Finite-temperature simulations of the scissors mode in Bose-Einstein condensed gases

The dynamics of a trapped Bose-condensed gas at finite temperatures is described by a generalized Gross-Pitaevskii equation for the condensate order parameter and a semi-classical kinetic equation for the thermal cloud, solved using $N$-body simulations. The two components are coupled by mean fields as well as collisional processes that transfer atoms between the two. We use this scheme to investigate scissors modes in anisotropic traps as a function of temperature. Frequency shifts and damping rates of the condensate mode are extracted, and are found to be in good agreement with recent experiments.Comment: 4 pages, 3 figure

Detection of circulating tumour DNA is associated with inferior outcomes in Ewing sarcoma and osteosarcoma: a report from the Children's Oncology Group.

BackgroundNew prognostic markers are needed to identify patients with Ewing sarcoma (EWS) and osteosarcoma unlikely to benefit from standard therapy. We describe the incidence and association with outcome of circulating tumour DNA (ctDNA) using next-generation sequencing (NGS) assays.MethodsA NGS hybrid capture assay and an ultra-low-pass whole-genome sequencing assay were used to detect ctDNA in banked plasma from patients with EWS and osteosarcoma, respectively. Patients were coded as positive or negative for ctDNA and tested for association with clinical features and outcome.ResultsThe analytic cohort included 94 patients with EWS (82% from initial diagnosis) and 72 patients with primary localised osteosarcoma (100% from initial diagnosis). ctDNA was detectable in 53% and 57% of newly diagnosed patients with EWS and osteosarcoma, respectively. Among patients with newly diagnosed localised EWS, detectable ctDNA was associated with inferior 3-year event-free survival (48.6% vs. 82.1%; p = 0.006) and overall survival (79.8% vs. 92.6%; p = 0.01). In both EWS and osteosarcoma, risk of event and death increased with ctDNA levels.ConclusionsNGS assays agnostic of primary tumour sequencing results detect ctDNA in half of the plasma samples from patients with newly diagnosed EWS and osteosarcoma. Detectable ctDNA is associated with inferior outcomes

Finite temperature hydrodynamic modes of trapped quantum gases

The hydrodynamic equations of an ideal fluid formed by a dilute quantum gas in a parabolic trapping potential are studied analytically and numerically. Due to the appearance of internal modes in the fluid stratified by the trapping potential, the spectrum of low-lying modes is found to be dense in the high-temperature limit, with an infinitely degenerate set of zero-frequency modes. The spectrum for Bose-fluids and Fermi-fluids is obtained and discussed.Comment: 26 pages, Late

Quantum Kinetic Theory of BEC Lattice Gas:Boltzmann Equations from 2PI-CTP Effective Action

We continue our earlier work [Ana Maria Rey, B. L. Hu, Esteban Calzetta, Albert Roura and Charles W. Clark, Phys. Rev. A 69, 033610 (2004)] on the nonequilibrium dynamics of a Bose Einstein condensate (BEC) selectively loaded into every third site of a one-dimensional optical lattice. From the two-particle irreducible (2PI) closed-time-path (CTP) effective action for the Bose- Hubbard Hamiltonian, we show how to obtain the Kadanoff-Baym equations of quantum kinetic theory. Using the quasiparticle approximation, we show that the local equilibrium solutions of these equations reproduce the second- order corrections to the self-energy originally derived by Beliaev. This work paves the way for the use of effective action methods in the derivation of quantum kinetic theory of many atom systems.Comment: 21 pages, 0 figures, minor editorial changes were mad

Quantum dynamics and thermalization for out-of-equilibrium phi^4-theory

The quantum time evolution of \phi^4-field theory for a spatially homogeneous system in 2+1 space-time dimensions is investigated numerically for out-of-equilibrium initial conditions on the basis of the Kadanoff-Baym equations including the tadpole and sunset self-energies. Whereas the tadpole self-energy yields a dynamical mass, the sunset self-energy is responsible for dissipation and an equilibration of the system. In particular we address the dynamics of the spectral (`off-shell') distributions of the excited quantum modes and the different phases in the approach to equilibrium described by Kubo-Martin-Schwinger relations for thermal equilibrium states. The investigation explicitly demonstrates that the only translation invariant solutions representing the stationary fixed points of the coupled equation of motions are those of full thermal equilibrium. They agree with those extracted from the time integration of the Kadanoff-Baym equations in the long time limit. Furthermore, a detailed comparison of the full quantum dynamics to more approximate and simple schemes like that of a standard kinetic (on-shell) Boltzmann equation is performed. Our analysis shows that the consistent inclusion of the dynamical spectral function has a significant impact on relaxation phenomena. The different time scales, that are involved in the dynamical quantum evolution towards a complete thermalized state, are discussed in detail. We find that far off-shell 1 3 processes are responsible for chemical equilibration, which is missed in the Boltzmann limit. Finally, we address briefly the case of (bare) massless fields. For sufficiently large couplings $\lambda$ we observe the onset of Bose condensation, where our scheme within symmetric \phi^4-theory breaks down.Comment: 77 pages, 26 figure

