Related papers: Directly measuring single molecule heterogeneity u…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…
Cell motility is one of the most fundamental phenomena underlying biological processes that maintain living organisms alive. Here we introduce a simple model to describe the motility of cells which include not only time-correlated internal…
We consider the asymptotic behavior of an evolving weakly coupled Fokker-Planck system of two equations set in a periodic environment. The magnitudes of the diffusion and the coupling are respectively proportional and inversely proportional…
Force versus extension curves measure entropic elasticity of single polymer chain in force spectroscopy experiments. A Worm-like Chain model is used to describe force extension experiments with an intrinsic chain parameter called…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
The recent experimental progresses in handling microscopic systems have allowed to probe them at levels where fluctuations are prominent, calling for stochastic modeling in a large number of physical, chemical and biological phenomena. This…
The effect of sequence heterogeneity on the dynamics of molecular motors is reviewed and analyzed using a set of recently introduced lattice models. First, we review results for the influence of heterogenous tracks such as a single-strand…
Cells sense external concentrations and, via biochemical signaling, respond by regulating the expression of target proteins. Both in signaling networks and gene regulation there are two main mechanisms by which the concentration can be…
A multispeckle technique for efficiently measuring correctly ensemble-averaged intensity autocorrelation functions of scattered light from non-ergodic and/or non-stationary systems is described. The method employs a CCD camera as a…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
We review the properties of biological motor proteins which move along linear filaments that are polar and periodic. The physics of the operation of such motors can be described by simple stochastic models which are coupled to a chemical…
Many proteins undergo conformational changes during their activity. A full understanding of the function of these proteins can only be obtained if different conformations and transitions between them can be monitored in aqueous solution,…
We show by means of experiments, theory and simulations, that the slow dynamics of coarsening systems displays dynamic heterogeneity similar to that observed in glass-forming systems. We measure dynamic heterogeneity via novel multi-point…
Force spectroscopy using magnetic tweezers (MT) is a powerful method to probe the physical characteristics of single polymers. Typically, molecules are functionalized for specific attachment to a glass surface at one end and a micron-scale…
We perform molecular dynamics simulations to characterize the occurrence of inhomogeneous shear flows in soft jammed materials. We use rough walls to impose a simple shear flow and study the athermal motion of jammed assemblies of soft…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
External biasing forces are often applied to enhance sampling in regions of phase space which would otherwise be rarely observed. While the typical goal of these experiments is to calculate the potential of mean force (PMF) along the…
Single molecule junctions exhibit dynamic structural configurations that strongly influence their electronic and thermoelectric properties. Here, we combine conductance (G) and Seebeck coefficient (S) measurements using the novel AC based…