Tracking excited states in wave function optimization using density matrices and variational principles

We present a method for finding individual excited states' energy stationary points in complete active space self-consistent field theory that is compatible with standard optimization methods and highly effective at overcoming difficulties due to root flipping and near-degeneracies. Inspired by both the maximum overlap method and recent progress in excited state variational principles, our approach combines these ideas in order to track individual excited states throughout the orbital optimization process. In a series of tests involving root flipping, near-degeneracies, charge transfers, and double excitations, we show that this approach is more effective for state-specific optimization than either the naive selection of roots based on energy ordering or a more direct generalization of the maximum overlap method. Furthermore, we provide evidence that this state-specific approach improves the performance of complete active space perturbation theory. With a simple implementation, a low cost, and compatibility with large active space methods, the approach is designed to be useful in a wide range of excited state investigations.Comment: 13 pages, submitted to JCT

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing.

Sequencing technologies have undergone a paradigm shift from bulk to single-cell resolution in response to an evolving understanding of the role of cellular heterogeneity in biological systems. However, single-cell sequencing of large populations has been hampered by limitations in processing genomes for sequencing. In this paper, we describe a method for single-cell genome sequencing (SiC-seq) which uses droplet microfluidics to isolate, amplify, and barcode the genomes of single cells. Cell encapsulation in microgels allows the compartmentalized purification and tagmentation of DNA, while a microfluidic merger efficiently pairs each genome with a unique single-cell oligonucleotide barcode, allowing >50,000 single cells to be sequenced per run. The sequencing data is demultiplexed by barcode, generating groups of reads originating from single cells. As a high-throughput and low-bias method of single-cell sequencing, SiC-seq will enable a broader range of genomic studies targeted at diverse cell populations

Brassica genomics: a complement to, and early beneficiary of, the Arabidopsis sequence.

Those studying the genus Brassica will be among the early beneficiaries of the now-completed Arabidopsis sequence. The remarkable morphological diversity of Brassica species and their relatives offers valuable opportunities to advance our knowledge of plant growth and development, and our understanding of rapid phenotypic evolution

Phase slip in a superfluid Fermi gas near a Feshbach resonance

In this paper, we study the properties of a phase slip in a superfluid Fermi gas near a Feshbach resonance. The phase slip can be generated by the phase imprinting method. Below the superfluid transition temperature, it appears as a dip in the density profile, and becomes more pronounced when the temperature is lowered. Therefore the phase slip can provide a direct evidence of the superfluid state. The condensation energy of the superfluid state can be extracted from the density profile of the phase slip, due to the unitary properties of the Fermi gas near the resonance. The width of the phase slip is proportional to the square root of the difference between the transition temperature and the temperature. The signature of the phase slip in the density profile becomes more robust across the BCS-BEC crossover.Comment: 5 pages, 2 figures, the density profile of a phase slip under experimental conditions was calculate

AMPHIBIAN DISTRIBUTION IN THE GEORGIA SEA ISLANDS: IMPLICATIONS FROM THE PAST AND FOR THE FUTURE

We summarized amphibian distributions for 12 coastal islands in Georgia, USA. Occurrence among islands was correlated with life history traits, habitats, island size, distance to other islands, and island geological age. Species’ distributions were determined from published literature. Island sizes and vegetation types were derived from 2011 Georgia Department of Natural Resources habitat maps, which included both federal and state vegetation classification systems. Species occurring on more islands tended to have greater total reproductive output (i.e., life span >4 years, and annual egg production >1,000 eggs) and adults had tolerance of brackish environs. Larger islands had great­er area of freshwater wetlands, predominantly short hydroperiod (<6 months). Species tied to long hydroperiod wetlands (>6 months) were more restricted in their distribution across islands. Overall, larger islands supported more species, but the correlation was weaker for geologically younger Ho­locene islands (age <11,000 years). While Euclidean distance between islands does not necessarily preclude inter-island dispersal, inhospitable habitat for amphibians (brackish tidal marshes and creeks interspersed with wide rivers) suggests that inter-island dispersal is very limited. The paucity of recent occurrence data for amphibians in this dynamic coastal region, let alone standardized annual moni­toring data, hinders efforts to model species’ vulnerability in a region susceptible to sea level rise and development pressure. The most common survey method, standardized amphibian vocal surveys, will detect Anuran reproductive efforts, but is unlikely to ascertain if breeding was successful or to detect salamanders. While it will not replace actual population data, consideration of critical life-history traits and breeding habitat availability can be used to direct management to support long-term species per­sistence in changing environs. Even common amphibians in coastal conservation areas of Georgia are vulnerable to increasing population isolation caused by unsuitable habitat

Intrinsic Cavity QED and Emergent Quasi-Normal Modes for Single Photon

We propose a special cavity design that is constructed by terminating a one-dimensional waveguide with a perfect mirror at one end and doping a two-level atom at the other. We show that this atom plays the intrinsic role of a semi-transparent mirror for single photon transports such that quasi-normal modes (QNM's) emerge spontaneously in the cavity system. This atomic mirror has its reflection coefficient tunable through its level spacing and its coupling to the cavity field, for which the cavity system can be regarded as a two-end resonator with a continuously tunable leakage. The overall investigation predicts the existence of quasi-bound states in the waveguide continuum. Solid state implementations based on a dc-SQUID circuit and a defected line resonator embedded in a photonic crystal are illustrated to show the experimental accessibility of the generic model.Comment: 4 pages,5 figures, Comments welcom

Meissner response of a bulk superconductor with an embedded sheet of reduced penetration depth

We calculate the change in susceptibility resulting from a thin sheet with reduced penetration depth embedded perpendicular to the surface of an isotropic superconductor, in a geometry applicable to scanning Superconducting QUantum Interference Device (SQUID) microscopy, by numerically solving Maxwell's and London's equations using the finite element method. The predicted stripes in susceptibility agree well in shape with the observations of Kalisky et al. of enhanced susceptibility above twin planes in the underdoped pnictide superconductor Ba(Fe1-xCox)2As2 (Ba-122). By comparing the predicted stripe amplitudes with experiment and using the London relation between penetration depth and superfluid density, we estimate the enhanced Cooper pair density on the twin planes, and the barrier force for a vortex to cross a twin plane. Fits to the observed temperature dependence of the stripe amplitude suggest that the twin planes have a higher critical temperature than the bulk, although stripes are not observed above the bulk critical temperature.Comment: 16 pages, 9 figure