Snakes and ladders: localized solutions of plane Couette flow

We demonstrate the existence of a large number of exact solutions of plane Couette flow, which share the topology of known periodic solutions but are localized in space. Solutions of different size are organized in a snakes-and-ladders structure strikingly similar to that observed for simpler pattern-forming PDE systems. These new solutions are a step towards extending the dynamical systems view of transitional turbulence to spatially extended flows.Comment: submitted to Physics Review Letter

Synthetic Gauge Fields for Vibrational Excitations of Trapped ions

The vibrations of a collection of ions in a microtrap array can be described in terms of hopping phonons. We show theoretically that the vibrational couplings may be tailored by using a gradient of the microtrap frequencies, together with a periodic driving of the trapping potential. These ingredients allow us to induce effective gauge fields on the vibrational excitations, such that phonons mimic the behavior of charged particles in a magnetic field. In particular, microtrap arrays are ideally suited to realize the famous Aharonov-Bohm effect, and observe the paradigmatic edge states typical from quantum-Hall samples and topological insulators.Comment: replaced with published versio

Bacteriophage and their potential roles in the human oral cavity.

The human oral cavity provides the perfect portal of entry for viruses and bacteria in the environment to access new hosts. Hence, the oral cavity is one of the most densely populated habitats of the human body containing some 6 billion bacteria and potentially 35 times that many viruses. The role of these viral communities remains unclear; however, many are bacteriophage that may have active roles in shaping the ecology of oral bacterial communities. Other implications for the presence of such vast oral phage communities include accelerating the molecular diversity of their bacterial hosts as both host and phage mutate to gain evolutionary advantages. Additional roles include the acquisitions of new gene functions through lysogenic conversions that may provide selective advantages to host bacteria in response to antibiotics or other types of disturbances, and protection of the human host from invading pathogens by binding to and preventing pathogens from crossing oral mucosal barriers. Recent evidence suggests that phage may be more involved in periodontal diseases than were previously thought, as their compositions in the subgingival crevice in moderate to severe periodontitis are known to be significantly altered. However, it is unclear to what extent they contribute to dysbiosis or the transition of the microbial community into a state promoting oral disease. Bacteriophage communities are distinct in saliva compared to sub- and supragingival areas, suggesting that different oral biogeographic niches have unique phage ecology shaping their bacterial biota. In this review, we summarize what is known about phage communities in the oral cavity, the possible contributions of phage in shaping oral bacterial ecology, and the risks to public health oral phage may pose through their potential to spread antibiotic resistance gene functions to close contacts

Coexistence in a One-Dimensional Cyclic Dominance Process

Cyclic (rock-paper-scissors-type) population models serve to mimic complex species interactions. Focusing on a paradigmatic three-species model with mutations in one dimension, we observe an interplay between equilibrium and non-equilibrium processes in the stationary state. We exploit these insights to obtain asymptotically exact descriptions of the emerging reactive steady state in the regimes of high and low mutation rates. The results are compared to stochastic lattice simulations. Our methods and findings are potentially relevant for the spatio-temporal evolution of other non-equilibrium stochastic processes.Comment: 4 pages, 4 figures and 2 pages of Supplementary Material. To appear in Physical Review

Octave Spanning Frequency Comb on a Chip

Optical frequency combs have revolutionized the field of frequency metrology within the last decade and have become enabling tools for atomic clocks, gas sensing and astrophysical spectrometer calibration. The rapidly increasing number of applications has heightened interest in more compact comb generators. Optical microresonator based comb generators bear promise in this regard. Critical to their future use as 'frequency markers', is however the absolute frequency stabilization of the optical comb spectrum. A powerful technique for this stabilization is self-referencing, which requires a spectrum that spans a full octave, i.e. a factor of two in frequency. In the case of mode locked lasers, overcoming the limited bandwidth has become possible only with the advent of photonic crystal fibres for supercontinuum generation. Here, we report for the first time the generation of an octave-spanning frequency comb directly from a toroidal microresonator on a silicon chip. The comb spectrum covers the wavelength range from 990 nm to 2170 nm and is retrieved from a continuous wave laser interacting with the modes of an ultra high Q microresonator, without relying on external broadening. Full tunability of the generated frequency comb over a bandwidth exceeding an entire free spectral range is demonstrated. This allows positioning of a frequency comb mode to any desired frequency within the comb bandwidth. The ability to derive octave spanning spectra from microresonator comb generators represents a key step towards achieving a radio-frequency to optical link on a chip, which could unify the fields of metrology with micro- and nano-photonics and enable entirely new devices that bring frequency metrology into a chip scale setting for compact applications such as space based optical clocks

An entropic approach to local realism and noncontextuality

For any Bell locality scenario (or Kochen-Specker noncontextuality scenario), the joint Shannon entropies of local (or noncontextual) models define a convex cone for which the non-trivial facets are tight entropic Bell (or contextuality) inequalities. In this paper we explore this entropic approach and derive tight entropic inequalities for various scenarios. One advantage of entropic inequalities is that they easily adapt to situations like bilocality scenarios, which have additional independence requirements that are non-linear on the level of probabilities, but linear on the level of entropies. Another advantage is that, despite the nonlinearity, taking detection inefficiencies into account turns out to be very simple. When joint measurements are conducted by a single detector only, the detector efficiency for witnessing quantum contextuality can be arbitrarily low.Comment: 12 pages, 8 figures, minor mistakes correcte

