Bose-Einstein condensation (BEC) has been observed in a dilute gas of sodium atoms. A Bose-Einstein condensate consists of a macroscopic population of the ground state of the system, and is a coherent state of matter. In an ideal gas, this phase transition is purely quantum-statistical. The study of BEC in weakly interacting systems which can be controlled and observed with precision holds the promise of revealing new macroscopic quantum phenomena that can be understood from first principles.

Bose-Einstein condensation in a gas of sodium atoms

Amino acid replacement matrices are an essential basis of protein phylogenetics. They are used to compute substitution probabilities along phylogeny branches and thus the likelihood of the data. They are also essential in protein alignment. A number of replacement matrices and methods to estimate these matrices from protein alignments have been proposed since the seminal work of Dayhoff et al. (1972). An important advance was achieved by Whelan and Goldman (2001) and their WAG matrix, thanks to an efficient maximum likelihood estimation approach that accounts for the phylogenies of sequences within each training alignment. We further refine this method by incorporating the variability of evolutionary rates across sites in the matrix estimation and using a much larger and diverse database than BRKALN, which was used to estimate WAG. To estimate our new matrix (called LG after the authors), we use an adaptation of the XRATE software and 3,912 alignments from Pfam, comprising approximately 50,000 sequences and approximately 6.5 million residues overall. To evaluate the LG performance, we use an independent sample consisting of 59 alignments from TreeBase and randomly divide Pfam alignments into 3,412 training and 500 test alignments. The comparison with WAG and JTT shows a clear likelihood improvement. With TreeBase, we find that 1) the average Akaike information criterion gain per site is 0.25 and 0.42, when compared with WAG and JTT, respectively; 2) LG is significantly better than WAG for 38 alignments (among 59), and significantly worse with 2 alignments only; and 3) tree topologies inferred with LG, WAG, and JTT frequently differ, indicating that using LG impacts not only the likelihood value but also the output tree. Results with the test alignments from Pfam are analogous. LG and a PHYML implementation can be downloaded from http://atgc.lirmm.fr/LG

https://hal-lirmm.ccsd.cnrs.fr/docs/00/72/82/46/PDF/LeGascuel_MBE08.pdf

An Improved General Amino Acid Replacement Matrix

Modern nanotechnology allows one to scale down various important devices (sensors, chips, fibers, etc.) and thus opens up new horizons for their applications. The efficiency of most of them is based on fundamental physical phenomena, such as transport of wave excitations and resonances. Short propagation distances make phase-coherent processes of waves important. Often the scattering of waves involves propagation along different paths and, as a consequence, results in interference phenomena, where constructive interference corresponds to resonant enhancement and destructive interference to resonant suppression of the transmission. Recently, a variety of experimental and theoretical work has revealed such patterns in different physical settings. The purpose of this review is to relate resonant scattering to Fano resonances, known from atomic physics. One of the main features of the Fano resonance is its asymmetric line profile. The asymmetry originates from a close coexistence of resonant transmission and resonant reflection and can be reduced to the interaction of a discrete (localized) state with a continuum of propagation modes. The basic concepts of Fano resonances are introduced, their geometrical and/or dynamical origin are explained, and theoretical and experimental studies of light propagation in photonic devices, charge transport through quantum dots, plasmon scattering in Josephson-junction networks, and matter-wave scattering in ultracold atom systems, among others are reviewed.

/pdf/fano-resonances-in-nanoscale-structures-2c8qeas3bm.pdf

Fano resonances in nanoscale structures

The development of wave optics for light brought many new insights into our understanding of physics, driven by fundamental experiments like the ones by Young, Fizeau, Michelson-Morley and others. Quantum mechanics, and especially the de Broglie’s postulate relating the momentum p of a particle to the wave vector k of an matter wave: k = 2 λ = p/ℏ, suggested that wave optical experiments should be also possible with massive particles (see table 1), and over the last 40 years electron and neutron interferometers have demonstrated many fundamental aspects of quantum mechanics [1].

/pdf/optics-and-interferometry-with-atoms-and-molecules-1vnuwajb51.pdf

Optics and interferometry with atoms and molecules

Deactivation of heterogeneous catalysts is a ubiquitous problem that causes loss of catalytic rate with time. This review on deactivation and regeneration of heterogeneous catalysts classifies deactivation by type (chemical, thermal, and mechanical) and by mechanism (poisoning, fouling, thermal degradation, vapor formation, vapor-solid and solid-solid reactions, and attrition/crushing). The key features and considerations for each of these deactivation types is reviewed in detail with reference to the latest literature reports in these areas. Two case studies on the deactivation mechanisms of catalysts used for cobalt Fischer-Tropsch and selective catalytic reduction are considered to provide additional depth in the topics of sintering, coking, poisoning, and fouling. Regeneration considerations and options are also briefly discussed for each deactivation mechanism.

/pdf/heterogeneous-catalyst-deactivation-and-regeneration-a-166g7jwbkh.pdf

Heterogeneous Catalyst Deactivation and Regeneration: A Review

Bose-Einstein condensation has been achieved in a magnetic surface microtrap with 4 x 10(5) (87)Rb atoms. The strongly anisotropic trapping potential is generated by a microstructure which consists of microfabricated linear copper conductor of widths ranging from 3 to 30 microm. After loading a high number of atoms from a pulsed thermal source directly into a magneto-optical trap the magnetically stored atoms are transferred into the microtrap by adiabatic transformation of the trapping potential. In the microtrap the atoms are cooled to condensation using forced rf-evaporation. The complete in vacuo trap design is compatible with ultrahigh vacuum below 2 x 10(-11) mbar.

https://arxiv.org/pdf/cond-mat/0109322.pdf

Bose-Einstein condensation in a surface microtrap.

Background
In general, the construction of trees is based on sequence alignments. This procedure, however, leads to loss of informationwhen parts of sequence alignments (for instance ambiguous regions) are deleted before tree building. To overcome this difficulty, one of us previously introduced a new and rapid algorithm that calculates dissimilarity matrices between sequences without preliminary alignment.

/pdf/comparing-sequences-without-using-alignments-application-to-8mvhba5f3e.pdf

Comparing sequences without using alignments: application to HIV/SIV subtyping.

We demonstrate the loading of a miniaturized magnetic guide for neutral atoms made of small-size current conductors. Cold rubidium atoms are initially stored in a shallow spherical quadrupole field and subsequently transferred into the magnetic guide by gradually transforming the trapping potential. Density, temperature, and atom number have been monitored in situ by absorption imaging with a charge-coupled device camera. A fraction of $14%$ of the initially trapped atoms has been transferred into the linear microtrap at a temperature of $39\ensuremath{\mu}\mathrm{K}$.

Miniaturized Wire Trap for Neutral Atoms

Potential-induced stress in the solid-liquid interface: Au(111) and Au(100) in an HClO4 electrolyte

We report an efficient method to load atoms into a magneto-optical trap. A resistively heated alkali metal dispenser, which is mounted close to the trapping region, serves as a compact, pulsed source for Rb atoms. The atoms are captured by the magneto-optical trap within less than 3 s at a loading rate of more than 107 atoms per second. The lifetime of the trapped atoms exceeds the filling time by about 30 s.

Alexander Grossmann

Papers

Bose-Einstein condensation in a surface microtrap.

Comparing sequences without using alignments: application to HIV/SIV subtyping.

Miniaturized Wire Trap for Neutral Atoms

Potential-induced stress in the solid-liquid interface: Au(111) and Au(100) in an HClO4 electrolyte

Fast loading of a magneto-optical trap from a pulsed thermal source