Related papers: Fluctuation Assisted Ejection of DNA From Bacterio…
We show that in experimental atomic force microscopy studies of the lifetime distribution of mechanically stressed folded proteins the effects of externally applied fluctuations can not be distinguished from those of internally present…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…
We propose a model Hamiltonian for charge transfer along the DNA double helix with temperature driven fluctuations in the base pair positions acting as the rate limiting factor for charge transfer between neighboring base pairs. We compare…
We measure the fluctuations of the position of a Brownian particle confined by an optical trap in an aging gelatin droplet after a fast quench. Its linear response to an external perturbation is also measured. We compute the spontaneous…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
An important question in the physics of superconducting nanostructures is the role of thermal fluctuations on superconductivity in the zero-dimensional limit. Here, we probe the evolution of superconductivity as a function of temperature…
Various charge migration mechanisms in the DNA are studied within the framework of the Peyrard-Bishop-Holstein model which has been widely used to address charge dynamics in this macromolecule. To analyze these mechanisms we consider…
We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed…
Biologically driven non-equilibrium fluctuations are often characterized by their non-Gaussianity or by an "effective temperature", which is frequency dependent and higher than the ambient temperature. We address these two measures…
The sources of wall-pressure fluctuations in turbulent channel flow are studied using a novel framework. The wall-pressure power spectral density (PSD) $(\phi_{pp}(\omega))$ is expressed as an integrated contribution from all wall-parallel…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in…
The Ludwig-Soret effect, the migration of a species due to a temperature gradient, has been extensively studied without a complete picture of its cause emerging. Here we investigate the dynamics of DNA and spherical particles sub jected to…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
We probe non-equilibrium properties of an active bacterial bath through measurements of correlations of passive tracer particles and the response function of a driven, optically trapped tracer. These measurements demonstrate violation of…
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…
We investigate the fluctuations of thermodynamic state-variables in compressible aerodynamic wall-turbulence, using results of direct numerical simulation (DNS) of compressible turbulent plane channel flow. The basic transport equations…
We investigate the translocation of a single stranded DNA (ssDNA) through a pore, which fluctuates between two conformations, by using coupled master equations (ME). The probability density function (PDF) of the first passage times (FPT) of…