Related papers: Frustration, dynamics and catalysis
We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
We reveal that the mechanical pulsation of locally synchronised particles is a generic route to propagate deformation waves. We consider a model of dense repulsive particles whose activity drives periodic change in size of each individual.…
Many transport processes in nature take place on substrates, often considered as unidimensional lanes. These unidimensional substrates are typically non-static: affected by a fluctuating environment, they can undergo conformational changes.…
Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…
We introduce a topology-based nonlinear network model of protein dynamics with the aim of investigating the interplay of spatial disorder and nonlinearity. We show that spontaneous localization of energy occurs generically and is a…
Living systems operate in a critical dynamical regime -- between order and chaos -- where they are both resilient to perturbation, and flexible enough to evolve. To characterize such critical dynamics, the established 'structural theory' of…
What features characterise complex system dynamics? Power laws and scale invariance of fluctuations are often taken as the hallmarks of complexity, drawing on analogies with equilibrium critical phenomena[1-3]. Here we argue that slow,…
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are…
The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as for instance the fluctuations in ribsome copy numbers for a gene regulatory network. While several…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
A number of factors, such as, cell-cell interactions and self-propulsion of cells driven by cytoskeletal forces determine tissue morphologies and dynamics. To explore the interplay between these factors in controlling the dynamics at the…
We derive an exact lower bound to a universal measure of frustration in degenerate ground states of quantum many-body systems. The bound results in the sum of two contributions: entanglement and classical correlations arising from local…
Active contributions to fluctuations are a direct consequence of metabolic energy consumption in living cells. Such metabolic processes continuously create active forces, which deform the membrane to control motility, proliferation as well…
Conformational fluctuations are believed to play an important role in the process by which transcription factor proteins locate and bind their target site on the genome of a bacterium. Using a simple model, we show that the binding time can…
Water plays a major role in bio-systems, greatly contributing to determine their structure, stability and even function. It is well know, for instance, that proteins require a minimum amount of water to be functionally active. Since the…
Nonnative residual interactions have attracted increasing attention in recent protein folding researches. Experimental and theoretical investigations had been set out to catch nonnative contacts that might dominate key events in protein…
Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…