Related papers: Group theory of icosahedral virus capsids: a dynam…
We derive a microscopic theory for the structural dynamics in the vicinity of the glass transition for a liquid exposed to a one-dimensional periodic potential. The periodic potential breaks translational invariance, in particular, the…
The rapid development of topological photonics and acoustics calls for accurate understanding of band topology in classical waves, which is not yet achieved in many situations. Here, we present the Wilson-loop approach for exact numerical…
Modeling the temporal behavior of data is of primordial importance in many scientific and engineering fields. Baseline methods assume that both the dynamic and observation equations follow linear-Gaussian models. However, there are many…
The features of topological physics can manifest in a variety of physical systems in distinct ways. Periodically driven systems, with the advantage of high flexibility and controllability, provide a versatile platform to simulate many…
We combine the hyper-netted chain approximation of liquid state theory with the mode-coupling theory of the glass transition to analyze the structure and dynamics of soft spheres interacting via harmonic repulsion. We determine the locus of…
A semiclassical model, based on a solution of the Vlasov equation for finite systems with moving-surface, is employed to study the isoscalar dipole modes in nuclei. It is shown that, by taking into account the surface degree of freedom, it…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
We present the applications of wavelet analysis methods in constrained variational framework to calculation of dynamical aperture. We construct represention via exact nonlinear high-localized periodic eigenmodes expansions, which allows to…
We study collective dynamical behavior of active particles with topological interactions and directional reversals. Surprising phenomena are shown to emerge as the interaction relaxation time is varied relative to the reversal rate, such as…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
Engineering dissipative dynamics in open quantum systems is under active focus, especially in topological settings where resilient edge modes are expected to exhibit decay rates distinct from the bulk. In this letter, we propose an…
In the frame of the Landau-Ginzburg formalism we propose a minimal phenomenological model for a morphological transformation in viral capsid shells. The transformation takes place during virus maturation process which renders virus…
Studies of periodically driven one-dimensional many-body systems have advanced our understanding of complex systems and stimulated promising developments in quantum simulation. It is hence of interest to go one step further, by…
We experimentally demonstrate a dynamical classification approach for investigation of topological quantum phases using a solid-state spin system through nitrogen-vacancy (NV) center in diamond. Similar to the bulkboundary correspondence in…
We address the problem of analytically extracting a countable infinity of flat, non-dispersive bands in a periodic array of cells that comprise branching Vicsek geometries of higher and higher generations. Through a geometric construction,…
An approach for simulating bionanosystems, such as viruses and ribosomes, is presented. This calibration-free approach is based on an all-atom description for bionanosystems, a universal interatomic force field, and a multiscale…
The collective motion of a finite nuclear system is investigated by numerical simulation and by linear response theory. Using a pseudo-particle simulation technique we analyze the giant resonances with a multipole decomposition scheme. We…
Mathematical models are formal and simplified representations of the knowledge related to a phenomenon. In classical epidemic models, a neglected aspect is the heterogeneity of disease transmission and progression linked to the viral load…
We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one…
A novel strategy for extracting axial (AV) and toroidal (TV) vortices in the magnetically-induced current density (MICD) in molecular systems is introduced, and its pilot application to LiH molecule is demonstrated. It exploits differences…