Related papers: Fluctuation Pressure Assisted Ejection of DNA From…
We study by simulation the effect of the diffusive motion of repressor molecules on the noise in mRNA and protein levels in the case of a repressed gene. We find that spatial fluctuations due to diffusion can drastically enhance the noise…
The occurrence of phase fluctuations due to thermal excitations in Bose-Einstein condensates (BECs) is studied for a variety of temperatures and trap geometries. We observe the statistical nature of the appearence of phase fluctuations and…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…
Direct numerical simulations (DNS) of turbulent channel flows up to $Re_{\tau} \approx 1000$ are conducted to investigate the three-dimensional (consisting of streamwise wavenumber, spanwise wavenumber and frequency) spectrum of wall…
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…
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…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
We report quantitative experimental results for the intensity of noise-induced fluctuations below the critical temperature difference $\Delta T_c$ for Rayleigh-B\'enard convection. The structure factor of the fluctuating convection rolls is…
Bacteria meticulously regulate their intracellular ion concentrations and create ionic concentration gradients across the bacterial membrane. These ionic concentration gradients provide free energy for many cellular processes and are…
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…
We explore how thermal fluctuations affect the mechanics of thin amorphous spherical shells. In flat membranes with a shear modulus, thermal fluctuations increase the bending rigidity and reduce the in-plane elastic moduli in a…
We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to…
Hydrated proteins undergo a transition in the deeply supercooled regime, which is attributed to rapid changes in hydration water and protein structural dynamics. Here, we investigate the nanoscale stress relaxation in hydrated lysozyme…
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…
We study the dynamics of a single trapped probe surrounded by self-propelled active particles in two dimensions. In the limit of large size separation, we perform an adiabatic elimination of the small active particles to obtain an effective…
A system of a solvated canonical B-DNA of 12 base pairs with the specified sequence is initially equilibrated in a state of zero external force $f$ acting on it. After equilibration, a switching experiment is performed over the system by…
The paper deals with the two-state (opening-closing of base pairs) model used to describe the fluctuation dynamics of a single bubble formation. We present an exact solution for the discrete and finite size version of the model that…
Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed…