Related papers: Synchronization as a unifying mechanism for protei…

Studies of how protein fold have shown that the way protein clumps form in the test tube is similar to how proteins form the so-called ``amyloid'' deposits that are the pathological signal of a variety of diseases, among them the memory…

We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…

Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…

A shell model can be considered as a chain of triads, where each triad can be interpreted as a nonlinear oscillator that can be mapped to a spinning top. Investigating the relation between phase dynamics and intermittency in a such a chain…

We report on a series of measurements aimed to characterize the development and the dynamics of the rhythmic applause in concert halls. Our results demonstrate that while this process shares many characteristics of other systems that are…

Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…

We propose a model for motor proteins based on a hierarchical Hamiltonian that we have previously introduced to describe protein folding. The proposed motor model has high efficiency and is consistent with a linear load-velocity response.…

Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…

The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…

Synchronization plays a crucial role in the dynamics of living organisms, from fireflies flashing in unison to pacemaker cells that jointly generate heartbeats. Uncovering the mechanism behind these phenomena requires an understanding of…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…

The Kuramoto model, which serves as a paradigm for investigating synchronization phenomenon of oscillatory system, is known to exhibit second-order, i.e., continuous, phase transitions in the macroscopic order parameter. Here, we generalize…

One of the main concerns of Anfinsen was to reveal the connection between the amino acid sequence and their biologically active conformation. This search gave rise to two crucial questions in structural biology, namely, why the proteins…

Coupled oscillators have been used to study synchronization in a wide range of social, biological, and physical systems, including pedestrian-induced bridge resonances, coordinated lighting up of firefly swarms, and enhanced output peak…

Synchronization occurs in many natural and technological systems, from cardiac pacemaker cells to coupled lasers. In the synchronized state, the individual cells or lasers coordinate the timing of their oscillations, but they do not move…

We study synchronization in a Kuramoto model of globally coupled phase oscillators with a bi-harmonic coupling function, in the thermodynamic limit of large populations. We develop a method for an analytic solution of self-consistent…

The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…

Synchronization is one of the paradigmatic phenomena in the study of complex systems. It has been explored theoretically and experimentally mostly to understand natural phenomena, but also in view of technological applications. Although…

We analyze populations of Kuramoto oscillators with a particular distribution of natural frequencies. Inspired by networks where there are two groups of nodes with opposite behaviors, as for instance in power-grids where energy is either…

Synchronization is ubiquitous in nature at various scales and fields. This phenomenon not only offers a window into the intrinsic harmony of complex systems, but also serves as a robust probe for many-body quantum systems. One such system…