ﻻ يوجد ملخص باللغة العربية
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the compressional elasticity of the bacterial nucleoid (DNA plus associated proteins), where DNA is confined into a cylindrical container and subjected to the action of a piston - a spherical bead to which an external force is applied. We quantify the effect of steric interactions (excluded volume) on the force-extension curves as the polymer is compressed. We find that non-DNA-binding proteins, even at low densities, exert an osmotic force which can be a lot larger than the entropic force exerted by the compressed DNA. The trends we observe are qualitatively robust with respect to changes in protein size, and are similar for neutral and charged proteins (and DNA). We also quantify the dynamics of DNA expansion following removal of the piston: while the expansion is well fitted by power laws, the apparent exponent depends on protein concentration, and protein-DNA interaction in a significant way. We further highlight an interesting kinetic process which we observe during the expansion of DNA interacting with DNA-binding proteins when the interaction strength is intermediate: the proteins bind while the DNA is packaged by the compression force, but they pop-off one-by-one as the force is removed, leading to a slow unzipping kinetics. Finally, we quantify the importance of supercoiling, which is an important feature of bacterial DNA in vivo.
Self-sustained turbulent structures have been observed in a wide range of living fluids, yet no quantitative theory exists to explain their properties. We report experiments on active turbulence in highly concentrated 3D suspensions of Bacillus subti
Colonies of bacterial cells endowed with a pili-based self-propulsion machinery represent an ideal model system for studying how active adhesion forces affect structure and dynamics of many-particle systems. As a novel computational tool, we describe
The thermal degradation of a graphene-like two-dimensional triangular membrane with bonds undergoing temperature-induced scission is studied by means of Molecular Dynamics simulation using Langevin thermostat. We demonstrate that the probability dist
We develop an explicit and tractable representation of a twist-grain-boundary phase of a smectic A liquid crystal. This allows us to calculate the interaction energy between grain boundaries and the relative contributions from the bending and compres
Frictional interfaces are abundant in natural and engineering systems, and predicting their behavior still poses challenges of prime scientific and technological importance. At the heart of these challenges lies the inherent coupling between the inte