Characterization of Binary Constraint System Games

We consider a class of nonlocal games that are related to binary constraint systems (BCSs) in a manner similar to the games implicit in the work of Mermin [N.D. Mermin, "Simple unified form for the major no-hidden-variables theorems," Phys. Rev. Lett., 65(27):3373-3376, 1990], but generalized to n binary variables and m constraints. We show that, whenever there is a perfect entangled protocol for such a game, there exists a set of binary observables with commutations and products similar to those exhibited by Mermin. We also show how to derive upper bounds strictly below 1 for the the maximum entangled success probability of some BCS games. These results are partial progress towards a larger project to determine the computational complexity of deciding whether a given instance of a BCS game admits a perfect entangled strategy or not.Comment: Revised version corrects an error in the previous version of the proof of Theorem 1 that arises in the case of POVM measurement

Tomographic Quantum Cryptography: Equivalence of Quantum and Classical Key Distillation

The security of a cryptographic key that is generated by communication through a noisy quantum channel relies on the ability to distill a shorter secure key sequence from a longer insecure one. For an important class of protocols, which exploit tomographically complete measurements on entangled pairs of any dimension, we show that the noise threshold for classical advantage distillation is identical with the threshold for quantum entanglement distillation. As a consequence, the two distillation procedures are equivalent: neither offers a security advantage over the other.Comment: 4 pages, 1 figur

Detection and classification of Bacteria using Raman Spectroscopy Combined with Multivariate Analysis

Vibrational spectroscopic techniques have advantages over conventional microbiological approaches towards identification & detection of pathogens. Since unique spectral fingerprint is obtained, one can identify very closely related bacteria using such methods. In this study Raman microspectroscopy in combination with chemometric method has been used to classify four strains of E. coli (two pathogenic & two non-pathogenic). Different multivariate approaches such as hierarchical cluster analysis, principal component analysis & linear discriminant analysis were explored to obtain efficient classification of the Raman signals obtained from the four strains of E.coli. It was observed that multivariate analysis was able to classify the bacteria at strain level. Linear discrimination analysis using PC scores (PC-LDA) was found to give very good result with as high as 100% accuracy. This hybrid technique (Raman spectroscopy & multivariate analysis) has tremendous potential to be developed as a tool for bacterial identification.

A Correlative Study Between Size of Tympanic Membrane Perforation, Pure Tone Audiometry and Intraoperative Findings in Tympanoplasty

Introduction             Chronic otitis media (COM) is a most common and prevalent disease of the middle ear. COM has been defined as a longstanding inflammatory condition of middle ear and mastoid, associated with perforation of the tympanic membrane. Tympanoplasties are common surgeries performed for chronic otitis media in inactive mucosal type. Any otological surgery may involve a menace/ hazard of hearing loss post operatively.             In this study, an attempt was made to correlate, size of tympanic membrane perforation, pure tone audiometry and intra-operative findings in tympanoplasties, results were analysed and conclusion drawn. Materials and Methods Forty patients attending ENT OPD with chronic otitis media (COM), inactive mucosal type, with conductive hearing loss undergoing tympanoplasties who were willing to participate in the study were selected.  Ear was examined pre-operatively to assess the size of perforation and then, pure tone audiometry (PTA) was done to assess the type of hearing loss and its severity. During tympanoplasty, middle ear was inspected for ossicular status and any other pathology was noted. Later, the size of tympanic membrane perforation, pure tone audiometry and intra operative findings were correlated with each other and analysed. Result  In small and medium sized perforation, PTA and intraoperative findings correlated with each other. Whereas, in large and subtotal perforation, there was no correlation. Conclusion             In small and medium sized perforation, middle ear inspection may not be necessary. Whereas, in large and subtotal perforation it is necessary

