National Center for Genome Analysis Program Year 2 Report – September 15, 2012 – September 14, 2013

On September 15, 2011, Indiana University (IU) received three years of support to establish the National Center for Genome Analysis Support (NCGAS). This technical report describes the activities of the second 12 months of NCGASThe facilities supported by the Research Technologies division at Indiana University are supported by a number of grants. The authors would like to acknowledge that although the National Center for Genome Analysis Support is funded by NSF 1062432, our work would not be possible without the generous support of the following awards received by our parent organization, the Pervasive Technology Institute at Indiana University. • The Indiana University Pervasive Technology Institute was supported in part by two grants from the Lilly Endowment, Inc. • NCGAS has also been supported directly by the Indiana METACyt Initiative. The Indiana METACyt Initiative of Indiana University is supported in part by the Lilly Endowment, Inc. • This material is based in part upon work supported by the National Science Foundation under Grant No. CNS-0521433. Any opinions, findings and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation (NSF)

Noncovariant gauge fixing in the quantum Dirac field theory of atoms and molecules

Starting from the Weyl gauge formulation of quantum electrodynamics (QED), the formalism of quantum-mechanical gauge fixing is extended using techniques from nonrelativistic QED. This involves expressing the redundant gauge degrees of freedom through an arbitrary functional of the gauge-invariant transverse degrees of freedom. Particular choices of functional can be made to yield the Coulomb gauge and Poincar\'{e} gauge representations. The Hamiltonian we derive therefore serves as a good starting point for the description of atoms and molecules by means of a relativistic Dirac field. We discuss important implications for the ontology of noncovariant canonical QED due to the gauge freedom that remains present in our formulation.Comment: 8 pages, 0 figure

Influence of the state of light on the optically induced interparticle interaction

A general expression for the energy of interparticle interaction induced by an arbitrary mode of light is determined using quantum electrodynamics, and it is shown that the Casimir-Polder potential is included within this quantum result. Equations are also derived for the corresponding coupling induced by multimode number states of light, and the dependence of the pair energy on the Poynting vector and polarization state is determined. Attention is then focused on the interactions between particles trapped in counterpropagating coherent beams, both with and without interference, and it is shown that the results afford insights into the multiparticle structures that can be optically fabricated with counterpropagating input. Brief consideration is also given to the effect of squeezing the optical coherent state. Extending previous studies of optical binding in Laguerre-Gaussian beams, results are given for the case of particles trapped at radially different locations within the beam structure. Finally, consideration is given to interparticle interactions induced by broadband light, and it is shown how the length of optically fabricated particle chains can be controlled by the use of wavelength filters

Enhanced optical activity using the orbital angular momentum of structured light

Recent molecular photonics studies have highlighted the significant role that phase-structured light possessing orbital angular momentum (OAM) can have when interacting with matter. These studies discovered chiroptical effects sensitive to both the magnitude and sign of the optical OAM in both the absorption and scattering of twisted photons by molecules and nanoparticles. Specifically, it has been shown how a structured beam engaging with electric-quadrupole transitions in the material allows a unique sensitivity to the helical-phase structure of twisted light. In this paper we highlight experimental methodologies and systems suitable to observe and quantify the chiroptical processes of Rayleigh and Raman optical activity, and the newly discovered circular-vortex differential scattering effect with structured light—including the importance of off-axis beam alignment, input beam intensity structure, multipolar moments, and scattering-angle dependencies. It is shown that with a judicious choice of experimental setup, chiroptical effects that scale with the topological charge or OAM of the input beam enable optical activity signals to be enhanced and significantly exceed those based solely on circularly polarized, unstructured light. The new technique thus offers a highly useful and important spectroscopic application of structured light. The more detailed role that perfect optical vortices with high OAM will play in such optical activity effects is now highlighted, to show where there is substantial scope for experimental application, specifically in vibrational optical activity and chiral spectroscopy

