Identifying short motifs by means of extreme value analysis

The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability can display large fluctuations from one putative binding site to another. Here we use a self-consistent statistical procedure that accounts correctly for the large deviations of the matching probability to predict the location of short binding sites. We apply it in two distinct situations: (a) the detection of the binding sites for three specific transcription factors on a set of 134 estrogen-regulated genes; (b) the identification, in a set of 138 possible transcription factors, of the ones binding a specific set of nine genes. In both instances, experimental findings are reproduced (when available) and the number of false positives is significantly reduced with respect to the other methods commonly employed.Comment: 6 pages, 5 figure

Chromomagnetism in nuclear matter

Quarks are color charged particles. Due to their motion there is a strong possibility of generation of color magnetic field. It is shown that however hadrons are color singlet particles they may have non-zero color magnetic moment. Due to this color magnetic moment hadrons can show color interaction. In this paper we have studied the chromomagnetic properties of nuclear matter.Comment: 6 pages, 1 figure, accepted for publication in Int. J. Theor. Phy

Phase Space Reduction and Vortex Statistics: An Anyon Quantization Ambiguity

We examine the quantization of the motion of two charged vortices in a Ginzburg--Landau theory for the fractional quantum Hall effect recently proposed by the first two authors. The system has two second-class constraints which can be implemented either in the reduced phase space or Dirac-Gupta-Bleuler formalism. Using the intrinsic formulation of statistics, we show that these two ways of implementing the constraints are inequivalent unless the vortices are quantized with conventional statistics; either fermionic or bosonic.Comment: 14 pages, PHYZZ

Nucleon to Delta Weak Excitation Amplitudes in the Non-relativistic Quark Model

We investigate the nucleon to Delta(1232) vector and axial vector amplitudes in the non-relativistic quark model of the Isgur-Karl variety. A particular interest is to investigate the SU(6) symmetry breaking, due to color hyperfine interaction. We compare the theoretical estimates to recent experimental investigation of the Adler amplitudes by neutrino scattering.Comment: \documentstyle[aps]{revtex}, 21pages; 11 postscript figures. Accepted for publication by Phys. Rev.

Preparation of biogenic gas vesicle nanostructures for use as contrast agents for ultrasound and MRI

Gas vesicles (GVs) are a unique class of gas-filled protein nanostructures that are detectable at subnanomolar concentrations and whose physical properties allow them to serve as highly sensitive imaging agents for ultrasound and MRI. Here we provide a protocol for isolating GVs from native and heterologous host organisms, functionalizing these nanostructures with moieties for targeting and fluorescence, characterizing their biophysical properties and imaging them using ultrasound and MRI. GVs can be isolated from natural cyanobacterial and haloarchaeal host organisms or from Escherichia coli expressing a heterologous GV gene cluster and purified using buoyancy-assisted techniques. They can then be modified by replacing surface-bound proteins with engineered, heterologously expressed variants or through chemical conjugation, resulting in altered mechanical, surface and targeting properties. Pressurized absorbance spectroscopy is used to characterize their mechanical properties, whereas dynamic light scattering (DLS)and transmission electron microscopy (TEM) are used to determine nanoparticle size and morphology, respectively. GVs can then be imaged with ultrasound in vitro and in vivo using pulse sequences optimized for their detection versus background. They can also be imaged with hyperpolarized xenon MRI using chemical exchange saturation transfer between GV-bound and dissolved xenon—a technique currently implemented in vitro. Taking 3–8 d to prepare, these genetically encodable nanostructures enable multimodal, noninvasive biological imaging with high sensitivity and potential for molecular targeting

Effective Lagrangian Approach to the Theory of Eta Photoproduction in the N∗(1535)N^{*}(1535) Region

We investigate eta photoproduction in the $N^{*}(1535)$ resonance region within the effective Lagrangian approach (ELA), wherein leading contributions to the amplitude at the tree level are taken into account. These include the nucleon Born terms and the leading $t$-channel vector meson exchanges as the non-resonant pieces. In addition, we consider five resonance contributions in the $s$- and $u$- channel; besides the dominant $N^{*}(1535)$, these are: $N^{*}(1440),N^{*}(1520),N^{*}(1650)$ and $N^{*}(1710)$. The amplitudes for the $\pi^\circ$ and the $\eta$ photoproduction near threshold have significant differences, even as they share common contributions, such as those of the nucleon Born terms. Among these differences, the contribution to the $\eta$ photoproduction of the $s$-channel excitation of the $N^{*}(1535)$ is the most significant. We find the off-shell properties of the spin-3/2 resonances to be important in determining the background contributions. Fitting our effective amplitude to the available data base allows us to extract the quantity $\sqrt{\chi \Gamma_\eta} A_{1/2}/\Gamma_T$, characteristic of the photoexcitation of the $N^{*}(1535)$ resonance and its decay into the $\eta$-nucleon channel, of interest to precise tests of hadron models. At the photon point, we determine it to be $(2.2\pm 0.2)\times 10^{-1} GeV^{-1}$ from the old data base, and $(2.2\pm 0.1) \times 10^{-1} GeV^{-1}$ from a combination of old data base and new Bates data. We obtain the helicity amplitude for $N^{*}(1535)\rightarrow \gamma p$ to be $A_{1/2}=(97\pm 7)\times 10^{-3} GeV^{-1/2}$ from the old data base, and $A_{1/2}=(97\pm 6)\times 10^{-3} GeV^{-1/2}$ from the combination of the old data base and new Bates data, compared with the results of the analysis of pion photoproduction yielding $74\pm 11$, in the same units.Comment: 43 pages, RevTeX, 9 figures available upon request, to appear in Phys. Rev.

Perturbative Renormalizations of Anyon Quantum Mechanics

In bosonic end perturbative calculations for quantum mechanical anyon systems a regularization and renormalization procedure, analogous to those used in field theory, is necessary. I examine the reliability and the physical interpretation of the most commonly used bosonic end regularization procedures. I then use the regularization procedure with the most transparent physical interpretation to derive some bosonic end perturbation theory results on anyon spectra, including a 3-anyon ground state energy.Comment: 19 pages, Plain LaTex, MIT-CTP-232

Approach to Perturbative Results in the N-Delta Transition

We show that constraints from perturbative QCD calculations play a role in the nucleon to Delta(1232) electromagnetic transition even at moderate momentum transfer scales. The pQCD constraints, tied to real photoproduction data and unseparated resonance response functions, lead to explicit forms for the helicity amplitudes wherein the E2/M1 ratio remains small at moderately large momentum transfer.Comment: 4 pages, 2 figures, ReVTe

Effects Of The Quantity σTS\sigma_{TS} On The Spin Structure Functions Of Nucleons In The Resonance Region

In this paper, we investigate the effects of the quantity $\sigma_{TS}$ on the spin-structure functions of nucleons in the resonance region. The Schwinger sum rule for the spin structure function $g_2(x,Q^2)$ at the real photon limit is derived for the nucleon treated as a composite system, and it provides a crucial constraint on the longitudinal transition operator which has not been treated consistently in the literature. The longitudinal amplitude $S_{\frac 12}$ is evaluated in the quark model with the transition operator that generates the Schwinger sum rule. The numerical results of the quantity $\sigma_{TS}$ are presented for both spin structure functions $g_1(x,Q^2)$ and $g_2(x,Q^2)$ in the resonance region. Our results show that this quantity plays an important role in the low $Q^2$ region, which can be tested in the future experiments at CEBAF.Comment: 20 pages, latex, 4 postscript figures can be obtained from the autho