WHIRLAWAY--A THREE-DIMENSIONAL, TWO-GROUP NEUTRON DIFFUSION CODE FOR THE IBM 7090 COMPUTER

WHIRLAWAY is an IBM 7090 FORTRAN programmed code for the solution of two- group neutron diffusion equations in xyz geometry. The code was designed to run under control of the IBM 7090 FORTRAN Monitor System on a machine with at least six tape units. The maximum number of mesh points is limited to 12,750. Arbitrary distributions of materials and mesh spacing are permitted. The boundary conditions are either zero flux or zero current at each of the six faces of the reactor, and the code will, if desired, compute the adjoint-flux and associated flux-adjoint-flux region integrals that are necessary for perturbation calculations. Computation time is approximately 0.006 sec per point iteration. Normally, running times are about 2 to 3 hr for a 10,000-point problem. (auth

Temperature dependence of the energy dissipation in dynamic force microscopy

The dissipation of energy in dynamic force microscopy is usually described in terms of an adhesion hysteresis mechanism. This mechanism should become less efficient with increasing temperature. To verify this prediction we have measured topography and dissipation data with dynamic force microscopy in the temperature range from 100 K up to 300 K. We used 3,4,9,10-perylenetetracarboxylic-dianhydride (PTCDA) grown on KBr(001), both materials exhibiting a strong dissipation signal at large frequency shifts. At room temperature, the energy dissipated into the sample (or tip) is 1.9 eV/cycle for PTCDA and 2.7 eV/cycle for KBr, respectively, and is in good agreement with an adhesion hysteresis mechanism. The energy dissipation over the PTCDA surface decreases with increasing temperature yielding a negative temperature coefficient. For the KBr substrate, we find the opposite behaviour: an increase of dissipated energy with increasing temperature. While the negative temperature coefficient in case of PTCDA agrees rather well with the adhesion hysteresis model, the positive slope found for KBr points to a hitherto unknown dissipation mechanism

Transcriptome analysis of bacteriophage communities in periodontal health and disease.

BackgroundThe role of viruses as members of the human microbiome has gained broader attention with the discovery that human body surfaces are inhabited by sizeable viral communities. The majority of the viruses identified in these communities have been bacteriophages that predate upon cellular microbiota rather than the human host. Phages have the capacity to lyse their hosts or provide them with selective advantages through lysogenic conversion, which could help determine the structure of co-existing bacterial communities. Because conditions such as periodontitis are associated with altered bacterial biota, phage mediated perturbations of bacterial communities have been hypothesized to play a role in promoting periodontal disease. Oral phage communities also differ significantly between periodontal health and disease, but the gene expression of oral phage communities has not been previously examined.ResultsHere, we provide the first report of gene expression profiles from the oral bacteriophage community using RNA sequencing, and find that oral phages are more highly expressed in subjects with relative periodontal health. While lysins were highly expressed, the high proportion of integrases expressed suggests that prophages may account for a considerable proportion of oral phage gene expression. Many of the transcriptome reads matched phages found in the oral cavities of the subjects studied, indicating that phages may account for a substantial proportion of oral gene expression. Reads homologous to siphoviruses that infect Firmicutes were amongst the most prevalent transcriptome reads identified in both periodontal health and disease. Some genes from the phage lytic module were significantly more highly expressed in subjects with periodontal disease, suggesting that periodontitis may favor the expression of some lytic phages.ConclusionsAs we explore the contributions of viruses to the human microbiome, the data presented here suggest varying expression of bacteriophage communities in oral health and disease

Age-Related Gene Expression Differences in Monocytes from Human Neonates, Young Adults, and Older Adults.

A variety of age-related differences in the innate and adaptive immune systems have been proposed to contribute to the increased susceptibility to infection of human neonates and older adults. The emergence of RNA sequencing (RNA-seq) provides an opportunity to obtain an unbiased, comprehensive, and quantitative view of gene expression differences in defined cell types from different age groups. An examination of ex vivo human monocyte responses to lipopolysaccharide stimulation or Listeria monocytogenes infection by RNA-seq revealed extensive similarities between neonates, young adults, and older adults, with an unexpectedly small number of genes exhibiting statistically significant age-dependent differences. By examining the differentially induced genes in the context of transcription factor binding motifs and RNA-seq data sets from mutant mouse strains, a previously described deficiency in interferon response factor-3 activity could be implicated in most of the differences between newborns and young adults. Contrary to these observations, older adults exhibited elevated expression of inflammatory genes at baseline, yet the responses following stimulation correlated more closely with those observed in younger adults. Notably, major differences in the expression of constitutively expressed genes were not observed, suggesting that the age-related differences are driven by environmental influences rather than cell-autonomous differences in monocyte development