Disorder in DNA-Linked Gold Nanoparticle Assemblies

We report experimental observations on the effect of disorder on the phase behavior of DNA-linked nanoparticle assemblies. Variation in DNA linker lengths results in different melting temperatures of the DNA-linked nanoparticle assemblies. We observed an unusual trend of a non-monotonic ``zigzag'' pattern in the melting temperature as a function of DNAlinker length. Linker DNA resulting in unequal DNA duplex lengths introduces disorder and lowers the melting temperature of the nanoparticle system. Comparison with free DNA thermodynamics shows that such an anomalous zigzag pattern does not exist for free DNA duplex melting, which suggests that the disorder introduced by unequal DNA duplex lengths results in this unusual collective behavior of DNA-linked nanoparticle assemblies.Comment: 4 pages, 4 figures, Phys.Rev.Lett. (2005), to appea

Peptide Mimicrying Between SARS Coronavirus Spike Protein and Human Proteins Reacts with SARS Patient Serum

Molecular mimicry, defined as similar structures shared by molecules from dissimilar genes or proteins, is a general strategy used by pathogens to infect host cells. Severe acute respiratory syndrome (SARS) is a new human respiratory infectious disease caused by SARS coronavirus (SARS-CoV). The spike (S) protein of SARS-CoV plays an important role in the virus entry into a cell. In this study, eleven synthetic peptides from the S protein were selected based on its sequence homology with human proteins. Two of the peptides D07 (residues 927–937) and D08 (residues 942–951) were recognized by the sera of SARS patients. Murine hyperimmune sera against these peptides bound to proteins of human lung epithelial cells A549. Another peptide D10 (residues 490–502) stimulated A549 to proliferate and secrete IL-8. The present results suggest that the selected S protein regions, which share sequence homology with human proteins, may play important roles in SARS-CoV infection

Enhanced J/psi suppression due to gluon depletion

The nonlinear effect of gluon depletion in the collision of large nuclei can be large. It is due to multiple scatterings among comoving partons initiated by primary scattering of partons in the colliding nuclei. The effect can give rise to substantial suppression of $J/\psi$ production in very large nuclei, even if the linear depletion effect is insignificant for the collisions of nuclei of smaller sizes. This mechanism offers a natural explanation of the enhanced suppression in the Pb-Pb data recently observed by NA50.Comment: 6 pages + 2 figures (in ps file), LaTex, submitted to Phys. Rev. Let

Disorder-Induced Depinning Transition

The competition in the pinning of a directed polymer by a columnar pin and a background of random point impurities is investigated systematically using the renormalization group method. With the aid of the mapping to the noisy-Burgers' equation and the use of the mode-coupling method, the directed polymer is shown to be marginally localized to an arbitrary weak columnar pin in 1+1 dimensions. This weak localization effect is attributed to the existence of large scale, nearly degenerate optimal paths of the randomly pinned directed polymer. The critical behavior of the depinning transition above 1+1 dimensions is obtained via an $\epsilon$-expansion.Comment: 47 pages in revtex; postscript files of 6 figures include

Recombination Models

We review the current status of recombination and coalescence models that have been successfully applied to describe hadronization in heavy ion collisions at RHIC energies. Basic concepts as well as actual implementations of the idea are discussed. We try to evaluate where we stand in our understanding at the moment and what remains to be done in the future.Comment: Plenary Talk at Quark Matter 2004, submitted to J. Phys. G, 8 pages, 3 figure

Phase Diagram for Splay Glass Superconductivity

Localization of flux lines to splayed columnar pins is studied. A sine-Gordon type renormalization group study reveals the existence of a Splay glass phase and yields an analytic form for the transition temperature into the glass phase. As an independent test, the $I-V$ characteristics are determined via a Molecular Dynamics code. The glass transition temperature supports the RG results convincingly. The full phase diagram of the model is constructed.Comment: 14 pages, uuencoded compressed tar file with 3 postscript figure

A variational study of the random-field XY model

A disorder-dependent Gaussian variational approach is applied to the $d$-dimensional ferromagnetic XY model in a random field. The randomness yields a non extensive contribution to the variational free energy, implying a random mass term in correlation functions. The Imry-Ma low temperature result, concerning the existence ($d>4$) or absence ($d < 4$) of long-range order is obtained in a transparent way. The physical picture which emerges below $d=4$ is that of a marginally stable mixture of domains. We also calculate within this variational scheme, disorder dependent correlation functions, as well as the probability distribution of the Imry-Ma domain size.Comment: 14 pages, latex fil

On the optical properties of Ag^{+15} ion-beam irradiated TiO_{2} and SnO_{2} thin films

The effects of 200-MeV Ag^{+15} ion irradiation on the optical properties of TiO_{2} and SnO_{2} thin films prepared by using the RF magnetron sputtering technique were investigated. These films were characterized by using UV-vis spectroscopy, and with increasing irradiation fluence, the transmittance for the TiO_{2} films was observed to increase systematically while that for SnO_{2} was observed to decrease. Absorption spectra of the irradiated samples showed minor changes in the indirect bandgap from 3.44 to 3.59 eV with increasing irradiation fluence for TiO_{2} while significant changes in the direct bandgap from 3.92 to 3.6 eV were observed for SnO_{2}. The observed modifications in the optical properties of both the TiO_{2} and the SnO_{2} systems with irradiation can be attributed to controlled structural disorder/defects in the system.Comment: 6 pages, ICAMD-201

Heterogeneous nuclear ribonucleoprotein A1 regulates rhythmic synthesis of mouse Nfil3 protein via IRES-mediated translation.

Nuclear factor, interleukin 3, regulated (Nfil3, also known as E4 Promoter-Binding Protein 4 (E4BP4)) protein is a transcription factor that binds to DNA and generally represses target gene expression. In the circadian clock system, Nfil3 binds to a D-box element residing in the promoter of clock genes and contributes to their robust oscillation. Here, we show that the 5&apos;-untranslated region (5&apos;-UTR) of Nfil3 mRNA contains an internal ribosome entry site (IRES) and that IRES-mediated translation occurs in a phase-dependent manner. We demonstrate that heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) binds to a specific region of Nfil3 mRNA and regulates IRES-mediated translation. Knockdown of hnRNP A1 almost completely abolishes protein oscillation without affecting mRNA oscillation. Moreover, we observe that intracellular calcium levels, which are closely related to bone formation, depend on Nfil3 levels in osteoblast cell lines. We suggest that the 5&apos;-UTR mediated cap-independent translation of Nfil3 mRNA contributes to the rhythmic expression of Nfil3 by interacting with the RNA binding protein hnRNP A1. These data provide new evidence that the posttranscriptional regulation of clock gene expression is important during bone metabolism.1131Ysciescopu

Anomalous Fluctuations of Directed Polymers in Random Media

A systematic analysis of large scale fluctuations in the low temperature pinned phase of a directed polymer in a random potential is described. These fluctuations come from rare regions with nearly degenerate ``ground states''. The probability distribution of their sizes is found to have a power law tail. The rare regions in the tail dominate much of the physics. The analysis presented here takes advantage of the mapping to the noisy-Burgers' equation. It complements a phenomenological description of glassy phases based on a scaling picture of droplet excitations and a recent variational approach with ``broken replica symmetry''. It is argued that the power law distribution of large thermally active excitations is a consequence of the continuous statistical ``tilt'' symmetry of the directed polymer, the breaking of which gives rise to the large active excitations in a manner analogous to the appearance of Goldstone modes in pure systems with a broken continuous symmetry.Comment: 59 pages including 8 figures ( REVTEX 3.0 )E-mail: [email protected]