Related papers: Synchronization as a unifying mechanism for protei…
Proteins can combine into functional elements in living cells or self-assemble into unwanted structures in a number of diseases. The resulting aggregates often display filamentous morphologies across a large range of protein shapes and…
The phenomenon of synchronization occurs universally across the natural sciences and provides critical insight into the behavior of coupled nonlinear dynamical systems. It also offers a powerful approach to robust frequency or temporal…
Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…
Synchronization is of importance in both fundamental and applied physics, but their demonstration at the micro/nanoscale is mainly limited to low-frequency oscillations like mechanical resonators. Here, we report the synchronization of two…
Recent advances in computational power and simulation programs finally delivered the first examples of reversible folding for small proteins with an all-atom description. But having at hand the atomistic details of the process did not lead…
We show that spontaneous density segregation in dense systems of aligning circle swimmers is a condensation phenomenon at odds with the phase separation scenarios usually observed in two-dimensional active matter. The condensates, which…
Synchronization of non-identical oscillators coupled through complex networks is an important example of collective behavior. It is interesting to ask how the structural organization of network interactions influences this process. Several…
Synchronization is a ubiquitous phenomenon in complex systems. The Kuramoto model serves as a paradigmatic framework for understanding how coupled oscillators achieve collective rhythm. Conventional approaches focus on pairwise…
Pattern formation and the mechanics of a mixture of actin filaments and myosin motors that is confined by a rigid membrane is investigated. By using a coarse-grained molecular dynamics model, we demonstrate that the competition between the…
A fundamental understanding of synchronized behavior in multi-agent systems can be acquired by studying analytically tractable Kuramoto models. However, such models typically diverge from many real systems whose dynamics evolve under…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
Amyloid fibrillation is a protein self-assembly phenomenon that is intimately related to well-known human neurodegenerative diseases. During the past few decades, striking advances have been achieved in our understanding of the physical…
We investigate the connection between the dynamics of synchronization and the modularity on complex networks. Simulating the Kuramoto's model in complex networks we determine patterns of meta-stability and calculate the modularity of the…
The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
In this work we study the synchronization of Kuramoto oscillators driven by external forces in complex modular networks. The motivation is the neuronal dynamics that takes place during information processing in the neural cortex. The neuron…
Synchronization commonly occurs in many natural and man-made systems, from neurons in the brain to cardiac cells to power grids to Josephson junction arrays. Transitions to or out of synchrony for coupled oscillators depend on several…
A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…
Nonlinear oscillations and synchronisation phenomena are ubiquitous in nature. We study the synchronization of self oscillating magneto-optically trapped cold atoms to a weak external driving. The oscillations arise from a dynamical…
A Newton's cradle is a device that demonstrates conservation of momentum using a series of identical colliding pendula. Despite being a famous example that demonstrates the concept of momentum conservation, extensive analysis of the system…