Different Functional Gene Clusters in Yeast have Different Spatial Distributions of the Transcription Factor Binding Sites

Transcription factors control gene expression by binding to short specific DNA sequences, called transcription factor binding sites (TFBSs), in the promoter of a gene. Thus, studying the spatial distribution of TFBSs in the promoters may provide insights into the molecular mechanisms of gene regulation. I developed a method to construct the spatial distribution of TFBSs for any set of genes of interest. I found that different functional gene clusters have different spatial distributions of TFBSs, indicating that gene regulation mechanisms may be very different among different functional gene clusters. I also found that the binding sites for different transcription factors (TFs) may have different spatial distributions: a sharp peak, a plateau or no dominant single peak. The spatial distributions of binding sites for many TFs derived from my analyses are valuable prior information for TFBS prediction algorithm because different regions of a promoter can assign different possibilities for TFBS occurrence

Sorption of Eu(III) on Attapulgite Studied by Batch, XPS and EXAFS Techniques.

The effects of pH, ionic strength and temperature on sorption of Eu(III) on attapulgite were investigated in the presence and absence of fulvic acid (FA) and humic acid (HA). The results indicated that the sorption of Eu(III) on attapulgite was strongly dependent on pH and ionic strength, and independent of temperature. In the presence of FA/HA, Eu(III) sorption was enhanced at pH 7. The X-ray photoelectron spectroscopy (XPS) analysis suggested that the sorption of Eu(III) might be expressed as ≡X3Eu0 ≡SwOHEu3+ and ≡SOEu-OOC-/HA in the ternary Eu/HA/attapulgite system. The extended X-ray absorption fine structure (EXAFS) analysis of Eu-HA complexes indicated that the distances of d(Eu-O) decreased from 2.451 to 2.360 Å with increasing pH from 1.76 to 9.50, whereas the coordination number (N) decreased from ~9.94 to ~8.56. Different complexation species were also found for the different addition sequences of HA and Eu(III) to attapulgite suspension. The results are important to understand the influence of humic substances on Eu(III) behavior in the natural environment

A MEMS device for continuously tunable optical buffering

We present design and fabrication of free-standing InP optical waveguides for MEMS-actuated optical buffering. A continuously tunable delay time of 10ps is predicted in a 1mm long device with the operation voltage of 3V

Search for TeV Scale Physics in Heavy Flavour Decays

The subject of heavy flavour decays as probes for physics beyond the TeV scale is covered from the experimental perspective. Emphasis is placed on the more traditional Beyond the Standard Model topics that have potential for impact in the short term, with the physics explained. We do unabashedly promote our own phemonenology work.Comment: 10 pages, 9 figures (now fixed); Submitted for the SUSY07 proceeding

The reaction Δ+N→N+N+ϕ\Delta+N\to N+N+\phi in ion-ion collisions

We study the threshold $\phi$-meson production in the process $\Delta+N\to N+N+\phi$, which appears as a possible important mechanism in high energy nuclei-nuclei collisions. The isotopic invariance of the strong interaction and the selection rules due to P-parity and total angular momentum result in a general and model independent parametrization of the spin structure of the matrix element in terms of three partial amplitudes. In the framework of one-pion exchange model these amplitudes can be derived in terms of the two threshold partial amplitudes for the process $\pi+N\to N+\phi$. We predict the ratio of cross sections for $\phi-$meson production in $pp$- and $\Delta N$-collisions and the polarization properties of the $\phi$-meson, in $\Delta+N\to N+N+\phi$, as a function of a single parameter, which characterizes the relative role of transversal and longitudinal $\phi$-meson polarizations in the process $\pi+N\to N+\phi$.Comment: 10 pages 3 figure

Charm multiplicity and the branching ratios of inclusive charmless b quark decays in the general two-Higgs-doublet models

