Absorption of hybrid fibre modes by Cs atoms in quadrupole transitions

We evaluate the rate of the absorption of an optical nanofibre mode by a Cs atom in an electric quadrupole transition. With the Cs atom localised near the outer surface of the optical nano-fibre, an interaction occurs between the atomic quadrupole tensor components and the gradients of the vector components of the electric field of a hybrid fibre mode. The absorption rate is evaluated as a function of the radial position of the atom from the fibre axis, assuming a specific value of the laser power and we use experimentally accessible parameters. We find that the absorption of the hybrid modes by the Cs atom decreases as the atom recedes away from the fibre axis and it formally vanishes at sufficiently large radial distances. Close to the fibre, however, the absorption rate for the input power chosen can be two orders of magnitude larger than the quadrupole de-excitation rate despite the moderate power used

Entanglement transfer between bipartite systems

The problem of a controlled transfer of an entanglement initially encoded into two two-level atoms that are successively sent through two single-mode cavities is investigated. The atoms and the cavity modes form a four qubit system and we demonstrate under which conditions the initial entanglement encoded into the atoms can be completely transferred to other pairs of qubits. We find that in the case of a nonzero detuning between the atomic transition frequencies and the cavity mode frequencies, no complete transfer of the initial entanglement is possible to any of the other pairs of qubits. In the case of exact resonance and equal coupling strengths of the atoms to the cavity modes, an initial maximally entangled state of the atoms can be completely transferred to the cavity modes. The complete transfer of the entanglement is restricted to the cavity modes only with the transfer to the other pairs being limited to up to 50%. We have found that the complete transfer of an initial entanglement to other pairs of qubits may take place if the initial state is not the maximally entangled state and the atoms couple to the cavity modes with unequal strengths. Depending on the ratio between the coupling strengths, the optimal entanglement can be created between the atoms and one of the cavity modes.Comment: 3 figures. Oral talk presented in CEWQO 18, Madrid 201

Qualitative aspects of the entanglement in the three-level model with photonic crystals

This communication is an enquiry into the circumstances under which concurrence and phase entropy methods can give an answer to the question of quantum entanglement in the composite state when the photonic band gap is exhibited by the presence of photonic crystals in a three-level system. An analytic approach is proposed for any three-level system in the presence of photonic band gap. Using this analytic solution, we conclusively calculate the concurrence and phase entropy, focusing particularly on the entanglement phenomena. Specifically, we use concurrence as a measure of entanglement for dipole emitters situated in the thin slab region between two semi-infinite one-dimensionally periodic photonic crystals, a situation reminiscent of planar cavity laser structures. One feature of the regime considered here is that closed-form evaluation of the time evolution may be carried out in the presence of the detuning and the photonic band gap, which provides insight into the difference in the nature of the concurrence function for atom-field coupling, mode frequency and different cavity parameters. We demonstrate how fluctuations in the phase and number entropies effected by the presence of the photonic-band-gap. The outcomes are illustrated with numerical simulations applied to GaAs. Finally, we relate the obtained results to instances of any three-level system for which the entanglement cost can be calculated. Potential experimental observations in solid-state systems are discussed and found to be promising.Comment: 28 pages, 10 figures: Accepted in Applied Physics B: Laser and Optic

Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs)

© 2019, The Author(s). Recent advancements in the use of microbial cells for scalable production of industrial enzymes encourage exploring new environments for efficient microbial cell factories (MCFs). Here, through a comparison study, ten newly sequenced Bacillus species, isolated from the Rabigh Harbor Lagoon on the Red Sea shoreline, were evaluated for their potential use as MCFs. Phylogenetic analysis of 40 representative genomes with phylogenetic relevance, including the ten Red Sea species, showed that the Red Sea species come from several colonization events and are not the result of a single colonization followed by speciation. Moreover, clustering reactions in reconstruct metabolic networks of these Bacillus species revealed that three metabolic clades do not fit the phylogenetic tree, a sign of convergent evolution of the metabolism of these species in response to special environmental adaptation. We further showed Red Sea strains Bacillus paralicheniformis (Bac48) and B. halosaccharovorans (Bac94) had twice as much secreted proteins than the model strain B. subtilis 168. Also, Bac94 was enriched with genes associated with the Tat and Sec protein secretion system and Bac48 has a hybrid PKS/NRPS cluster that is part of a horizontally transferred genomic region. These properties collectively hint towards the potential use of Red Sea Bacillus as efficient protein secreting microbial hosts, and that this characteristic of these strains may be a consequence of the unique ecological features of the isolation environment

Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle.

