Related papers: Synchronization as a unifying mechanism for protei…
Synchronization is a ubiquitous phenomenon occurring in social, biological, and technological systems when the internal rhythms of their constituents are adapted to be in unison as a result of their coupling. This natural tendency towards…
Predicting the three-dimensional (3D) functional structures of proteins remains an important computational milestone in molecular biology to be achieved. This feat is hinged on a clear understanding of the mechanism which proteins use to…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
The features of animal population dynamics, for instance, flocking and migration, are often synchronized for survival under large-scale climate change or perceived threats. These coherent phenomena have been explained using synchronization…
The cluster synchronization is a very important characteristic for the higher harmonic coupling Kuramoto system. A novel transformation is provided, and it gives cluster synchronization by the periodic properties of the density function.…
Protein folding is the intricate process by which a linear sequence of amino acids self-assembles into a unique three-dimensional structure. Protein folding kinetics is the study of pathways and time-dependent mechanisms a protein undergoes…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
A novel approach to protein folding dynamics is presented. We suggest that folding of protein may be mediated via interaction with solitons which propagate along the molecular chain. A simple toy model is presented in which a Sine-Gordon…
Based on recent advances in fibration symmetry theory, we investigate how structural symmetries influence synchronization in systems with higher-order interactions (HOI). Using bipartite graph representations, we identify a node partition…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
After decades of study, there are only two known mechanisms to induce global synchronization in a population of oscillators: deterministic coupling and common forcing. The inclusion of independent random forcing in these models typically…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Synchronization is an omnipresent collective phenomenon in nature and technology, whose understanding is in particular for real-world systems still elusive. We study the synchronization transition in a phase oscillator system with two…
The collective motion of dust particles during the mode-coupling induced melting of a two-dimensional plasma crystal is explored in molecular dynamics simulations. The crystal is compressed horizontally by an anisotropic confinement. This…
We investigate in depth the synchronization of coupled oscillators on top of complex networks with different degrees of heterogeneity within the context of the Kuramoto model. In a previous paper [Phys. Rev. Lett. 98, 034101 (2007)], we…
The understanding of synchronization ranging from natural to social systems has driven the interests of scientists from different disciplines. Here, we have investigated the synchronization dynamics of the Kuramoto dynamics departing from…