Detection of a pH-dependent conformational change in azurin by time-resolved phosphorescence

Azurin, a blue copper protein from the bacterial species Pseudomonas aeruginosa, contains a single tryptophan residue. Previous fluorescence measurements indicate that this residue is highly constrained and unusually inaccessible to water. In the apoprotein this residue also possesses a long-lived room-temperature phosphorescence (RTP), the nonexponential decay of which can be resolved into two major components associated with lifetimes of 417 and 592 ms, which likely originate from at least two conformations of the protein. The relative weights of these two decay components change with pH in good correlation with a change in protonation of His-35, which has been studied in Cu(II) azurin. Interestingly, the structural changes characterized in earlier work have little effect on the fluorescence decay and appear to occur away from the tryptophan residue. However, in the present work, the two RTP lifetimes suggest conformations with different structural rigidities in the vicinity of the tryptophan residue. The active conformation that predominates below a pH of 5.6 has the shorter lifetime and is less rigid. Phosphorescence decays of several metal derivatives of azurin were also measured and revealed strong similarities to that of apoazurin, indicating that the structural constraints upon the metal-binding site are imposed predominately by the protein

Macroscopic Quantum Fluctuations in the Josephson Dynamics of Two Weakly Linked Bose-Einstein Condensates

We study the quantum corrections to the Gross-Pitaevskii equation for two weakly linked Bose-Einstein condensates. The goals are: 1) to investigate dynamical regimes at the borderline between the classical and quantum behaviour of the bosonic field; 2) to search for new macroscopic quantum coherence phenomena not observable with other superfluid/superconducting systems. Quantum fluctuations renormalize the classical Josephson oscillation frequencies. Large amplitude phase oscillations are modulated, exhibiting collapses and revivals. We describe a new inter-well oscillation mode, with a vanishing (ensemble averaged) mean value of the observables, but with oscillating mean square fluctuations. Increasing the number of condensate atoms, we recover the classical Gross-Pitaevskii (Josephson) dynamics, without invoking the symmetry-breaking of the Gauge invariance.Comment: Submitte

Alignment-Free Phylogenetic Reconstruction

14th Annual International Conference, RECOMB 2010, Lisbon, Portugal, April 25-28, 2010. ProceedingsWe introduce the first polynomial-time phylogenetic reconstruction algorithm under a model of sequence evolution allowing insertions and deletions (or indels). Given appropriate assumptions, our algorithm requires sequence lengths growing polynomially in the number of leaf taxa. Our techniques are distance-based and largely bypass the problem of multiple alignment

Ultrafast laser inscribed integrated photonics: material science to device development

Detailed studies of intense light – material interactions has led to new insights into fs laser induced refractive index change in a range of glass types. This body of knowledge enables the development of advanced processing methodologies, resulting in novel planar and 3D guided wave devices. We will review the chemistry and morphology associated with fs laser induced refractive index change in multi-component glasses such as ZBLAN, phosphates and silicates, and discuss how these material changes inform our research programs developing a range of active and passive lightwave systems.S. Gross, T. D. Meany, A. Arriola, C. Miese, R. J. Williams, Y. Duan, Q. Liu, I. Spaleniak, M. Ams, P. Dekker, N. Jovanovic, A. Fuerbach, M. Ireland, M. J. Steel, D. G. Lancaster, H. Ebendorff Heidepriem, T. M. Monro, and M. J. Withfor

Theory of Quantum Optical Control of Single Spin in a Quantum Dot

We present a theory of quantum optical control of an electron spin in a single semiconductor quantum dot via spin-flip Raman transitions. We show how an arbitrary spin rotation may be achieved by virtual excitation of discrete or continuum trion states. The basic physics issues of the appropriate adiabatic optical pulses in a static magnetic field to perform the single qubit operation are addressed

The evolution of language: a comparative review

For many years the evolution of language has been seen as a disreputable topic, mired in fanciful "just so stories" about language origins. However, in the last decade a new synthesis of modern linguistics, cognitive neuroscience and neo-Darwinian evolutionary theory has begun to make important contributions to our understanding of the biology and evolution of language. I review some of this recent progress, focusing on the value of the comparative method, which uses data from animal species to draw inferences about language evolution. Discussing speech first, I show how data concerning a wide variety of species, from monkeys to birds, can increase our understanding of the anatomical and neural mechanisms underlying human spoken language, and how bird and whale song provide insights into the ultimate evolutionary function of language. I discuss the ‘‘descended larynx’ ’ of humans, a peculiar adaptation for speech that has received much attention in the past, which despite earlier claims is not uniquely human. Then I will turn to the neural mechanisms underlying spoken language, pointing out the difficulties animals apparently experience in perceiving hierarchical structure in sounds, and stressing the importance of vocal imitation in the evolution of a spoken language. Turning to ultimate function, I suggest that communication among kin (especially between parents and offspring) played a crucial but neglected role in driving language evolution. Finally, I briefly discuss phylogeny, discussing hypotheses that offer plausible routes to human language from a non-linguistic chimp-like ancestor. I conclude that comparative data from living animals will be key to developing a richer, more interdisciplinary understanding of our most distinctively human trait: language