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Bending of worm-like polymers carries an energy penalty which results in the appearance of a persistence length l p such that the polymer is straight on length scales smaller than l p and bends only on length scales larger than this length. Intuitively, this leads us to expect that the most probable value of the local curvature of a worm-like polymer(More)
We have used the nanometer scale alpha-Hemolysin pore to study the unzipping kinetics of individual DNA hairpins under constant force or constant loading rate. Using a dynamic voltage control method, the entry rate of polynucleotides into the pore and the voltage pattern applied to induce hairpin unzipping are independently set. Thus, hundreds of unzipping(More)
Solid-state nanopores are sensors capable of analysing individual unlabelled DNA molecules in solution. Although the critical information obtained from nanopores (for example, DNA sequence) comes from the signal collected during DNA translocation, the throughput of the method is determined by the rate at which molecules arrive and thread into the pores.(More)
A new approach to polymer simulation well suited to massively parallel architectures is presented. The approach is based on a novel two-space algorithm that enables 50% of the monomers to be updated in parallel. The simplicity of this algorithm enables implementation and comparison of different platforms. Such comparisons are relevant to a wide variety of(More)
Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule inside. In the presence of DNA, the counterions condense on the stretched macromolecule effectively neutralizing it, and(More)
We generate two-dimensional Lennard-Jones networks with random topology by preparing a perfect four-functional network of identical harmonic springs and randomly cutting some of the springs. Using molecular-dynamics simulations we find that the fraction p of active springs affects both the temperature of phase separation and the type of structures observed(More)
Solid-state nanopores are sensors capable of analyzing individual unlabelled DNA molecules in solution. While the critical information obtained from nanopores (e.g., DNA sequence) is the signal collected during DNA translocation, the throughput of the method is determined by the rate at which molecules arrive and thread into the pores. Here we study the(More)
We use Monte-Carlo simulations to study the effect of variable rigidity on plectoneme formation and localization in supercoiled double-stranded DNA. We show that the presence of soft sequences increases the number of plectoneme branches and that the edges of the branches tend to be localized at these sequences. We propose an experimental approach to test(More)
Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal measurements of protein content, showing accumulation and division across generations. Here we present a stochastic(More)
We study the effects of thermal fluctuations on elastic rings. Analytical expressions are derived for correlation functions of Euler angles, mean-square distance between points on the ring contour, radius of gyration, and probability distribution of writhe fluctuations. Since fluctuation amplitudes diverge in the limit of vanishing twist rigidity, twist(More)