Calculating Biological Behaviors of Epigenetic States in Phage lambda Life Cycle

Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function. However, its stability and robustness for both wild type and mutants has been a notorious theoretical/mathematical problem. In this paper we report our successful calculation on the properties of this gene regulatory network. We believe it is of its first kind. Our success is of course built upon numerous previous theoretical attempts, but following 3 features make our modeling uniqu: 1) A new modeling method particular suitable for stability and robustness study; 2) Paying a close attention to the well-known difference of in vivo and in vitro; 3) Allowing more important role for noise and stochastic effect to play. The last two points have been discussed by two of us (Ao and Yin, cond-mat/0307747), which we believe would be enough to make some of previous theoretical attempts successful, too. We hope the present work would stimulate a further interest in the emerging field of gene regulatory network.Comment: 16 pages, 3 figures, 1 tabl

Scanning Tunneling Spectroscopy and Vortex Imaging in the Iron-Pnictide Superconductor BaFe1.8_{1.8}Co0.2_{0.2}As2_2

We present an atomic resolution scanning tunneling spectroscopy study of superconducting BaFe$_{1.8}$Co$_{0.2}$As$_2$ single crystals in magnetic fields up to $9 \text{Tesla}$. At zero field, a single gap with coherence peaks at $\overline{\Delta}=6.25 \text{meV}$ is observed in the density of states. At $9 \text{T}$ and $6 \text{T}$, we image a disordered vortex lattice, consistent with isotropic, single flux quantum vortices. Vortex locations are uncorrelated with strong scattering surface impurities, demonstrating bulk pinning. The vortex-induced sub-gap density of states fits an exponential decay from the vortex center, from which we extract a coherence length $\xi=27.6\pm 2.9 \text{\AA}$, corresponding to an upper critical field $H_{c2}=43 \text{T}$.Comment: 4 pages, 4 figure

Proximity and anomalous field-effect characteristics in double-wall carbon nanotubes

Proximity effect on field-effect characteristic (FEC) in double-wall carbon nanotubes (DWCNTs) is investigated. In a semiconductor-metal (S-M) DWCNT, the penetration of electron wavefunctions in the metallic shell to the semiconducting shell turns the original semiconducting tube into a metal with a non-zero local density of states at the Fermi level. By using a two-band tight-binding model on a ladder of two legs, it is demonstrated that anomalous FEC observed in so-called S-M type DWCNTs can be fully understood by the proximity effect of metallic phases.Comment: 4 pages, 4 figure

Dinitrosyl formation as an intermediate stage of the reduction of NO in the presence of MoO_3

We present first-principles calculations in the framework of density-functional theory and the pseudopotential approach, aiming to model the intermediate stages of the reduction of NO in the presence of MoO$_3$(010). In particular, we study the formation of dinitrosyl, which proves to be an important intermediate stage in the catalytic reduction. We find that the replacement of an oxygen of MoO$_3$ by NO is energetically favorable, and that the system lowers further its energy by the formation of (NO)$_2$. Moreover, the geometry and charge distribution for the adsorbed dinitrosyl indicates a metal-oxide mediated coupling between the two nitrogen and the two oxygen atoms. We discuss the mechanisms for the dinitrosyl formation and the role of the oxide in the reaction.Comment: 6 pages, 4 figs, RevTeX. To be published in J. Chem. Phy

The correlations between the twin kHz QPO frequencies of LMXBs

We analyzed the recently published kHz QPO data in the neutron star low-mass X-ray binaries (LMXBs), in order to investigate the different correlations of the twin peak kilohertz quasi-eriodic oscillations (kHz QPOs) in bright Z sources and in the less luminous Atoll sources. We find that a power-law relation \no\sim\nt^{b} between the upper and the lower kHz QPOs with different indices: $b\simeq$1.5 for the Atoll source 4U 1728-34 and $b\simeq$1.9 for the Z source Sco X-1. The implications of our results for the theoretical models for kHz QPOs are discussed.Comment: 6 pages, accepted by MNRA