Related papers: Synchronization as a unifying mechanism for protei…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
Coordination is ubiquitous in living systems. Existing theoretical models of coordination -- from bacteria to brains -- focus on either gross statistics in large-scale systems ($N\rightarrow\infty$) or detailed dynamics in small-scale…
The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…
Many coordination phenomena are based on a synchronisation process, whose global behaviour emerges from the interactions among the individual parts. Often in Nature, such self-organising mechanism allows the system to behave as a whole and…
Suppose we are given a system of coupled oscillators on an unknown graph along with the trajectory of the system during some period. Can we predict whether the system will eventually synchronize? Even with a known underlying graph…
Many natural and human-made complex systems feature group interactions that adapt over time in response to their dynamic states. However, most of the existing adaptive network models fall short of capturing these group dynamics, as they…
We present a rigorous mathematical framework establishing the equivalence of four classical notions of synchronization full phase-locking, phase-locking, frequency synchronization, and order parameter synchronization in generalized Kuramoto…
Swarmalators, entities that combine the properties of swarming particles with synchronized oscillations, represent a novel and growing area of research in the study of collective behavior. This review provides a comprehensive overview of…
A model to describe the mechanism of conformational dynamics in secondary protein based on matter interactions is proposed. The approach deploys the lagrangian method by imposing certain symmetry breaking. The protein backbone is initially…
We study the phase synchronization of Kuramoto's oscillators in small parts of networks known as motifs. We first report on the system dynamics for the case of a scale-free network and show the existence of a non-trivial critical point. We…
We analyze the collective behavior of a lattice model of pulse-coupled oscillators. By means of computer simulations we find the relation between the intrinsic dynamics of each member of the population and their mutual interaction that…
The simplest prescription for building a patterned structure from its constituents is to add particles, one at a time, to an appropriate template. However, self-organizing molecular and colloidal systems in nature can evolve in much more…
Cellular appendages conferring motility, such as flagella or cilia, are known to synchronise their periodic beats. The origin of synchronisation is a combination of long-range hydrodynamic interactions with physical mechanisms allowing the…
We introduce the concept of synchronization bombs as large networks of coupled heterogeneous oscillators that operate in a bistable regime and abruptly transit from incoherence to phase-locking (or vice-versa) by adding (or removing) one or…
Synchronization is a widespread phenomenon observed across natural and artificial networked systems. It often manifests itself by clusters of units exhibiting coincident dynamics. These clusters are a direct consequence of the organization…