Related papers: Synchronization as a unifying mechanism for protei…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
We present a model of systems of cells with intracellular oscillators (`clocks'). This is motivated by examples from developmental biology and from the behavior of organisms on the threshold to multicellularity. Cells undergo random motion…
Imagine a group of oscillators, each endowed with their own rhythm or frequency, be it the ticking of a biological clock, the swing of a pendulum, or the glowing of fireflies. While these individual oscillators may seem independent of one…
Synchronization underlies phenomena including memory and perception in the brain, coordinated motion of animal flocks, and stability of the power grid. These synchronization phenomena are often modeled through networks of phase-coupled…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
The Kuramoto model captures various synchronization phenomena in biological and man-made systems of coupled oscillators. It is well-known that there exists a critical coupling strength among the oscillators at which a phase transition from…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
A generalized Kuramoto model of coupled phase oscillators with slowly varying coupling matrix is studied. The dynamics of the coupling coefficients is driven by the phase difference of pairs of oscillators in such a way that the coupling…
When modeling the classical Kuramoto model, one of the key features is the tendency to synchronize. Accordingly, the most well-adopted choice of the coupling function is the sine function. Due to the oddness of the sine function, the…
We present a novel interdisciplinary framework that bridges synchronization theory and multi-agent AI systems by adapting the Kuramoto model to describe the collective dynamics of heterogeneous AI agents engaged in complex task execution.…
We discuss in detail a human scale example of the synchronization phenomenon, namely the dynamics of the rhythmic applause. After a detailed experimental investigation, we describe the phenomenon with an approach based on the classical…
Synchronization systems with effective inertia, such as power grid networks and coupled electromechanical oscillators, are commonly modeled by the second-order Kuramoto model. In the forward process, numerical simulations exhibit a…
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
Synchronization of coupled oscillators is a ubiquitous phenomenon found throughout nature. Its robust realization is crucial to our understanding of various nonlinear systems, ranging from biological functions to electrical engineering. On…
The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this…
Chromatin and associated proteins constitute the highly folded structure of chromosomes. We consider a self-avoiding polymer model of the chromatin, segments of which may get cross-linked via protein binders that repel each other. The…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
A new collective behavior of resonant synchronization is discovered and the ability to retrieve information from brain memory is proposed based on this mechanism. We use modified Kuramoto phase oscillator to simulate the dynamics of a…
We study a Kuramoto-like model of coupled identical phase oscillators on a network, where attractive and repulsive couplings are balanced dynamically due to nonlinearity in interaction. Under a week force, an oscillator tends to follow the…