Related papers: Persistence Length Changes Dramatically as RNA Fol…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
We study spatial permutations with cycle weights that are bounded or slowly diverging. We show that a phase transition occurs at an explicit critical density. The long cycles are macroscopic and their cycle lengths satisfy a…
We study a matrix model of RNA in which an external perturbation acts on n nucleotides of the polymer chain. The effect of the perturbation appears in the exponential generating function of the partition function as a factor…
Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer…
The persistent motion of bacteria produces clusters with a stationary cluster size distribution (CSD). Here we develop a minimal model for bacteria in a narrow channel to assess the relative importance of motility diversity (i.e.…
Background: Microbiota have evolved to acclimate themselves to many environments. Humanity is become ever increasingly medicated and many of those medications are antibiotics. Sadly, Microbiota are adapting to medication and with each…
We report on the observation of a change in the bend angle of an RNA kissing complex upon Rop binding using single-molecular-pair FRET. The angular relationship between the dyes, rather than the distance between them, is shown to be…
We report molecular dynamics simulations of the segregation of two overlapping chains in cylindrical confinement. We find that the entropic repulsion between the chains can be sufficiently strong to cause segregation on a time scale that is…
Motivated by novel results in the theory of correlated sequences, we analyze the dynamics of random walks with long-term memory (binary chains with long-range correlations). In our model, the probability for a unit bit in a binary string…
The growing importance of microfluidic and nanofluidic devices to the study of biological processes has highlighted the need to better understand how confinement affects the behavior of polymers in flow. In this paper we explore one aspect…
The equilibrium distance between two lipid bilayers stable in bulk water and in proximity of a substrate was investigated. Samples consisted of a homogeneous lipid bilayer, floating near an identical bilayer deposited on the hydrophilic…
A Poisson-Boltzmann approach is used to determine the double-layer integral and differential capacitances in a finite-length situation for an electrolytic cell. By means of simple analytical calculations, it is shown how these quantities…
The variability of the high-frequency peaked BL Lac object PKS 2155-304 is studied using almost 10 years of optical, X-ray and gamma-rays data. Publicly available data have been gathered and analyzed with the aim to characterize the…
The localization length for isotopically disordered harmonic one-dimensional chains is calculated for arbitrary impurity concentration and scattering cross section. The localization length depends on the scattering cross section of a single…
The supercell method is used to study the variation of the photonic bandgaps in one-dimensional photonic crystals under random perturbations to thicknesses of the layers. The results of both plane wave and analytical band structure and…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
We investigate the effect of sequentiallydisrupting the shortest path of percolation clusters at criticality by comparing it with the shortest alternative path. We measure the difference in length and the enclosed area between the two…
The formation of (bio)molecular condensates via liquid-liquid phase separation in cells has received increasing attention, as these coacervates play important functional and regulatory roles within biological systems. However, the majority…
On the basis of the thermodynamic theory of the excluded volume effects, we show that the size exponent varies abruptly, depending on the change of the segment concentration. For linear polymers, the exponent changes discontinuously from…
We consider dynamics of an isolated polymer chain with a chemically active end-bead on a 2D solid substrate containing immobile, randomly placed chemically active sites (traps). For a particular situation when the end-bead can be…