Despite half a century of research, the biology of dinoflagellates remains enigmatic: they defy many functional and genetic traits attributed to typical eukaryotic cells. Genomic approaches to study dinoflagellates are often stymied due to their large, multi-gigabase genomes. Members of the genus Symbiodinium are photosynthetic endosymbionts of stony corals that provide the foundation of coral reef ecosystems. Their smaller genome sizes provide an opportunity to interrogate evolution and functionality of dinoflagellate genomes and endosymbiosis. We sequenced the genome of the ancestral Symbiodinium microadriaticum and compared it to the genomes of the more derived Symbiodinium minutum and Symbiodinium kawagutii and eukaryote model systems as well as transcriptomes from other dinoflagellates. Comparative analyses of genome and transcriptome protein sets show that all dinoflagellates, not only Symbiodinium, possess significantly more transmembrane transporters involved in the exchange of amino acids, lipids, and glycerol than other eukaryotes. Importantly, we find that only Symbiodinium harbor an extensive transporter repertoire associated with the provisioning of carbon and nitrogen. Analyses of these transporters show species-specific expansions, which provides a genomic basis to explain differential compatibilities to an array of hosts and environments, and highlights the putative importance of gene duplications as an evolutionary mechanism in dinoflagellates and Symbiodinium

Multiphoton Bloch-Siegert shifts and level-splittings in a three-level system

In previous work we studied the spin-boson model in the multiphoton regime, using a rotation that provides a separation between terms that contribute most of the level energies away from resonance, and terms responsible for the level splittings at the anticrossing. Here, we consider a generalization of the spin-boson model consisting of a three-level system coupled to an oscillator. We construct a similar rotation and apply it to the more complicated model. We find that the rotation provides a useful approximation to the energy levels in the multiphoton region of the new problem. We find that good results can be obtained for the level splittings at the anticrossings for resonances involving the lower two levels in regions away from accidental or low-order resonances of the upper two levels.Comment: 29 pages, 13 figure

Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces

<p>Abstract</p> <p>Background</p> <p>Empirical binding models have previously been investigated for the energetics of protein complexation (ΔG models) and for the influence of mutations on complexation (i.e. differences between wild-type and mutant complexes, ΔΔG models). We construct binding models to directly compare these processes, which have generally been studied separately.</p> <p>Results</p> <p>Although reasonable fit models were found for both ΔG and ΔΔG cases, they differ substantially. In a dataset curated for the absence of mainchain rearrangement upon binding, non-polar area burial is a major determinant of ΔG models. However this ΔG model does not fit well to the data for binding differences upon mutation. Burial of non-polar area is weighted down in fitting of ΔΔG models. These calculations were made with no repacking of sidechains upon complexation, and only minimal packing upon mutation. We investigated the consequences of more extensive packing changes with a modified mean-field packing scheme. Rather than emphasising solvent exposure with relatively extended sidechains, rotamers are selected that exhibit maximal packing with protein. This provides solvent accessible areas for proteins that are much closer to those of experimental structures than the more extended sidechain regime. The new packing scheme increases changes in non-polar burial for mutants compared to wild-type proteins, but does not substantially improve agreement between ΔG and ΔΔG binding models.</p> <p>Conclusion</p> <p>We conclude that solvent accessible area, based on modelled mutant structures, is a poor correlate for ΔΔG upon mutation. A simple volume-based, rather than solvent accessibility-based, model is constructed for ΔG and ΔΔG systems. This shows a more consistent behaviour. We discuss the efficacy of volume, as opposed to area, approaches to describe the energetic consequences of mutations at interfaces. This knowledge can be used to develop simple computational screens for binding in comparative modelled interfaces.</p

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

Background: The increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions. Results: We report the complete circular and annotated genomes of two Red Sea strains, B. paralicheniformis Bac48 isolated from mangrove mud and B. paralicheniformis Bac84 isolated from microbial mat collected from Rabigh Harbor Lagoon in Saudi Arabia. Comparing the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 with nine publicly available complete genomes of B. licheniformis and three genomes of B. paralicheniformis, revealed that all of the B. paralicheniformis strains in this study are more enriched in nonribosomal peptides (NRPs). We further report the first computationally identified trans-acyltransferase (trans-AT) nonribosomal peptide synthetase/polyketide synthase (PKS/ NRPS) cluster in strains of this species. Conclusions:B. paralicheniformis species have more genes associated with biosynthesis of antimicrobial bioactive compounds than other previously characterized species of B. licheniformis, which suggests that these species are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked to adaptations that strains surviving in the Red Sea underwent to survive in the relatively hot and saline ecosystems

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.Peer reviewe