Exclusive Decay of 1−−1^{--} Quarkonia and BcB_c Meson into a Lepton Pair Combined with Two Pions

We study the exclusive decay of $J/\Psi$, $\Upsilon$ and $B_c$ into a lepton pair combined with two pions in the two kinematic regions. One is specified by the two pions having large momenta, but a small invariant mass. The other is specified by the two pions having small momenta. In both cases we find that in the heavy quark limit the decay amplitude takes a factorized form, in which the nonperturbative effect related to heavy meson is represented by a NRQCD matrix element. The nonperturbative effects related to the two pions are represented by some universal functions characterizing the conversion of gluons into the pions. Using models for these universal functions and chiral perturbative theory we are able to obtain numerical predictions for the decay widths. Our numerical results show that the decay of \jpsi is at order of $10^{-5}$ with reasonable cuts and can be observed at BES II and the proposed BES III and CLEO-C. For other decays the branching ratio may be too small to be measured.Comment: 19 pages, Latex 2e file, 12 EPS figures (included). Replaced with version to appear in Eur. Phys. J. C,published online: 8 May 200

Ultrasensitive detections in atomic and molecular physics: demonstration in molecular overtone spectroscopy

We consider several highly sensitive techniques commonly used in detection of atomic and molecular absorptions. Their basic operating principles and corresponding performances are summarized and compared. We then present our latest results on the ultrasensitive detection of molecular overtone transitions to illustrate the principle and application of the cavity-enhanced frequency-modulation (FM) spectroscopy. An external cavity is used to enhance the molecular response to the light field, and an FM technique is applied for shot-noise-limited signal recovery. A perfect match between the FM sideband frequency and the cavity free spectral range makes the detection process insensitive to the laser-frequency noise relative to the cavity, and, at the same time, overcomes the cavity bandwidth limit. Working with a 1.064-µm Nd:YAG laser, we obtained sub-Doppler overtone resonances of C2HD, C2H2, and CO2 molecules. A detection sensitivity of 5 x 10^-13 of integrated absorption (1 x 10^-14/cm) over 1-s averaging time has been achieved

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This paper presents a new homology detection method MRFalign, consisting of three key components: 1) a Markov Random Fields (MRF) representation of a protein family; 2) a scoring function measuring similarity of two MRFs; and 3) an efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning two MRFs. Compared to HMM that can only model very short-range residue correlation, MRFs can model long-range residue interaction pattern and thus, encode information for the global 3D structure of a protein family. Consequently, MRF-MRF comparison for remote homology detection shall be much more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign outperforms several popular HMM or PSSM-based methods in terms of both alignment accuracy and remote homology detection and that MRFalign works particularly well for mainly beta proteins. For example, tested on the benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM succeed on 48% and 52% of proteins, respectively, at superfamily level, and on 15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign succeeds on 57.3% and 42.5% of proteins at superfamily and fold level, respectively. This study implies that long-range residue interaction patterns are very helpful for sequence-based homology detection. The software is available for download at http://raptorx.uchicago.edu/download/.Comment: Accepted by both RECOMB 2014 and PLOS Computational Biolog