Optical Thomas-Reiche-Kuhn sum rules

The Thomas-Reiche-Kuhn sum rule is a fundamental consequence of the position-momentum commutation relation for an atomic electron and it provides an important constraint on the transition matrix elements for an atom. Analogously, the commutation relations for the electromagnetic field operators in a magnetodielectric medium constrain the properties of the dispersion relations for the medium through four sum rules for the allowed phase and group velocities for polaritons propagating through the medium. These rules apply to all bulk media including the metamaterials designed to provide negative refractive indices. An immediate consequence of this is that it is not possible to construct a medium in which all the polariton modes for a given wavelength lie in the negative-index region

Spontaneous decay of an excited atom in an absorbing dielectric

Starting from the quantized version of Maxwell's equations for the electromagnetic field in an arbitrary linear Kramers-Kronig dielectric, spontaneous decay of the excited state of a two-level atom embedded in a dispersive and absorbing medium is studied and the decay rate is calculated. The calculations are performed for both the (Clausius-Mosotti) virtual cavity model and the (Glauber-Lewenstein) real cavity model. It is shown that owing to nonradiative decay associated with absorption the rate of spontaneous decay sensitively depends on the cavity radius when the atomic transition frequency approaches an absorption band of the medium. Only when the effect of absorption is fully disregarded, then the familiar local-field correction factors are recovered.Comment: 28 pages, 6 figures, typeset using RevTe

Raman Optical Activity Using Twisted Photons

Raman optical activity underpins a powerful vibrational spectroscopic technique for obtaining detailed structural information about chiral molecular species. The effect centers on the discriminatory interplay between the handedness of material chirality with that of circularly polarized light. Twisted light possessing an optical orbital angular momentum carries helical phase fronts that screw either clockwise or anticlockwise and, thus, possess a handedness that is completely distinct from the polarization. Here a novel form of Raman optical activity that is sensitive to the handedness of the incident twisted photons through a spin-orbit interaction of light is identified, representing a new chiroptical spectroscopic technique

Pseudovector components of the pion, pi^0 -> gamma gamma, and F_pi(q^2)

As a consequence of dynamical chiral symmetry breaking the pion Bethe-Salpeter amplitude necessarily contains terms proportional to gamma_5 gamma.P and gamma_5 gamma.k, where k is the relative and P the total momentum of the constituents. These terms are essential for the preservation of low energy theorems, such as the Gell-Mann--Oakes-Renner relation and those describing anomalous decays of the pion, and to obtaining an electromagnetic pion form factor that falls as 1/q^2 for large q^2, up to calculable ln(q^2)-corrections. In a simple model, which correlates low- and high-energy pion observables, we find q^2 F_pi(q^2) ~ 0.12 - 0.19 GeV^2 for q^2 >~10 GeV^2.Comment: 15 pages, 2 figures, REVTE

Depletion of a Bose-Einstein condensate by laser-iduced dipole-dipole interactions

We study a gaseous Bose-Einstein condensate with laser-induced dipole-dipole interactions using the Hartree-Fock-Bogoliubov theory within the Popov approximation. The dipolar interactions introduce long-range atom-atom correlations, which manifest themselves as increased depletion at momenta similar to that of the laser wavelength, as well as a "roton" dip in the excitation spectrum. Surprisingly, the roton dip and the corresponding peak in the depletion are enhanced by raising the temperature above absolute zero.Comment: 10 pages, 6 figure

Theory of radiation pressure on magneto–dielectric materials

We present a classical linear response theory for a magneto–dielectric material and determine the polariton dispersion relations. The electromagnetic field fluctuation spectra are obtained and polariton sum rules for their optical parameters are presented. The electromagnetic field for systems with multiple polariton branches is quantized in three dimensions and field operators are converted to 1–dimensional forms appropriate for parallel light beams. We show that the field–operator commutation relations agree with previous calculations that ignored polariton effects. The Abraham (kinetic) and Minkowski (canonical) momentum operators are introduced and their corresponding single–photon momenta are identified. The commutation relations of these and of their angular analogues support the identification, in particular, of the Minkowski momentum with the canonical momentum of the light. We exploit the Heaviside–Larmor symmetry of Maxwell's equations to obtain, very directly, the Einsetin–Laub force density for action on a magneto–dielectric. The surface and bulk contributions to the radiation pressure are calculated for the passage of an optical pulse into a semi–infinite sample