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

A numerical algorithm for endochronic plasticity and comparison with experiment

A numerical algorithm based on the finite element method of analysis of the boundary value problem in a continuum is presented, in the case where the plastic response of the material is given in the context of endochronic plasticity. The relevant constitutive equation is expressed in incremental form and plastic effects are accounted for by the method of an induced pseudo-force in the matrix equations. The results of the analysis are compared with observed values in the case of a plate with two symmetric notches and loaded longitudinally in its own plane. The agreement between theory and experiment is excellent

The Radio and Gamma-Ray Luminosities of Blazars

Based on the $\gamma$-ray data of blazars in the third EGRET catalog and radio data at 5 GHz, we studied the correlation between the radio and $\gamma$-ray luminosities using two statistical methods. The first method was the partial correlation analysis method, which indicates that there exist correlations between the radio and $\gamma$-ray luminosities in both high and low states as well as in the average case. The second method involved a comparison of expected $\gamma$-ray luminosity distribution with the observed data using the Kolmogorov-- Smirnov (KS) test. In the second method, we assumed that there is a correlation between the radio and $\gamma$-ray luminosities and that the $\gamma$-ray luminosity function is proportional to the radio luminosity function. The KS test indicates that the expected gamma-ray luminosity distributions are consistent with the observed data in a reasonable parameter range. Finally, we used different $\gamma$-ray luminosity functions to estimate the possible 'observed' $\gamma$-ray luminosity distributions by GLAST.Comment: 8 pages, 4 figures, one table, PASJ, 53 (2001

Polarization and Variations of BL Lacertae Objects

BL Lacertae objects are an extreme subclass of AGNs showing rapid and large-amplitude variability, high and variable polarization, and core-dominated radio emissions. If a strong beaming effect is the cause of the extreme observation properties, one would expect that these properties would be correlated with each other. Based on the relativistic beaming model, relationships between the polarization and the magnitude variation in brightness, as well as the core- dominance parameter are derived and used statistically to compare with the observational data of a BL Lacertae object sample. The statistical results are consistent with these correlations, which suggests that the polarization, the variation, and the core-dominance parameter are possible indications of the beaming effect.Comment: 6 pages, two figures, one table, some revisions. PASJ, 53 (2001

Basic properties of Gamma-ray loud blazars

In this paper, a method is proposed to determine the basic properties of $\gamma$-ray loud blazars, among them the central black hole mass, M, the Doppler factor, $\delta$, the propagation angle of the $\gamma$-rays with respect to the symmetric axis of a two-temperature accretion disk, $\Phi$, and the distance (i.e. the height above the accretion disk), d at which the $\gamma$-rays are created, for seven $\gamma$-ray loud blazars with available GeV variability timescales and in which the absorption effect of a $\gamma$-ray and the beaming effect have been taken into account. Our results indicate that, if we take the intrinsic $\gamma$-ray luminosity to be $\lambda$ times the Eddington luminosity, $L_{\gamma}^{in} = \lambda L_{Edd.}$, the masses of the blazars are in the range of $(4 \sim 131)\times 10^{7}M_{\odot}$, the Doppler factors ($\delta$) lie in the range of 0.57 to 5.33 the angle ($\Phi$) is in the range of $13^{\circ}$ to 43$^{\circ}$ and the distance (d) is in the range of 26R_{g} to 411R_{g}. Our model results are independent of $\gamma$-ray emission mechanisms but they do depend on the X-ray emission mechanism of the accretion disk.Comment: 14 pages, 3 tables, A&A accepte

Effects of the complex mass distribution of dark matter halos on weak lensing cluster surveys

Gravitational lensing effects arise from the light ray deflection by all of the mass distribution along the line of sight. It is then expected that weak lensing cluster surveys can provide us true mass-selected cluster samples. With numerical simulations, we analyze the correspondence between peaks in the lensing convergence $\kappa$-map and dark matter halos. Particularly we emphasize the difference between the peak $\kappa$ value expected from a dark matter halo modeled as an isolated and spherical one, which exhibits a one-to-one correspondence with the halo mass at a given redshift, and that of the associated $\kappa$-peak from simulations. For halos with the same expected $\kappa$, their corresponding peak signals in the $\kappa$-map present a wide dispersion. At an angular smoothing scale of $\theta_G=1\hbox{arcmin}$, our study shows that for relatively large clusters, the complex mass distribution of individual clusters is the main reason for the dispersion. The projection effect of uncorrelated structures does not play significant roles. The triaxiality of dark matter halos accounts for a large part of the dispersion, especially for the tail at high $\kappa$ side. Thus lensing-selected clusters are not really mass-selected. (abridged)Comment: ApJ accepte

Quantitative analysis of acetyl-CoA production in hypoxic cancer cells reveals substantial contribution from acetate

Background Cell growth requires fatty acids for membrane synthesis. Fatty acids are assembled from 2-carbon units in the form of acetyl-CoA (AcCoA). In nutrient and oxygen replete conditions, acetyl-CoA is predominantly derived from glucose. In hypoxia, however, flux from glucose to acetyl-CoA decreases, and the fractional contribution of glutamine to acetyl-CoA increases. The significance of other acetyl-CoA sources, however, has not been rigorously evaluated. Here we investigate quantitatively, using 13C-tracers and mass spectrometry, the sources of acetyl-CoA in hypoxia.<p></p> Results In normoxic conditions, cultured cells produced more than 90% of acetyl-CoA from glucose and glutamine-derived carbon. In hypoxic cells, this contribution dropped, ranging across cell lines from 50% to 80%. Thus, under hypoxia, one or more additional substrates significantly contribute to acetyl-CoA production. 13C-tracer experiments revealed that neither amino acids nor fatty acids are the primary source of this acetyl-CoA. Instead, the main additional source is acetate. A large contribution from acetate occurs despite it being present in the medium at a low concentration (50–500 μM).<p></p> Conclusions Acetate is an important source of acetyl-CoA in hypoxia. Inhibition of acetate metabolism may impair tumor growth.<p></p&gt