Related papers: Persistence Length Changes Dramatically as RNA Fol…
The evolution of drug resistance in HIV occurs by the fixation of specific, well-known, drug-resistance mutations, but the underlying population genetic processes are not well understood. By analyzing within-patient longitudinal sequence…
Both multi-cell biochemical assays and single cell fluorescence measurements have revealed that the elongation rate of Polymerase II (PolII) in eukaryotes varies largely across different cell types and genes. However, there is not yet a…
A collection of spherical particles can be packed tightly together into an amorphous packing known as "random close packing" (RCP). This structure is of interest as a model for the arrangement of molecules in simple liquids and glasses, as…
We study how varying the P \'eclet number (Pe) affects the steady state sedimentation of colloidal particles that interact through short-ranged attractions. By employing a hybrid molecular dynamics simulation method we demonstrate that the…
Motivated both by theoretical and practical considerations in topological data analysis, we generalize the $p$-Wasserstein distance on barcodes to multiparameter persistence modules. For each $p\in [1,\infty]$, we in fact introduce two such…
In a recent Letter Bray and Blythe have shown that the survival probability P(t) of an A particle diffusing with a diffusion coefficient D_A in a 1D system with diffusive traps B is independent of D_A in the asymptotic limit t \to \infty…
We consider a single Rouse polymer chain in two dimensions in presence of a transverse shear flow along the $x$ direction and calculate the persistence probability $P_0(t)$ that the $x$ coordinate of a bead in the bulk of the chain does not…
The effective elasticity of highly charged stiff polyelectrolytes is studied in the presence of counterions, with and without added salt. The rigid polymer conformations may become unstable due to an effective attraction induced by…
A wide spectrum of Peritrichous bacteria undergo considerable physiological changes when they are inoculated onto nutrition-rich surfaces and exhibit a rapid and collective migration denoted as swarming. Thereby, the length of such swarmer…
We investigate the lifetimes of complexes formed in ultracold molecule collisions. Employing both transition-state-theory and an optical model approach we examine processes that can extend the lifetime of complexes beyond that predicted by…
In cond-mat/9907125 the low-temperature behavior of a model for RNA secondary structure was studied. It is claimed that the model exhibits a breaking of the replica symmetry, since the width of the distribution P(q) of overlaps may converge…
We study the survival versus disruption of the giant clumps in high-redshift disc galaxies, short-lived (S) versus long-lived (L) clumps and two L sub-types, via analytic modeling tested against simulations. We develop a criterion for clump…
Emulsions ripen with an average droplet size increasing in time. In chemically active emulsions, coarsening can be absent, leading to a non-equilibrium steady state with mono-disperse droplet sizes. By considering a minimal model for phase…
Persistence in coarsening 1D spin systems with a power law interaction $r^{-1-\sigma}$ is considered. Numerical studies indicate that for sufficiently large values of the interaction exponent $\sigma$ ($\sigma\geq 1/2$ in our simulations),…
Given an autoregressive process X of order p (i.e. X_n = a_1 X_{n-1} + ...+ a_p X_{n_p} + Y_n where the random variables Y_1, Y_2, ... are i.i.d.), we study the asymptotic behaviour of the probability that the process does not exceed a…
We investigate the conformations of DNA-like stiff chains, characterized by contour length ($L$) and persistence length ($l_p$), in a variety of crowded environments containing mono disperse soft spherical (SS) and spherocylindrical (SC)…
Sensitive sequencing of biopolymers by nanopore-based translocation techniques requires extension of the time spent by the molecule in the pore. We develop an electrostatic theory of polymer translocation to show that the translocation time…
The present paper investigates the extension behavior of a wormlike chain with varied persistence length under the confinement of a cylindrical tube. Based on Odijk theory of a confined polymer chain, we have developed a theory which can…
The theory of first order density-driven phase transitions with frustration due to the long range Coulomb (LRC) interaction develop on paper I of this series is applied to the following physical systems: i) the low density electron gas ii)…
The nature and the universal properties of DNA thermal denaturation are investigated by Monte Carlo simulations. For suitable lattice models we determine the exponent c describing the decay of the probability distribution of denaturated…