Related papers: Dynamic transition from $\alpha$-helices to $\beta…
At temperatures well below their glass transition, the deformation properties of bulk metallic glasses are characterised by a sharp transition from elasticity to plasticity, a reproducible yield stress, and an approximately linear decrease…
Many bacteria use rotating helical flagellar filaments to swim. The filaments undergo polymorphic transformations in which the helical pitch and radius change abruptly. These transformations arise in response to mechanical loading, changes…
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…
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…
Elasto-plastic models are among the most successful ways to study the critical properties of the plastic yielding transition of amorphous solids. Typically these models are studied under a condition of constant transition rates from one…
Recent experiments and simulations of amorphous solids plastically deformed by oscillatory drive have foundsurprising behavior - for small strain amplitudes the dynamics can be reversible, which is contrary to the usual notion of plasticity…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
The plastic response of beryllium was investigated during loading by laser-induced shock waves, using surface velocimetry and in-situ x-ray diffraction. Results from loading by thermal x-rays (hohlraum) were consistent with more extensive…
All-atom molecular dynamics simulations of an elastohydrodynamic lubrication oil film are performed to study the effect of pressure. Fluid molecules of n-hexane are confined between two solid plates under a constant normal force of 0.1--8.0…
In this work, the nonequilibrium pathways of the collapse of the helix-forming biopolymer polyalanine are investigated. To this end, the full time evolution of the helix-coil transition is simulated using molecular dynamics simulations. At…
Instability patterns of rolling up a sleeve appear more intricate than the ones of walking over a rug on floor, both characterized as uniaxially compressed soft-film/stiff-substrate systems. This can be explained by curvature effects. To…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
For the finite element simulation of thin soft biological tissues in dynamics, shell elements, compared to volume elements, can capture the whole tissue thickness at once, and feature larger critical time steps. However, the capabilities of…
We show that two-dimensional systems of deformable particles undergo a continuous liquid-hexatic transition upon compression or cooling, but no hexatic-solid transition-even at zero temperature and high density. Numerical simulations reveal…
Hard helices can be regarded as a paradigmatic elementary model for a number of natural and synthetic soft matter systems, all featuring the helix as their basic structural unit: from natural polynucleotides and polypeptides to synthetic…
We systematically study phase transformations from one helical structure to another. Motivated in part by recent work that relates the presence of compatible interfaces with properties such as the hysteresis and reversibility of a phase…
Elastic interactions arising from a difference of lattice spacing between two coherent phases can have a strong influence on the phase separation (coarsening) of alloys. If the elastic moduli are different in the two phases, the elastic…
Ferroelasticity describes a phenomenon in which a material exhibits two or more equally stable orientation variants and can be switched from one form to another under an applied stress. Recent works have demonstrated that two-dimensional…
In this paper, we present a 2D numerical model developed to simulate the dynamics of soft, deformable particles. To accommodate significant particle deformations, the particle surface is represented as a narrow shell composed of mass points…
We analyze a bubble forming system composed of particles with competing long range repulsive and short range attractive interactions driven over a quasi-one-dimensional periodic substrate. We find various pinned and sliding phases as a…