Related papers: Persistence Length Changes Dramatically as RNA Fol…
We calculate the dependence of the electrostatic persistence length, l_e, of weakly charged flexible polyelectrolyte chains using a self-consistent variational theory. The variation of l_e with \kappa, the inverse Debye screening length, is…
Using high-throughput Tethered Particle Motion single molecule experiments, the double-stranded DNA persistence length, $L_p$, is measured in solutions with Na$^+$ and Mg$^{2+}$ ions of various ionic strengths, $I$. Several theoretical…
Monte Carlo simulations and variational calculations using a Gaussian ansatz are applied to a model consisting of a flexible linear polyelectrolyte chain as well as to an intrinsically stiff chain with up to 1000 charged monomers. Addition…
Even though the persistence length $L_P$ of double-stranded DNA plays a pivotal role in cell biology and nanotechnologies, its dependence on ionic strength $I$ lacks a consensual description. Using a high-throughput single-molecule…
Chain-like macromolecules in solution, whether biological or synthetic, transform from an extended conformation to a compact one when temperature or other system parameters change. This collapse transition is relevant in various phenomena,…
The authors measure the persistence and contour lengths of DNA-psoralen complexes, as a function of psoralen concentration, for intercalated and crosslinked complexes. In both cases, the persistence length monotonically increases until a…
The highly charged RNA molecules, with each phosphate carrying a single negative charge, cannot fold into well-defined architectures with tertiary interactions, in the absence of ions. For ribozymes, divalent cations are known to be more…
According to classical electrolyte theories interactions in dilute (low ion density) electrolytes decay exponentially with distance, with the Debye screening length the characteristic length-scale. This decay length decreases monotonically…
We use optical tweezers to perform stretching experiments on DNA molecules when interacting with the drugs daunomycin and ethidium bromide, which intercalate the DNA molecule. These experiments are performed in the low-force regime from…
The aim of this paper is to study two models for a bacterial population subject to antibiotic treatments. It is known that some bacteria are sensitive to antibiotics. These bacteria are in a state called persistence and each bacterium can…
Dynamics of reentry are studied in a one dimensional loop of model cardiac cells with discrete intercellular gap junction resistance ($R$). Each cell is represented by a continuous cable with ionic current given by a modified Beeler-Reuter…
Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher…
Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of…
Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped…
We study the effect of electrostatic interactions on the distribution function of the end-to-end distance of a single polyelectrolyte chain in the rodlike limit. The extent to which the radial distribution function of a polyelectrolyte is…
The persistence length of a single, intrinsically rigid polyelectrolyte chain, above the Manning condensation threshold is investigated theoretically in presence of added salt. Using a loop expansion method, the partition function is…
We address the long standing problem of the dependence of the electrostatic persistence length $l_e$ of a flexible polyelectrolyte (PE) on the screening length $r_s$ of the solution within the linear Debye-Huckel theory. The standard Odijk,…
By using high molecular weight fluorescent passive tracers with different diffusion coefficients and by changing the fluid velocity we study dependence of a characteristic mixing length on the Peclet number, $Pe$, which controls the mixing…
We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the…
We consider an i.i.d. supercritical bond percolation on Z^d , every edge is open with a probability p > p\_c (d), where p\_c (d) denotes the critical parameter for this percolation. We know that there exists almost surely a unique infinite…