Related papers: Synchronization as a unifying mechanism for protei…
We analyze the physical mechanisms leading either to synchronization or to the formation of spatio-temporal patterns in a lattice model of pulse-coupled oscillators. In order to make the system tractable from a mathematical point of view we…
Synchronization is a fundamental phenomenon in complex systems, observed across a wide range of natural and engineered contexts. The Kuramoto model provides a foundational framework for understanding synchronization among coupled…
Synchronization of an ensemble of oscillators is an emergent phenomenon present in several complex systems, ranging from social and physical to biological and technological systems. The most successful approach to describe how coherent…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Synchronization of actively oscillating organelles such as cilia and flagella facilitates self-propulsion of cells and pumping fluid in low Reynolds number environments. To understand the key mechanism behind synchronization induced by…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
Synchronization is of central importance in power distribution, telecommunication, neuronal, and biological networks. Many networks are observed to produce patterns of synchronized clusters, but it has been difficult to predict these…
Synchronization and desynchronization are the two ends on the spectrum of emergent phenomena that somehow often coexist in biological, neuronal, and physical networks. However, previous studies essentially regard their coexistence as a…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
Systems of mobile physical entities exchanging information with their neighborhood can be found in many different situations. The understanding of their emergent cooperative behaviour has become an important issue across disciplines,…
Self-synchronization is a ubiquitous phenomenon in nature, in which oscillators are collectively locked in frequency and phase through mutual interactions. While self-synchronization requires the forced excitation of at least one of the…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
All cells must keep time to consistently perform vital biological functions. To that end, the coupling and interrelatedness of diverse subsecond events in the complex cellular environment, such as protein folding or translation rates,…
A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected…
Adaptive dynamical networks are ubiquitous in real-world systems. This paper aims to explore the synchronization dynamics in networks of adaptive oscillators based on a paradigmatic system of adaptively coupled phase oscillators. Our…
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…
A class of adaptation functions is found for which a synchronous oscillation mode exists in the network of phase oscillators with triadic couplings. It is shown that the destruction of the synchronous mode occurs differently for networks…
Synchronization is a phenomenon where interacting particles lock their motion and display non-trivial dynamics. Despite intense efforts studying synchronization in systems without clear classical limits, no comprehensive theory has been…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…