Finite Temperature Models of Bose-Einstein Condensation

The theoretical description of trapped weakly-interacting Bose-Einstein condensates is characterized by a large number of seemingly very different approaches which have been developed over the course of time by researchers with very distinct backgrounds. Newcomers to this field, experimentalists and young researchers all face a considerable challenge in navigating through the `maze' of abundant theoretical models, and simple correspondences between existing approaches are not always very transparent. This Tutorial provides a generic introduction to such theories, in an attempt to single out common features and deficiencies of certain `classes of approaches' identified by their physical content, rather than their particular mathematical implementation. This Tutorial is structured in a manner accessible to a non-specialist with a good working knowledge of quantum mechanics. Although some familiarity with concepts of quantum field theory would be an advantage, key notions such as the occupation number representation of second quantization are nonetheless briefly reviewed. Following a general introduction, the complexity of models is gradually built up, starting from the basic zero-temperature formalism of the Gross-Pitaevskii equation. This structure enables readers to probe different levels of theoretical developments (mean-field, number-conserving and stochastic) according to their particular needs. In addition to its `training element', we hope that this Tutorial will prove useful to active researchers in this field, both in terms of the correspondences made between different theoretical models, and as a source of reference for existing and developing finite-temperature theoretical models.Comment: Detailed Review Article on finite temperature theoretical techniques for studying weakly-interacting atomic Bose-Einstein condensates written at an elementary level suitable for non-experts in this area (e.g. starting PhD students). Now includes table of content

Characterizing RecA-Independent Induction of Shiga toxin2-Encoding Phages by EDTA Treatment

Background: The bacteriophage life cycle has an important role in Shiga toxin (Stx) expression. The induction of Shiga toxin-encoding phages (Stx phages) increases toxin production as a result of replication of the phage genome, and phage lysis of the host cell also provides a means of Stx toxin to exit the cell. Previous studies suggested that prophage induction might also occur in the absence of SOS response, independently of RecA. Methodology/Principal Findings: The influence of EDTA on RecA-independent Stx2 phage induction was assessed, in laboratory lysogens and in EHEC strains carrying Stx2 phages in their genome, by Real-Time PCR. RecA-independent mechanisms described for phage l induction (RcsA and DsrA) were not involved in Stx2 phage induction. In addition, mutations in the pathway for the stress response of the bacterial envelope to EDTA did not contribute to Stx2 phage induction. The effect of EDTA on Stx phage induction is due to its chelating properties, which was also confirmed by the use of citrate, another chelating agent. Our results indicate that EDTA affects Stx2 phage induction by disruption of the bacterial outer membrane due to chelation of Mg 2+. In all the conditions evaluated, the pH value had a decisive role in Stx2 phage induction. Conclusions/Significance: Chelating agents, such as EDTA and citrate, induce Stx phages, which raises concerns due to their frequent use in food and pharmaceutical products. This study contributes to our understanding of the phenomenon o

The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution

Exploiting evolutionary steering to induce collateral drug sensitivity in cancer

Drug resistance mediated by clonal evolution is arguably the biggest problem in cancer therapy today. However, evolving resistance to one drug may come at a cost of decreased fecundity or increased sensitivity to another drug. These evolutionary trade-offs can be exploited using 'evolutionary steering' to control the tumour population and delay resistance. However, recapitulating cancer evolutionary dynamics experimentally remains challenging. Here, we present an approach for evolutionary steering based on a combination of single-cell barcoding, large populations of 108-109 cells grown without re-plating, longitudinal non-destructive monitoring of cancer clones, and mathematical modelling of tumour evolution. We demonstrate evolutionary steering in a lung cancer model, showing that it shifts the clonal composition of the tumour in our favour, leading to collateral sensitivity and proliferative costs. Genomic profiling revealed some of the mechanisms that drive evolved sensitivity. This approach allows modelling evolutionary steering strategies that can potentially control treatment resistance