Quantum dynamics of the avian compass

The ability of migratory birds to orient relative to the Earth's magnetic field is believed to involve a coherent superposition of two spin states of a radical electron pair. However, the mechanism by which this coherence can be maintained in the face of strong interactions with the cellular environment has remained unclear. This Letter addresses the problem of decoherence between two electron spins due to hyperfine interaction with a bath of spin 1/2 nuclei. Dynamics of the radical pair density matrix are derived and shown to yield a simple mechanism for sensing magnetic field orientation. Rates of dephasing and decoherence are calculated ab initio and found to yield millisecond coherence times, consistent with behavioral experiments

Limits of the Plane Wave Approximation in the Measurement of Molecular Properties

Rescattering electrons offer great potential as probes of molecular properties on ultrafast timescales. The most famous example is molecular tomography, in which high harmonic spectra of oriented molecules are mapped to ``tomographic images'' of the relevant molecular orbitals. The accuracy of such reconstructions may be greatly affected by the distortion of scattering wavefunctions from their asymptotic forms due to interactions with the parent ion. We investigate the validity of the commonly used plane wave approximation in molecular tomography, showing how such distortions affect the resulting orbital reconstructions

High Harmonic Generation in SF6_{6}: Raman-excited Vibrational Quantum Beats

In a recent experiment (N. Wagner et al., PNAS v103, p13279) on SF$_{6}$, a high-harmonic generating laser pulse is preceded by a pump pulse which stimulates Raman-active modes in the molecule. Varying the time delay between the two pulses modulates high harmonic intensity, with frequencies equal to the vibration frequencies of the Raman-active modes. We propose an explanation of this modulation as a quantum interference between competing pathways that occur via adjacent vibrational states of the molecule. The Raman and high harmonic processes act as beamsplitters, producing vibrational quantum beats among the Raman-active vibrational modes that are excited by the first pulse. We introduce a rigorous treatment of the electron-ion recombination process and the effect of the ionic Coulomb field in the electron propagation outside the molecule, improving over the widely-used three-step model.Comment: submitted to PR

Vibrational interference of Raman and high-harmonic generation pathways

Experiments have shown that the internal vibrational state of a molecule can affect the intensity of high harmonic light generated from that molecule. This paper presents a model which explains this modulation in terms of interference between different vibrational states occurring during the high harmonic process. In addition, a semiclassical model of the continuum electron propagation is developed which connects with rigorous treatments of the electron-ion scattering

Interaction of intense vuv radiation with large xenon clusters

The interaction of atomic clusters with short, intense pulses of laser light to form extremely hot, dense plasmas has attracted extensive experimental and theoretical interest. The high density of atoms within the cluster greatly enhances the atom--laser interaction, while the finite size of the cluster prevents energy from escaping the interaction region. Recent technological advances have allowed experiments to probe the laser--cluster interaction at very high photon energies, with interactions much stronger than suggested by theories for lower photon energies. We present a model of the laser--cluster interaction which uses non-perturbative R-matrix techniques to calculate inverse bremsstrahlung and photoionization cross sections for Herman-Skillman atomic potentials. We describe the evolution of the cluster under the influence of the processes of inverse bremsstrahlung heating, photoionization, collisional ionization and recombination, and expansion of the cluster. We compare charge state distribution, charge state ejection energies, and total energy absorbed with the Hamburg experiment of Wabnitz {\em et al.} [Nature {\bf 420}, 482 (2002)] and ejected electron spectra with Laarmann {\em et al.} [Phys. Rev. Lett. {\bf 95}, 063402 (2005)]

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas