Discovery of the Acoustic Faraday Effect in Superfluid 3He-B

We report the discovery of the acoustic Faraday effect in superfluid 3He-B. The observation of this effect provides the first direct evidence for propagating transverse acoustic waves in liquid 3He, a mode first predicted by Landau in 1957. The Faraday rotation is large and observable because of spontaneously broken spin-orbit symmetry in 3He-B. We compare the experimental observations with a simulation of the transverse acoustic impedance that includes the field-induced circular birefringence of transverse waves.Comment: 4 pages in RevTex plus 3 postscript figures; new version includes: minor corrections to the text and an updated of list of reference

Allowed and forbidden transitions in artificial hydrogen and helium atoms

The strength of radiative transitions in atoms is governed by selection rules. Spectroscopic studies of allowed transitions in hydrogen and helium provided crucial evidence for the Bohr's model of an atom. Forbidden transitions, which are actually allowed by higher-order processes or other mechanisms, indicate how well the quantum numbers describe the system. We apply these tests to the quantum states in semiconductor quantum dots (QDs), which are regarded as artificial atoms. Electrons in a QD occupy quantized states in the same manner as electrons in real atoms. However, unlike real atoms, the confinement potential of the QD is anisotropic, and the electrons can easily couple with phonons of the material. Understanding the selection rules for such QDs is an important issue for the manipulation of quantum states. Here we investigate allowed and forbidden transitions for phonon emission in one- and two-electron QDs (artificial hydrogen and helium atoms) by electrical pump-and-probe experiments, and find that the total spin is an excellent quantum number in artificial atoms. This is attractive for potential applications to spin based information storage.Comment: slightly longer version of Nature 419, 278 (2002

Anyons in a weakly interacting system

We describe a theoretical proposal for a system whose excitations are anyons with the exchange phase pi/4 and charge -e/2, but, remarkably, can be built by filling a set of single-particle states of essentially noninteracting electrons. The system consists of an artificially structured type-II superconducting film adjacent to a 2D electron gas in the integer quantum Hall regime with unit filling fraction. The proposal rests on the observation that a vacancy in an otherwise periodic vortex lattice in the superconductor creates a bound state in the 2DEG with total charge -e/2. A composite of this fractionally charged hole and the missing flux due to the vacancy behaves as an anyon. The proposed setup allows for manipulation of these anyons and could prove useful in various schemes for fault-tolerant topological quantum computation.Comment: 7 pages with 3 figures. For related work and info visit http://www.physics.ubc.ca/~fran

Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives

BACKGROUND: Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the predicted 3D structures. The correlated mutations (CM) method serves as the most promising approach and it has been used to predict amino acids pairs that are distant in the primary sequence but form contacts in the native 3D structure of homologous proteins. RESULTS: Here we report a new implementation of the CM method with an added set of selection rules (filters). The parameters of the algorithm were optimized against fifteen high resolution crystal structures with optimization criterion that maximized the confidentiality of the predictions. The optimization resulted in a true positive ratio (TPR) of 0.08 for the CM without filters and a TPR of 0.14 for the CM with filters. The protocol was further benchmarked against 65 high resolution structures that were not included in the optimization test. The benchmarking resulted in a TPR of 0.07 for the CM without filters and to a TPR of 0.09 for the CM with filters. CONCLUSION: Thus, the inclusion of selection rules resulted to an overall improvement of 30%. In addition, the pair-wise comparison of TPR for each protein without and with filters resulted in an average improvement of 1.7. The methodology was implemented into a web server that is freely available to the public. The purpose of this implementation is to provide the 3D structure predictors with a tool that can help with ranking alternative models by satisfying the largest number of predicted contacts, as well as it can provide a confidence score for contacts in cases where structure is known

Size-Dependent Materials Properties Toward a Universal Equation

Due to the lack of experimental values concerning some material properties at the nanoscale, it is interesting to evaluate this theoretically. Through a “top–down” approach, a universal equation is developed here which is particularly helpful when experiments are difficult to lead on a specific material property. It only requires the knowledge of the surface area to volume ratio of the nanomaterial, its size as well as the statistic (Fermi–Dirac or Bose–Einstein) followed by the particles involved in the considered material property. Comparison between different existing theoretical models and the proposed equation is done

Discovery of an excited pair state in superfluid 3He

Order parameter collective modes are the fingerprint of a condensed phase. The spectroscopy of these modes in superfluid $^3$He and unconventional superconductors can provide key information on the symmetry of the condensate as well as the microscopic pairing mechanism responsible for the ground state and excitation energies. We report the discovery of a new collective mode in superfluid $^3$He-B which we identify as an excited bound state of Cooper pairs. We use interferometry within an acoustic cavity that is very sensitive to changes in the velocity of transverse sound. Our measurements of sound velocity and mode frequency, together with the observation of acoustic birefringence indicate that this new mode is weakly bound with an excitation energy within 1% of the pair-breaking edge of $2\Delta$. Based on the selection rules for coupling of transverse sound to a collective mode in $^3$He-B, combined with the observation of acoustic birefringence near the collective mode frequency, we infer that the new mode is most likely a spin-triplet (S=1), $f$-wave pair exciton (L=3) with total angular momentum, J=4. The existence of a pair exciton with J=4 suggests an attractive, sub-dominant, $f$-wave pairing interaction in liquid $^3$He

Computing Highly Correlated Positions Using Mutual Information and Graph Theory for G Protein-Coupled Receptors

G protein-coupled receptors (GPCRs) are a superfamily of seven transmembrane-spanning proteins involved in a wide array of physiological functions and are the most common targets of pharmaceuticals. This study aims to identify a cohort or clique of positions that share high mutual information. Using a multiple sequence alignment of the transmembrane (TM) domains, we calculated the mutual information between all inter-TM pairs of aligned positions and ranked the pairs by mutual information. A mutual information graph was constructed with vertices that corresponded to TM positions and edges between vertices were drawn if the mutual information exceeded a threshold of statistical significance. Positions with high degree (i.e. had significant mutual information with a large number of other positions) were found to line a well defined inter-TM ligand binding cavity for class A as well as class C GPCRs. Although the natural ligands of class C receptors bind to their extracellular N-terminal domains, the possibility of modulating their activity through ligands that bind to their helical bundle has been reported. Such positions were not found for class B GPCRs, in agreement with the observation that there are not known ligands that bind within their TM helical bundle. All identified key positions formed a clique within the MI graph of interest. For a subset of class A receptors we also considered the alignment of a portion of the second extracellular loop, and found that the two positions adjacent to the conserved Cys that bridges the loop with the TM3 qualified as key positions. Our algorithm may be useful for localizing topologically conserved regions in other protein families