Related papers: Fluctuations, correlations and the estimation of c…
The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…
Cells generally change their internal state to adapt to an environmental change, and accordingly evolve in response to the new conditions. This process involves phenotypic changes that occur over several different time scales, ranging from…
We investigate the propagation of random fluctuations through biochemical networks in which the concentrations of species are large enough so that the unperturbed problem is well-described by ordinary differential equation. We characterize…
In biological cells and novel diagnostic devices biochemical receptors need to be sensitive to extremely small concentration changes of signaling molecules. The accuracy of such molecular signaling is ultimately limited by the counting…
We study fluctuations of particle number in the presence of critical point by utilizing molecular dynamics simulations of the classical Lennard-Jones fluid in a periodic box. The numerical solution of the $N$-body problem naturally…
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…
The stability of a flexible fluid membrane containing a distribution of mobile, active proteins (e.g. proton pumps) is shown to depend on the structure and functional asymmetry of the proteins. A stable active membrane is in a…
Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of…
Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules…
In this perspective we consider how modern statistical mechanics and response theory can be applied to understand the response of polar molecules to an applied electric field and the fluctuations in these systems. Results that are…
Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct…
Fluctuation in fluorescence emission of immobilized single molecule is typically ascribed to the chromophore's intrinsic structural conformations and the influence of local environmental factors. Despite extensive research over several…
The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…
Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers…
We study fluctuations in diffusion-limited reaction systems driven out of their stationary state. Using a numerically exact method, we investigate fluctuation ratios in various systems which differ by their level of violation of microscopic…
It is shown, by considering the case of the harmonic oscillator, that quantum fluctuations may be the most significant contribution to the random walk of a single molecule. From this point, the controversy on the existence of a standard…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
The rate at which individual bacterial cells grow depends on the concentrations of cellular components such as ribosomes and proteins. These concentrations continuously fluctuate over time and are inherited from mother to daughter cells,…
Cells adapt to changing environments by sensing ligand concentrations using specific receptors. The accuracy of sensing is ultimately limited by the finite number of ligand molecules bound by receptors. Previously derived physical limits to…
Chemically active systems such as living cells are maintained out of thermal equilibrium due to chemical events which generate heat and lead to active fluctuations. A key question is to understand on which time and length scales active…