Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.     

Two-photon resonant three-photon ionization with ultrashort pulses

The problem of two-photon resonant three-photon ionization is analysed for the case of ultrashort ionizing pulses. An analytic solution to the problem is obtained and discussed. A simple experiment is proposed which would demonstrate the effect of optical nutation on the photoelectron flux.     

Self-injection length in La0.7Ca0.3MnO3-YBa2Cu3O7-δ ferromagnet-superconductor multilayer thin films

We have carried out extensive studies on the self-injection problem in barrierless heterojunctions between La_0.7Ca_0.3MnO₃ (LCMO) and YBa₂Cu₃O_7-δ (YBCO) thin films. The heterojunctions were formed in situ by sequentially growing LCMO and YBCO films on 〈100〉 LaAlO₃ (LAO) substrate using a pulsed laser deposition (PLD) system. YBCO micro-bridges with 64 μm width were patterned both on the LAO (control) and LCMO side of the substrate. Critical current, I _c, was measured at 77 K on both the control side as well as the LCMO side for different YBCO film thickness. It was observed that while the control side showed a J _c of ∼ 2 × 10⁶ A/cm², the LCMO side showed about half the value for the same thickness (1800 ?). The difference in J _c indicates that a certain thickness of YBCO has become ‘effectively’ normal due to self-injection. From the measurement of J _c at two different thicknesses (1800 ? and 1500 ?) of YBCO films both on the LAO as well as the LCMO side, the value of self-injection length (at 77 K) was estimated to be ∼ 900 ?. To the authors’ best knowledge, this is the first time that self-injection length has been quantified. A control experiment carried out with LaNiO₃ deposited by PLD on YBCO did not show any evidence of self-injection.     

The role of the interactive Kerr effect in two-photon optical multistability

We show that bistable behaviour in a two-photon resonant system within a cavity may be attributed to interactive mode-pulling via the two-photon optical Kerr effect and also to absorptive bleaching (atomic saturation). The interactive Kerr process may be regarded as giving rise to a new category of optical bistability. Moreover, a mechanism for the recently-predicted tristability can be found in terms of simultaneous competition between the interactive Kerr effect and bleaching.     

Incompatibility of polarization-division multiplexing with wavelength-division multiplexing in soliton-transmission systems

In a recent experiment it was demonstrated that polarization-division multiplexing was incompatible with wavelength-division multiplexing. We discuss a theoretical model that explains this result.     

Structure-function correlations in Iron(II) tris(pyrazolyl)borate spin-state crossover complexes

Iron(II) poly(pyrazolyl)borate complexes have been investigated to determine the impact of substituent effects, intramolecular ligand distortions, and intermolecular supramolecular structures on the spin-state crossover (SCO) behavior. The molecular structure of Fe[HB(3,4,5-Me3pz)3]2 (pz = pyrazolyl ring), a complex known to remain high spin when the temperature is lowered, reveals that this complex has an intramolecular ring-twist distortion that is not observed in analogous complexes that do exhibit a SCO at low temperatures, thus indicating that this distortion greatly influences the properties of these complexes. The structure of Fe[B(3-(cy)Prpz)4]2.(CH3OH) ((cy)Pr = cyclopropyl ring) at 294 K has two independent molecules in the unit cell, both of which are high spin; only one of these high-spin iron(II) sites, the site with the lesser ring-twist distortion, is observed to be low-spin iron(II) in the 90 K structure. A careful evaluation of the supramolecular structures of these complexes and several similar complexes reported previously revealed no strong correlation between the supramolecular packing forces and their SCO behavior. Magnetic and M?ssbauer spectral measurements on Fe[B(3-(cy)Prpz)4]2 and Fe[HB(3-(cy)Prpz)3]2 indicate that both complexes exhibit a partial SCO from fully high-spin iron(II) at higher temperatures, respectively, to a 50:50 high-spin/low-spin mixture of iron(II) below 100 K. These results may be understood, in the former case, by the differences in ring-twisting and, in the latter case, by a phase transition; in all complexes in which a phase transition is observed, this change dominates the SCO behavior. A comparison of the M?ssbauer spectral properties of these two complexes and of Fe[HB(3-Mepz)3]2 with that of other complexes reveals correlations between the M?ssbauer-effect isomer shift and the average Fe-N bond distance and between the quadrupole splitting and the average FeN-NB intraligand dihedral torsion angles and the distortion of the average N-Fe-N intraligand bond angles.     

Statistical properties in the chaotic regime of the Maxwell-Bloch equations

The statistical properties of the electric field solution of the Maxwell-Bloch equations describing a single mode, homogeneously broadened laser in the mean field limit are investigated in the strange attractor regime. The electric field distribution sis calculated and it is found that the low order intensity moments are somewhat higher than those for thermal-chaotic light whilst the higher order moments are substantially lower. The field and intensity correlation functions are also calculated and found to exhibit radically different behaviour. The results are interpreted in terms of iterative map which is dederived using multiple time-scale perturbation theory. It is shown that a simple random phasor model is compatible with the numerical data.