In the framework of general two-Higgs-doublet models, we calculate the branching ratios of various inclusive charmless b decays by using the low energy effective Hamiltonian including next-to-leading order QCD corrections, and examine the current status and the new physics effects on the determination of the charm multiplicity $n_c$ and semileptonic branching ratio $B_{SL}$. Within the considered parameter space, the enhancement to the ratio $BR(b \to s g)$ due to the charged-Higgs penguins can be as large as a factor of 8 (3) in the model III (II), while the ratio $BR(b \to no charm)$ can be increased from the standard model prediction of 2.49% to 4.91% (2.99%) in the model III (II). Consequently, the value of $B_{SL}$ and $n_c$ can be decreased simultaneously in the model III. The central value of $B_{SL}$ will be lowered slightly by about 0.003, but the ratio $n_c$ can be reduced significantly from the theoretical prediction of $n_c= 1.28 \pm 0.05$ in the SM to $n_c= 1.23 \pm 0.05$, $1.18 \pm 0.05$ for $m_{H^+}=200, 100$ GeV, respectively. We find that the predicted $n_c$ and the measured $n_c$ now agree within roughly one standard deviation after taking into account the effects of gluonic charged Higgs penguins in the model III with a relatively light charged Higgs boson.Comment: 25 pages, Latex file, axodraw.sty, 6 figures. Final version to be published in Phys.Rev.

Complete population transfer in a degenerate 3-level atom

We find conditions required to achieve complete population transfer, via coherent population trapping, from an initial state to a designated final state at a designated time in a degenerate 3-level atom, where transitions are caused by an external interaction. Complete population transfer from an initially occupied state 1 to a designated state 2 occurs under two conditions. First, there is a constraint on the ratios of the transition matrix elements of the external interaction. Second, there is a constraint on the action integral over the interaction, or "area", corresponding to the phase shift induced by the external interaction. Both conditions may be expressed in terms of simple odd integers.Comment: 22 pages, 4 figure

Test for entanglement using physically observable witness operators and positive maps

Motivated by the Peres-Horodecki criterion and the realignment criterion we develop a more powerful method to identify entangled states for any bipartite system through a universal construction of the witness operator. The method also gives a new family of positive but non-completely positive maps of arbitrary high dimensions which provide a much better test than the witness operators themselves. Moreover, we find there are two types of positive maps that can detect 2xN and 4xN bound entangled states. Since entanglement witnesses are physical observables and may be measured locally our construction could be of great significance for future experiments.Comment: 6 pages, 1 figure, revtex4 styl

Muon anomalous magnetic moment in the standard model with two Higgs doublets

The muon anomalous magnetic moment is investigated in the standard model with two Higgs doublets (S2HDM) motivated from spontaneous CP violation. Thus all the effective Yukawa couplings become complex. As a consequence of the non-zero phase in the couplings, the one loop contribution from the neutral scalar bosons could be positive and negative relying on the CP phases. The interference between one and two loop diagrams can be constructive in a large parameter space of CP-phases. This will result in a significant contribution to muon anomalous magnetic moment even in the flavor conserving process with a heavy neutral scalar boson ($m_h \sim$ 200 GeV) once the effective muon Yukawa coupling is large ($|\xi_\mu|\sim 50$). In general, the one loop contributions from lepton flavor changing scalar interactions become more important. In particular, when all contributions are positive in a reasonable parameter space of CP phases, the recently reported 2.6 sigma experiment vs. theory deviation can be easily explained even for a heavy scalar boson with a relative small Yukawa coupling in the S2HDM.Comment: 8 pages, RevTex file, 5 figures, published version Phys. Rev. D 54 (2001) 11501

Delocalization and spin-wave dynamics in ferromagnetic chains with long-range correlated random exchange

We study the one-dimensional quantum Heisenberg ferromagnet with exchange couplings exhibiting long-range correlated disorder with power spectrum proportional to $1/k^{\alpha}$, where $k$ is the wave-vector of the modulations on the random coupling landscape. By using renormalization group, integration of the equations of motion and exact diagonalization, we compute the spin-wave localization length and the mean-square displacement of the wave-packet. We find that, associated with the emergence of extended spin-waves in the low-energy region for $\alpha > 1$, the wave-packet mean-square displacement changes from a long-time super-diffusive behavior for $\alpha <1$ to a long-time ballistic behavior for $\alpha > 1$. At the vicinity of $\alpha =1$, the mobility edge separating the extended and localized phases is shown to scale with the degree of correlation as $E_c\propto (\alpha -1)^{1/3}$.Comment: PRB to appea