Related papers: Synchronization as a unifying mechanism for protei…
A family of stochastic processes has quasi-cycle oscillations if the oscillations are sustained by noise. For such a family we define a Kuramoto-type coupling of both phase and amplitude processes. We find that synchronization, as measured…
Elongation is a fundament process in amyloid fiber growth, which is normally characterized by a linear relationship between the fiber elongation rate and the monomer concentration. However, in high concentration regions, a sub-linear…
Synchronization phenomena are pervasive in biology. In neuronal networks, the mechanisms of synchronization have been extensively studied from both physiological and computational viewpoints. The functional role of synchronization has also…
In this work, we study the synchronization of coupled phase oscillators on the underlying topology of scale-free networks. In particular, we assume that each network's component is an oscillator and that each interacts with the others…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
The spontaneous emergence of coherent behavior through synchronization plays a key role in neural function, and its anomalies often lie at the basis of pathologies. Here we employ a parsimonious (mesoscopic) approach to study analytically…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
Proteinaceous aggregation occurs through self-assembly-- a process not entirely understood. In a recent article [1], an analytical theory for amyloid fibril growth via secondary rather than primary nucleation was presented. Remarkably, with…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
Cytoskeletal networks, which are essentially motor-filament assemblies, play a major role in many developmental processes involving structural remodeling and shape changes. These are achieved by nonequilibrium self-organization processes…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
In order to understand the nuclei which develop during the course of protein folding and unfolding, we examine phase segregation of a single heteropolymer chain which occurs in equilibrium. These segregated conformations are characterized…
Spatial organisation is a hallmark of all living cells, and recreating it in model systems is a necessary step in the creation of synthetic cells. It is therefore of both fundamental and practical interest to better understand the basic…
Recent studies of dynamic properties in complex systems point out the profound impact of hidden geometry features known as simplicial complexes, which enable geometrically conditioned many-body interactions. Studies of collective behaviours…
Synchronization processes are ubiquitous despite the many connectivity patterns that complex systems can show. Usually, the emergence of synchrony is a macroscopic observable, however, the microscopic details of the system, as e.g. the…
We investigate synchronization in a Kuramoto-like model with nearest neighbour coupling. Upon analyzing the behaviour of individual oscillators at the onset of complete synchronization, we show that the time interval between bursts in the…
Synchronisation of coupled oscillators is a ubiquitous phenomenon, occurring in topics ranging from biology and physics, to social networks and technology. A fundamental and long-time goal in the study of synchronisation has been to find…