A multi-photon Stokes-parameter invariant for entangled states

We consider the Minkowskian norm of the n-photon Stokes tensor, a scalar invariant under the group realized by the transformations of stochastic local quantum operations and classical communications (SLOCC). This invariant is offered as a candidate entanglement measure for n-qubit states and discussed in relation to measures of quantum state entanglement for certain important classes of two-qubit and three-qubit systems. This invariant can be directly estimated via a quantum network, obviating the need to perform laborious quantum state tomography. We also show that this invariant directly captures the extent of entanglement purification due to SLOCC filters.Comment: 9 pages, 0 figures, Accepted for publication in Physical Review

Nonlinear Coherent Modes of Trapped Bose-Einstein Condensates

Nonlinear coherent modes are the collective states of trapped Bose atoms, corresponding to different energy levels. These modes can be created starting from the ground state condensate that can be excited by means of a resonant alternating field. A thorough theory for the resonant excitation of the coherent modes is presented. The necessary and sufficient conditions for the feasibility of this process are found. Temporal behaviour of fractional populations and of relative phases exhibits dynamic critical phenomena on a critical line of the parametric manifold. The origin of these critical phenomena is elucidated by analyzing the structure of the phase space. An atomic cloud, containing the coherent modes, possesses several interesting features, such as interference patterns, interference current, spin squeezing, and massive entanglement. The developed theory suggests a generalization of resonant effects in optics to nonlinear systems of Bose-condensed atoms.Comment: 26 pages, Revtex, no figure

Functional Diversity and Structural Disorder in the Human Ubiquitination Pathway

The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred - E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions. © 2013 Bhowmick et al

Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability

BACKGROUND: The emergence of eukaryotes was characterized by the expansion and diversification of several ancient RNA-binding domains and the apparent de novo innovation of new RNA-binding domains. The identification of these RNA-binding domains may throw light on the emergence of eukaryote-specific systems of RNA metabolism. RESULTS: Using sensitive sequence profile searches, homology-based fold recognition and sequence-structure superpositions, we identified novel, divergent versions of the Sm domain in the Scd6p family of proteins. This family of Sm-related domains shares certain features of conventional Sm domains, which are required for binding RNA, in addition to possessing some unique conserved features. We also show that these proteins contain a second previously uncharacterized C-terminal domain, termed the FDF domain (after a conserved sequence motif in this domain). The FDF domain is also found in the fungal Dcp3p-like and the animal FLJ22128-like proteins, where it fused to a C-terminal domain of the YjeF-N domain family. In addition to the FDF domains, the FLJ22128-like proteins contain yet another divergent version of the Sm domain at their extreme N-terminus. We show that the YjeF-N domains represent a novel version of the Rossmann fold that has acquired a set of catalytic residues and structural features that distinguish them from the conventional dehydrogenases. CONCLUSIONS: Several lines of contextual information suggest that the Scd6p family and the Dcp3p-like proteins are conserved components of the eukaryotic RNA metabolism system. We propose that the novel domains reported here, namely the divergent versions of the Sm domain and the FDF domain may mediate specific RNA-protein and protein-protein interactions in cytoplasmic ribonucleoprotein complexes. More specifically, the protein complexes containing Sm-like domains of the Scd6p family are predicted to regulate the stability of mRNA encoding proteins involved in cell cycle progression and vesicular assembly. The Dcp3p and FLJ22128 proteins may localize to the cytoplasmic processing bodies and possibly catalyze a specific processing step in the decapping pathway. The explosive diversification of Sm domains appears to have played a role in the emergence of several uniquely eukaryotic ribonucleoprotein complexes, including those involved in decapping and mRNA stability

Big Domains Are Novel Ca2+-Binding Modules: Evidences from Big Domains of Leptospira Immunoglobulin-Like (Lig) Proteins

binds to a Big domains, which would provide a novel functional role of the proteins containing Big fold. with dissociation constants of 2–4 µM. Lig A9 and Lig A10 domains fold well with moderate thermal stability, have β-sheet conformation and form homodimers. Fluorescence spectra of Big domains show a specific doublet (at 317 and 330 nm), probably due to Trp interaction with a Phe residue. Equilibrium unfolding of selected Big domains is similar and follows a two-state model, suggesting the similarity in their fold. binding