Related papers: DNA-Protein Binding Rates: Bending Fluctuation and…
Protein molecules often self-assemble by means of non-covalent physical bonds to form extended filaments, such as amyloids, F-actin, intermediate filaments, and many others. The kinetics of filament growth is limited by the disassembly…
We extend the Saffman theory of membrane hydrodynamics to account for the correlated motion of membrane proteins, along with the effect of protein concentration on that correlation and on the response of the membrane to stresses.…
The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking non-monotonic dependence of the long-time self-diffusion on the concentration of the DNA in low-salt conditions. This generic non-monotonic…
The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles respectively, when the strands of the DNA are subjected to a force along the same…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We observed reptation of single DNA molecules in fused silica nanoslits of sub-30 nm height. The reptation behavior and the effect of confinement are quantitatively characterized using orientation correlation and transverse fluctuation…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
Transcription factors are able to associate to their binding sites on DNA faster than the physical limit posed by diffusion. Such high association rates can be achieved by alternating between three-dimensional diffusion and one-dimensional…
The reaction-diffusion waves of proteins are known to be involved in fundamental cellular functions, such as cell migration, cell division, and vesicular transportation. In some of these phenomena, pattern formation on the membranes is…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very…
The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection…
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…
We recently introduced a model of an asymmetric dumbbell made of two hydrodynamically coupled subunits as a minimal model for a macromolecular complex, in order to explain the observation of enhanced diffusion of catalytically active…
A theoretical model for the effect of water hydrogen bonding on the thermodynamics of hydrophobic hydration is proposed as a combination of the classical density functional theory with the recently developed probabilistic approach to water…
In this work we develop a theory of interaction of randomly patterned surfaces as a generic prototype model of protein-protein interactions. The theory predicts that pairs of randomly superimposed identical (homodimeric) random patterns…