Related papers: Dynamic transition from $\alpha$-helices to $\beta…
Recently the materials possessing structure of molecular and supramolecular matrix are more and more actively studied. They are relative to many polymeric materials of a technological origin, such as rubber, and living biological tissues.…
Folded protein hydrogels are prime candidates as tuneable biomaterials but it is unclear to what extent their mechanical properties have mesoscopic, as opposed to molecular origins. To address this, we probe hydrogels of the muscle-derived…
Compressive mechanical stress exceeding a critical value leads to the formation of periodic surface buckling patterns in film-substrate systems. A comprehensive understanding of this buckling phenomenon is desired in applications where the…
In recent work we revisited the phase diagram of hard ellipsoids of revolution (spheroids) by means of replica exchange Monte Carlo simulations. This was done by setting random initial configurations, and allows to confirm the formation of…
In this letter, we adopt a new approach combining theoretical modeling with silk stretching measurements to explore the mystery of the structures between silkworm and spider silks, leading to the differences in mechanical response against…
We introduce and investigate a coarse-grained model for quasi one-dimensional ferrogels. In our description the magnetic particles are represented by hard spheres with a magnetic dipole moment in their centers. Harmonic springs connecting…
We have investigated the potential energy surfaces for glycine 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…
Configurations of a single semiflexible polymer is studied when it is pushed into a nanochannel in the case where the polymer persistence length $l_p$ is much longer than the channel diameter $D$, i.e. $l_p/D \gg 1$. Using numerical…
Motivated by the intriguing motility of spirochetes (helically-shaped bacteria that screw through viscous fluids due to the action of internal periplasmic flagella), we examine the fundamental fluid dynamics of superhelices translating and…
When an amorphous solid is deformed homogeneously, the response exhibits heterogeneous plastic instabilities with localized cooperative rearrangement of cluster of particles. The heterogeneous behavior plays an important role in deciding…
We analyze experimentally the shape of a long elastic filament rotating in a viscous liquid. We identify a continuous but sharp transition from a straight to an helical shape, resulting from the competition between viscous stresses and…
We consider a model of an extensible semiflexible filament moving in two dimensions on a motility assay of motor proteins represented explicitly as active harmonic linkers. Their heads bind stochastically to polymer segments within a…
We use numerical simulations to study the dynamics of dense assemblies of self-propelled particles in the limit of extremely large, but finite, persistence times. In this limit, the system evolves intermittently between mechanical…
We develop a model for the gliding of dislocations and plasticity in solid He-4. This model takes into account the Peierls barrier, multiplication and interaction of dislocations, as well as classical thermally and mechanically activated…
The size and shape of a large variety of polymeric particles, including biological cells, star polymers, dendrimes, and microgels, depend on the applied stresses as the particles are extremely soft. In high-density suspensions these…
The presence of low dimensional chaos in the protein secondary structures, using the binary coded $\alpha$-helices and $\beta$-sheet motifs, has been investigated. In order to analyse symbolic DNA/RNA sequences the assignment, based on the…
The power of polymorphism in carbon is vividly manifested by the numerous applications of carbon-based nano-materials. Ranging from environmental issues to biomedical applications, it has the potential to address many of today's dire…
Characteristic shock effects in silica serve as a key indicator of historical impacts at geological sites. Despite this geological significance, atomistic details of structural transformations under high pressure and shock compression…
The quasistatic behavior of a simple 2D model of a cohesive powder under isotropic loads is investigated by Discrete Element simulations. The loose packing states, as studied in a previous paper, undergo important structural changes under…
Predicting protein secondary structures such as alpha helices, beta sheets, and coils from amino acid sequences is essential for understanding protein function. This work presents a transformer-based model that applies attention mechanisms…