which can be exploited for various…
Large scale numerical simulations are used to study the elastic dynamics of two-dimensional vortex lattices driven on a disordered medium in the case of weak disorder. We investigate the so-called elastic depinning transition by decreasing…
We formulate a phenomenological elasto-plastic theory to describe a solid undergoing a structural transition from a square (p4mm) to an oblique (p2) lattice in two dimensions. Within our theory, the components of the strain may be…
In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of…
A mesoscopic model of amorphous plasticity is discussed in the context of depinning models. After embedding in a d + 1 dimensional space, where the accumulated plastic strain lives along the additional dimension, the gradual plastic…
We performed an X-ray diffraction experiment while palladium bulk absorbed and desorbed hydrogen to investigate the behavior of the crystalline lattice during the phase transition between the $\alpha$ phase and $\beta$ phase. Fast growth of…
The role of active stress on the conformational dynamics of a polymer has drawn significant interest due to its potential applications in understanding the energy landscape of protein structures, buckling of biopolymers, genomic spatial…
We use numerical simulations to show how a fully flexible filament binding to a deformable cylindrical surface may acquire a macroscopic persistence length and a helical conformation. This is a result of the nontrivial elastic response to…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
Amorphization during severe plastic deformation has been observed in various crystalline materials, yet its underlying mechanisms remain poorly understood. This study introduces a novel phase-field model at the mesoscale, integrating…
Using numerical simulations, we study the dynamical evolution of particles interacting via competing long-range repulsion and short-range attraction in two dimensions. The particles are compressed using a time-dependent quasi-one…
An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good…
Soft colloids allow to explore high density states well beyond random close packing. An important open question is whether softness controls the dynamics under these dense conditions. While experimental works reported conflicting results,…
We develop an energy-landscape based elasto-plastic model to understand the behaviour of amorphous solids under uniform and cyclic shear. Amorphous solids are modeled as being composed of mesoscopic sub-volumes, each of which may occupy…
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are…
Force-induced reversible transformations between coiled and normal polymorphs of bacterial flagella have been observed in recent optical-tweezer experiment. We introduce a discrete elastic rod model with two competing helical states…
Helical objects are often implemented in electronic or mechanical micro-systems, requiring a precise understanding of their mechanical properties. While helices formed by cylindrical filaments have been intensely investigated, little is…