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

Inferring DNA sequences from mechanical unzipping: an ideal-case study

We introduce and test a method to predict the sequence of DNA molecules from in silico unzipping experiments. The method is based on Bayesian inference and on the Viterbi decoding algorithm. The probability of misprediction decreases exponentially with the number of unzippings, with a decay rate depending on the applied force and the sequence content.Comment: Source as TeX file with ps 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

Unzipping DNA with Optical Tweezers: High Sequence Sensitivity and Force Flips

AbstractForce measurements are performed on single DNA molecules with an optical trapping interferometer that combines subpiconewton force resolution and millisecond time resolution. A molecular construction is prepared for mechanically unzipping several thousand-basepair DNA sequences in an in vitro configuration. The force signals corresponding to opening and closing the double helix at low velocity are studied experimentally and are compared to calculations assuming thermal equilibrium. We address the effect of the stiffness on the basepair sensitivity and consider fluctuations in the force signal. With respect to earlier work performed with soft microneedles, we obtain a very significant increase in basepair sensitivity: presently, sequence features appearing at a scale of 10 basepairs are observed. When measured with the optical trap the unzipping force exhibits characteristic flips between different values at specific positions that are determined by the base sequence. This behavior is attributed to bistabilities in the position of the opening fork; the force flips directly reflect transitions between different states involved in the time-averaging of the molecular system

Electron-Phonon Interacation in Quantum Dots: A Solvable Model

The relaxation of electrons in quantum dots via phonon emission is hindered by the discrete nature of the dot levels (phonon bottleneck). In order to clarify the issue theoretically we consider a system of $N$ discrete fermionic states (dot levels) coupled to an unlimited number of bosonic modes with the same energy (dispersionless phonons). In analogy to the Gram-Schmidt orthogonalization procedure, we perform a unitary transformation into new bosonic modes. Since only $N(N+1)/2$ of them couple to the fermions, a numerically exact treatment is possible. The formalism is applied to a GaAs quantum dot with only two electronic levels. If close to resonance with the phonon energy, the electronic transition shows a splitting due to quantum mechanical level repulsion. This is driven mainly by one bosonic mode, whereas the other two provide further polaronic renormalizations. The numerically exact results for the electron spectral function compare favourably with an analytic solution based on degenerate perturbation theory in the basis of shifted oscillator states. In contrast, the widely used selfconsistent first-order Born approximation proves insufficient in describing the rich spectral features.Comment: 8 pages, 4 figure

Carrier relaxation in GaAs v-groove quantum wires and the effects of localization

Carrier relaxation processes have been investigated in GaAs/AlGaAs v-groove quantum wires (QWRs) with a large subband separation (46 meV). Signatures of inhibited carrier relaxation mechanisms are seen in temperature-dependent photoluminescence (PL) and photoluminescence-excitation (PLE) measurements; we observe strong emission from the first excited state of the QWR below ~50 K. This is attributed to reduced inter-subband relaxation via phonon scattering between localized states. Theoretical calculations and experimental results indicate that the pinch-off regions, which provide additional two-dimensional confinement for the QWR structure, have a blocking effect on relaxation mechanisms for certain structures within the v-groove. Time-resolved PL measurements show that efficient carrier relaxation from excited QWR states into the ground state, occurs only at temperatures > 30 K. Values for the low temperature radiative lifetimes of the ground- and first excited-state excitons have been obtained (340 ps and 160 ps respectively), and their corresponding localization lengths along the wire estimated.Comment: 9 pages, 8 figures, submitted to Phys. Rev. B Attempted to correct corrupt figure

Multiband theory of multi-exciton complexes in self-assembled quantum dots

We report on a multiband microscopic theory of many-exciton complexes in self-assembled quantum dots. The single particle states are obtained by three methods: single-band effective-mass approximation, the multiband $k\cdot p$ method, and the tight-binding method. The electronic structure calculations are coupled with strain calculations via Bir-Pikus Hamiltonian. The many-body wave functions of $N$ electrons and $N$ valence holes are expanded in the basis of Slater determinants. The Coulomb matrix elements are evaluated using statically screened interaction for the three different sets of single particle states and the correlated $N$-exciton states are obtained by the configuration interaction method. The theory is applied to the excitonic recombination spectrum in InAs/GaAs self-assembled quantum dots. The results of the single-band effective-mass approximation are successfully compared with those obtained by using the of $k\cdot p$ and tight-binding methods.Comment: 10 pages, 8 figure

Transient current spectroscopy of a quantum dot in the Coulomb blockade regime

Transient current spectroscopy is proposed and demonstrated in order to investigate the energy relaxation inside a quantum dot in the Coulomb blockade regime. We employ a fast pulse signal to excite an AlGaAs/GaAs quantum dot to an excited state, and analyze the non-equilibrium transient current as a function of the pulse length. The amplitude and time-constant of the transient current are sensitive to the ground and excited spin states. We find that the spin relaxation time is longer than, at least, a few microsecond.Comment: 5 pages, 3 figure