Localized Joule heating produced by ion current focusing through micron-size holes

We provide an experimental demonstration that the focusing of ionic currents in a micron size hole connecting two chambers can produce local temperature increases of up to $100^\circ$ C with gradients as large as $1^\circ$ K$\mu m^{-1}$. We find a good agreement between the measured temperature profiles and a finite elements-based numerical calculation. We show how the thermal gradients can be used to measure the full melting profile of DNA duplexes within a region of 40 $\mu$m. The possibility to produce even larger gradients using sub-micron pores is discussed.Comment: 3 pages, accepted to Appl. Phys. Lett

Unzipping Dynamics of Long DNAs

The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For unzipping of 50 kilobase DNAs at less than about 1000 bases per second, thermal equilibrium-based theory applies. However, for higher unzipping velocities, rotational viscous drag creates a buildup of elastic torque to levels above kBT in the dsDNA region, causing the unzipping force to be well above or well below the equilibrium unzipping force during respectively unzipping and rezipping, in accord with recent experimental results of Thomen et al. [Phys. Rev. Lett. 88, 248102 (2002)]. Our analysis includes the effect of sequence on unzipping and rezipping, and the transient delay in buildup of the unzipping force due to the approach to the steady state.Comment: 15 pages Revtex file including 9 figure

Probing the mechanical unzipping of DNA

A study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique that allows accurate determination of the dependence of the unzipping forces on unzipping speed and temperature. Our findings agree quantitatively with experimental results for homogeneous DNA, and for $\lambda$-phage DNA we reproduce the recently obtained experimental force-temperature phase diagram. Finally, we argue that there may be fundamental differences between {\em in vivo} and {\em in vitro} DNA unzipping

Bar-Halo Friction in Galaxies II: Metastability

It is well-established that strong bars rotating in dense halos generally slow down as they lose angular momentum to the halo through dynamical friction. Angular momentum exchanges between the bar and halo particles take place at resonances. While some particles gain and others lose, friction arises when there is an excess of gainers over losers. This imbalance results from the generally decreasing numbers of particles with increasing angular momentum, and friction can therefore be avoided if there is no gradient in the density of particles across the major resonances. Here we show that anomalously weak friction can occur for this reason if the pattern speed of the bar fluctuates upwards. After such an event, the density of resonant halo particles has a local inflexion created by the earlier exchanges, and bar slowdown can be delayed for a long period; we describe this as a metastable state. We show that this behavior in purely collisionless N-body simulations is far more likely to occur in methods with adaptive resolution. We also show that the phenomenon could arise in nature, since bar-driven gas inflow could easily raise the bar pattern speed enough to reach the metastable state. Finally, we demonstrate that mild external, or internal, perturbations quickly restore the usual frictional drag, and it is unlikely therefore that a strong bar in a galaxy having a dense halo could rotate for a long period without friction.Comment: 13 pages, 11 figures, to appear in Ap

Valence band spectroscopy in V-grooved quantum wires

We present a combined theoretical and experimental study of the anisotropy in the optical absorption of V-shaped quantum wires. By means of realistic band structure calculations for these structures, we show that detailed information on the heavy- and light-hole states can be singled out from the anisotropy spectra {\em independently of the electron confinement}, thus allowing accurate valence band spectroscopy.Comment: To be published in Appl. Phys. Lett. (8 pages in REVTeX, two postscipt figures

Revealing the Competition between Peeled-Ssdna, Melting Bubbles and S-DNA during DNA Overstretching using Fluorescence Microscopy

Understanding the structural changes occurring in double-stranded (ds)DNA during mechanical strain is essential to build a quantitative picture of how proteins interact and modify DNA. However, the elastic response of dsDNA to tension is only well-understood for forces < 65 pN. Above this force, torsionally unconstrained dsDNA gains ∼70% of its contour length, a process known as overstretching. The structure of overstretched DNA has proved elusive, resulting in a rich and controversial debate in recent years. At the centre of the debate is the question of whether overstretching yields a base-paired elongated structure, known as S-DNA, or instead forms single-stranded (ss)DNA via base-pair cleavage. Here, we show clearly, using a combination of fluorescence microscopy and optical tweezers, that both S-DNA and base-pair melted structures can exist, often concurrently, during overstretching. The balance between the two models is affected strongly by temperature and ionic strength. Moreover, we reveal, for the first time, that base-pair melting can proceed via two entirely different processes: progressive strand unpeeling from a free end in the backbone, or by the formation of ‘bubbles' of ssDNA, nucleating initially in AT-rich regions. We demonstrate that the mechanism of base-pair melting is governed by DNA topology: strand unpeeling is favored when there are free ends in the DNA backbone. Our studies settle a long running debate, and unite the contradictory dogmas of DNA overstretching. These findings have important implications for both medical and biological sciences. Force-induced melting transitions (yielding either peeled-ssDNA or melting bubbles) may play active roles in DNA replication and damage repair. Further, the ability to switch easily from DNA containing melting bubbles to S-DNA may be particularly advantageous in the cell, for instance during the formation of RNA within transcription bubbles. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved

Revealing the Competition between Peeled-Ssdna, Melting Bubbles and S-DNA during DNA Overstretching using Fluorescence Microscopy

Understanding the structural changes occurring in double-stranded (ds)DNA during mechanical strain is essential to build a quantitative picture of how proteins interact and modify DNA. However, the elastic response of dsDNA to tension is only well-understood for forces < 65 pN. Above this force, torsionally unconstrained dsDNA gains ∼70% of its contour length, a process known as overstretching. The structure of overstretched DNA has proved elusive, resulting in a rich and controversial debate in recent years. At the centre of the debate is the question of whether overstretching yields a base-paired elongated structure, known as S-DNA, or instead forms single-stranded (ss)DNA via base-pair cleavage. Here, we show clearly, using a combination of fluorescence microscopy and optical tweezers, that both S-DNA and base-pair melted structures can exist, often concurrently, during overstretching. The balance between the two models is affected strongly by temperature and ionic strength. Moreover, we reveal, for the first time, that base-pair melting can proceed via two entirely different processes: progressive strand unpeeling from a free end in the backbone, or by the formation of ‘bubbles' of ssDNA, nucleating initially in AT-rich regions. We demonstrate that the mechanism of base-pair melting is governed by DNA topology: strand unpeeling is favored when there are free ends in the DNA backbone. Our studies settle a long running debate, and unite the contradictory dogmas of DNA overstretching. These findings have important implications for both medical and biological sciences. Force-induced melting transitions (yielding either peeled-ssDNA or melting bubbles) may play active roles in DNA replication and damage repair. Further, the ability to switch easily from DNA containing melting bubbles to S-DNA may be particularly advantageous in the cell, for instance during the formation of RNA within transcription bubbles. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved