Use of high throughput sequencing to observe genome dynamics at a single cell level

With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions. Here, we sequenced several genomes of Escherichia coli from colonies obtained after chemical mutagenesis and observed a strikingly nonrandom distribution of the induced mutations. These include long stretches of exclusively G to A or C to T transitions along the genome and orders of magnitude intra- and inter-genomic differences in mutation density. Whereas most of these observations can be explained by the known features of enzymatic processes, the others could reflect stochasticity in the molecular processes at the single-cell level. Our results demonstrate how analysis of the molecular records left in the genomes of the descendants of an individual mutagenized cell allows for genome-scale observations of fixation and segregation of mutations, as well as recombination events, in the single genome of their progenitor.Comment: 22 pages, 9 figures (including 5 supplementary), one tabl

Soft X-ray seeding studies for the SLAC Linac Coherent Light Source II

We present the results from studies of soft X-ray seeding options for the LCLS-II X-ray free electron laser (FEL) at SLAC. The LCLS-II will use superconducting accelerator technology to produce X-ray pulses at up to 1 MHz repetition rate using 4 GeV electron beams. If properly seeded, these pulses will be nearly fully coherent, and highly stable in photon energy, bandwidth, and intensity, thus enabling unique experiments with intense high-resolution soft X-rays. Given the expected electron beam parameters from start to end simulations and predicted FEL performance, our studies reveal echo enabled harmonic generation (EEHG) and soft X-ray self-seeding (SXRSS) as promising and complementary seeding methods. We find that SXRSS has the advantage of simplicity and will deliver 5-35 times higher spectral brightness than EEHG in the 1-2 nm range, but lacks some of the potential for phase-stable multipulse and multicolor FEL operations enabled by external laser seeding with EEHG

Measuring photon anti-bunching from continuous variable sideband squeezing

We present a technique for measuring the second-order coherence function $g^{(2)}(\tau)$ of light using a Hanbury-Brown Twiss intensity interferometer modified for homodyne detection. The experiment was performed entirely in the continuous variable regime at the sideband frequency of a bright carrier field. We used the setup to characterize $g^{(2)}(\tau)$ for thermal and coherent states, and investigated its immunity to optical loss. We measured $g^{(2)}(\tau)$ of a displaced squeezed state, and found a best anti-bunching statistic of $g^{(2)}(0) = 0.11 \pm 0.18$.Comment: 4 pages, 4 figure

Quantum Noise Correlation Experiments with Ultracold Atoms

Noise correlation analysis is a detection tool for spatial structures and spatial correlations in the in-trap density distribution of ultracold atoms. In this book chapter, we discuss the implementation, properties and limitations of the method applied to ensembles of ultracold atoms in optical lattices, and describe some instances where it has been applied.Comment: 26 pages, 14 figures - To appear as Chapter 8 in "Quantum gas experiments - exploring many-body states," P. T\"orm\"a, K. Sengstock, eds. (Imperial College Press, to be published 2014

Bunches of misfit dislocations on the onset of relaxation of Si0.4_{0.4}Ge0.6_{0.6}/Si(001) epitaxial films revealed by high-resolution x-ray diffraction

The experimental x-ray diffraction patterns of a Si$_{0.4}$Ge$_{0.6}$/Si(001) epitaxial film with a low density of misfit dislocations are modeled by the Monte Carlo method. It is shown that an inhomogeneous distribution of 60$^\circ$ dislocations with dislocations arranged in bunches is needed to explain the experiment correctly. As a result of the dislocation bunching, the positions of the x-ray diffraction peaks do not correspond to the average dislocation density but reveal less than a half of the actual relaxation

Blue-Light-Emitting Color Centers in High-Quality Hexagonal Boron Nitride

Light emitters in wide band gap semiconductors are of great fundamental interest and have potential as optically addressable qubits. Here we describe the discovery of a new color center in high-quality hexagonal boron nitride (h-BN) with a sharp emission line at 435 nm. The emitters are activated and deactivated by electron beam irradiation and have spectral and temporal characteristics consistent with atomic color centers weakly coupled to lattice vibrations. The emitters are conspicuously absent from commercially available h-BN and are only present in ultra-high-quality h-BN grown using a high-pressure, high-temperature Ba-B-N flux/solvent, suggesting that these emitters originate from impurities or related defects specific to this unique synthetic route. Our results imply that the light emission is activated and deactivated by electron beam manipulation of the charge state of an impurity-defect complex

Efficient Stark deceleration of cold polar molecules

Stark deceleration has been utilized for slowing and trapping several species of neutral, ground-state polar molecules generated in a supersonic beam expansion. Due to the finite physical dimension of the electrode array and practical limitations of the applicable electric fields, only molecules within a specific range of velocities and positions can be efficiently slowed and trapped. These constraints result in a restricted phase space acceptance of the decelerator in directions both transverse and parallel to the molecular beam axis; hence, careful modeling is required for understanding and achieving efficient Stark decelerator operation. We present work on slowing of the hydroxyl radical (OH) elucidating the physics controlling the evolution of the molecular phase space packets both with experimental results and model calculations. From these results we deduce experimental conditions necessary for efficient operation of a Stark decelerator.Comment: 8 pages, 9 figure

Strongly Correlated Two-Photon Transport in One-Dimensional Waveguide Coupled to A Two-Level System

We show that two-photon transport is strongly correlated in one-dimensional waveguide coupled to a two-level system. The exact S-matrix is constructed using a generalized Bethe-Ansatz technique. We show that the scattering eigenstates of this system include a two-photon bound state that passes through the two-level system as a composite single particle. Also, the two-level system can induce effective attractive or repulsive interactions in space for photons. This general procedure can be applied to the Anderson model as well.Comment: 12 pages. 3 figures. Accepted by Physical Review Letter