Modeling two-state cooperativity in protein folding

A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical characteristics and free energy profile show a well-defined two-state behavior and cooperativity of folding for such a model. As a comparison, related simulations for the usual G\={o} model, where the interaction energies are independent of the local conformations, are also made. Our results indicate that the evolution of interactions during the folding process plays an important role in the two-state cooperativity in protein folding.Comment: 5 figure

Electronic bandstructure and optical gain of lattice matched III-V dilute nitride bismide quantum wells for 1.55 μ\mum optical communication systems

Dilute nitride bismide GaNBiAs is a potential semiconductor alloy for near- and mid-infrared applications, particularly in 1.55 $\mu$m optical communication systems. Incorporating dilute amounts of Bismuth (Bi) into GaAs reduces the effective bandgap rapidly, while significantly increasing the spin-orbit-splitting energy. Additional incorporation of dilute amounts of Nitrogen (N) helps to attain lattice matching with GaAs, while providing a route for flexible bandgap tuning. Here we present a study of the electronic bandstructure and optical gain of the lattice matched GaN$_x$Bi$_y$As$_{1-x-y}$/GaAs quaternary alloy quantum well (QW) based on the 16-band k$\cdot$p model. We have taken into consideration the interactions between the N and Bi impurity states with the host material based on the band anticrossing (BAC) and valence band anticrossing (VBAC) model. The optical gain calculation is based on the density matrix theory. We have considered different lattice matched GaNBiAs QW cases and studied their energy dispersion curves, optical gain spectrum, maximum optical gain and differential gain; and compared their performances based on these factors. The thickness and composition of these QWs were varied in order to keep the emission peak fixed at 1.55 $\mu$m. The well thickness has an effect on the spectral width of the gain curves. On the other hand, a variation in the injection carrier density has different effects on the maximum gain and differential gain of QWs of varying thicknesses. Among the cases studied, we found that the 6.3 nm thick GaN$_3$Bi$_{5.17}$As$_{91.83}$ lattice matched QW was most suited for 1.55 $\mu$m (0.8 eV) GaAs-based photonic applications.Comment: Accepted in AIP Journal of Applied Physic

Air-snow exchange of HNO3 and NOy at Summit, Greenland

Ice core records of NO3− deposition to polar glaciers could provide unrivaled information on past photochemical status and N cycling dynamics of the troposphere, if the ice core records could be inverted to yield concentrations of reactive N oxides in the atmosphere at past times. Limited previous investigations at Summit, Greenland, have suggested that this inversion may be difficult, since the levels of HNO3 and aerosol-associated NO3− over the snow are very low in comparison with those of NO3− in the snow. In addition, it appears that some fraction of the NO3− in snow may be reemitted to the atmosphere after deposition. Here we report on extensive measurements of HNO3, including vertical gradients between 1.5 and 7 m above the snow, made during the summers of 1994 and 1995 at Summit. These HNO3 data are compared with NO3− concentrations in surface snow and the first measurements of the concentrations and fluxes of total reactive nitrogen oxides (Ny) on a polar glacier. Our results confirm that HNO3 concentrations are quite low (mean 0.5 nmol m−3) during the summer, while NO3− is the dominant ion in snow. Daytime peaks in HNO3− appear to be due at least partly to emissions from the snow, an assertion supported by gradients indicating a surface source for HNO3− on many days. Observed short-term increases in NO3− inventory in the snow can be too large to be readily attributed to deposition of HNO3− suggesting that deposition of one or more other N oxides must be considered. We found that the apparent fluxes of HNO3 and NOy were in opposite directions during about half the intervals when both were measured, with more cases of HNO3 leaving the snow, against an NOy flux into the snow, than the reverse. The concentrations of NOy are generally about 2 orders of magnitude greater than those of HNO3; hence deposition of only a small, non-HNO3, fraction of this pool could dominate NO3− in snow, if the depositing species converted to NO3−, either in the snowpack or upon melting for analysis

Inversion formula and Parsval theorem for complex continuous wavelet transforms studied by entangled state representation

In a preceding Letter (Opt. Lett. 32, 554 (2007)) we have proposed complex continuous wavelet transforms (CCWTs) and found Laguerre--Gaussian mother wavelets family. In this work we present the inversion formula and Parsval theorem for CCWT by virtue of the entangled state representation, which makes the CCWT theory complete. A new orthogonal property of mother wavelet in parameter space is revealed.Comment: 4 pages no figur

Concentrations and snow-atmosphere fluxes of reactive nitrogen at Summit, Greenland

Concentrations and fluxes of NOy (total reactive nitrogen), ozone concentrations and fluxes of sensible heat, water vapor, and momentum were measured from May 1 to July 20, 1995 at Summit, Greenland. Median NOy concentrations declined from 947 ppt in May to 444 ppt by July. NOy fluxes were observed into and out of the snow, but the magnitudes were usually below 1 μmol m−2 h−1 because of the low HNO3 concentration and weak turbulence over the snow surface. Some of the highest observed fluxes may be due to temporary storage by equilibrium sorption of peroxyacetylnitrate (PAN) or other organic nitrogen species on ice surfaces in the upper snowpack. Sublimation of snow at the surface or during blowing snow events is associated with efflux of NOy from the snowpack. Because the NOy fluxes during summer at Summit are bidirectional and small in magnitude, the net result of turbulent NOyexchange is insignificant compared to the 2 μmol m−2 d−1 mean input from fresh snow during the summer months. If the arctic NOy reservoir is predominantly PAN (or compounds with similar properties), thermal dissociation of this NOy is sufficient to support the observed flux of nitrate in fresh snow. Very low HNO3 concentrations in the surface layer (1% of total NOy) reflect the poor ventilation of the surface layer over the snowpack combined with the relatively rapid uptake of HNO3 by fog, falling snow, and direct deposition to the snowpack

High energy neutrino early afterglows from gamma-ray bursts revisited

The high energy neutrino emission from gamma-ray bursts (GRBs) has been expected in various scenarios. In this paper, we study the neutrino emission from early afterglows of GRBs, especially under the reverse-forward shock model and late prompt emission model. In the former model, the early afterglow emission occurs due to dissipation made by an external shock with the circumburst medium (CBM). In the latter model, internal dissipation such as internal shocks produces the shallow decay emission in early afterglows. We also discuss implications of recent Swift observations for neutrino signals in detail. Future neutrino detectors such as IceCube may detect neutrino signals from early afterglows, especially under the late prompt emission model, while the detection would be difficult under the reverse-forward shock model. Contribution to the neutrino background from the early afterglow emission may be at most comparable to that from the prompt emission unless the outflow making the early afterglow emission loads more nonthermal protons, and it may be important in the very high energies. Neutrino-detections are inviting because they could provide us with not only information on baryon acceleration but also one of the clues to the model of early afterglows. Finally, we compare various predictions for the neutrino background from GRBs, which are testable by future neutrino-observations.Comment: 18 pages, 12 figures, accepted for publication in PR