1,721,545 research outputs found
Conformational changes of neuromedin B and delta sleep-inducing peptide induced by their interaction with lipid membranes as revealed by spectroscopic techniques and molecular dynamics simulation.
No full textStatic and dynamic spectroscopic properties of the tryptophanil emission in conjunction with circular dichroism (CD) spectroscopy and molecular dynamics are used to investigate the interactions of the neuropeptide neuromedin B (NMB) and the membrane-permeable δ sleep-inducing peptide (DSIP) with the membrane lipid phase. Our data indicate that in solution both peptides exist in energetically equivalent conformations, whereas in the presence of the membrane specific conformational states are stabilized. By changing from the aqueous to the lipid phase, the static and the dynamic fluorescence properties of the NMB's tryptophan residue are clearly affected: the fluorescence steady-state spectrum as well as the resolved fluorescence decay-associated spectra (DAS) are shifted to the blue with a significant increase of the fluorescence intensity of the second lifetime component (τ2-DAS). On the other hand, in the lipid environment the same parameters of DSIP are negligibly affected as compared to the aqueous buffer. The CD and molecular dynamics analyses are consistent with these results and indicate that, while NMB assumes a helix-like conformation with the tryptophan residue in the apolar surface, DSIP adopts a globule-like structure with the indole ring that is surface-exposed. As previously found for neuromedin C (Polverini, E., Neyroz, P., Fariselli, P., Casadio, R., and Masotti, L., Biochem. Biophys. Res. Commun. 214, 663-668, 1995), for NMB the stabilized 'lipophilic' structure also may favor the correct peptide-receptor contact and recognition. For DSIP, the lipid-stabilized conformation does not support an amphiphilic structure-driven peptide-membrane interaction and suggests a hydrophobicity-driven diffusion across the bilayer
On dispersion relations and the statistical mechanics of Hawking radiation
No full textWe analyse the interplay between dispersion relations for the spectrum of Hawking quanta and the statistical mechanics of such a radiation. We first find the general relation between the occupation number density and the energy spectrum of Hawking quanta and then study several cases in detail. We show that both the canonical and the microcanonical picture of the evaporation lead to the same linear dispersion relation for relatively large black holes. We also compute the occupation number obtained instead by assuming that the spectrum levels out (and eventually falls to zero) for very large momenta and show that the luminosity of black holes is not appreciably affected by the modified statistics
Hamiltonian formalism for the Oppenheimer-Snyder model
No full textAn effective action in Hamiltonian form is derived for a self-gravitating sphere of isotropic homogeneous dust. Starting from the Einstein-Hilbert action for baryotropic perfect fluids and making use of the symmetry and equation of state of the matter distribution we obtain a family of reduced actions for two canonical variables, namely, the radius of the sphere and its ADM energy, the latter being conserved along trajectories of the former. These actions differ by the value of the (conserved) geodesic energy of the radius of the sphere which defines (disconnected) classes of solutions in correspondence to the inner geometry and proper volume of the sphere. By replacing the (fixed) geodesic energy with its expression in terms of the Schwarzschild time at the surface of the sphere and treating the latter as a further canonical variable we finally obtain an extended action which covers the full space of solutions. Generalization to the (inhomogeneous) Tolman model is shown to be straightforward. Quantization is also discussed. © 1998 The American Physical Society
On brane-world black holes and short scale physics
No full textThere is evidence that trans-Planckian physics does not affect the Hawking radiation in four dimensions and, consequently, deviations from the linear dispersion relation (for massless particles) at very high energies cannot be revealed using four-dimensional black holes. We study this issue in the context of models with extra-spatial dimensions and show that small black holes that could be produced in accelerators might also provide a chance of testing the high energy regime where non-linear dispersion relations are generally expected. © 2003 Elsevier Science (USA). All rights reserved
BLACK HOLES: A WINDOW INTO STRONG (QUANTUM?) GRAVITY
No full textBlack holes are regions of space-time where gravity becomes so strong to confine everything. Their classical general relativistic description however shows critical aspects when faced with the established quantum nature of matter. Alternative approaches and descriptions, like the horizon quantum mechanics and corpuscular models, have therefore been proposed in order to investigate their quantum structure, and search for new phenomenological signatures
QUANTUM ROTATING BLACK HOLES (RECOVERING GEOMETRY IN A QUANTUM WORLD)
No full textClassical geometries for spherically symmetric systems can be effectively obtained from quantum coherent states for the relevant degrees of freedom. This description replaces the classical singularity of black holes with integrable structures in which tidal forces remain finite, and there is no inner Cauchy horizon. It is then shown how the extension to rotating systems can avoid the classical inner horizon provided the rotation is not ultra-rigid
Topology prediction for helical transmembrane proteins at 86% accuracy
No full textPreviously, we introduced a neural network system predicting locations of transmembrane helices (HTMs) based on evolutionary profiles (PHDhtm, Rest B, Casadio R, Fariselli P, Sander C, 1995, Protein Sci 4:521-533). Here, we describe an improvement and an extension of that system. The improvement is achieved by a dynamic programming-like algorithm that optimizes helices compatible with the neural network output. The extension is the prediction of topology (orientation of first loop region with respect to membrane) by applying to the refined prediction the observation that positively charged residues are more abundant in extra-cytoplasmic regions. Furthermore, we introduce a method to reduce the number of false positives, i.e., proteins falsely predicted with membrane helices. The evaluation of prediction accuracy is based on a cross-validation and a double-blind test set (in total 131 proteins). The final method appears to be more accurate than other methods published: (1) For almost 89% (+/-3%) of the test proteins, all HTMs are predicted correctly. (2) For more than 86% (+/-3%) of the proteins, topology is predicted correctly. (3) We define reliability indices that correlate with prediction accuracy: for one half of the proteins, segment accuracy raises to 98%; and for two-thirds, accuracy of topology prediction is 95%. (4) The rate of proteins for which HTMs are predicted falsely is below 2% (+/-1%). Finally, the method is applied to 1,616 sequences of Haemophilus influenzae. We predict 19% of the genome sequences to contain one or more HTMs. This appears to be lower than what we predicted previously for the yeast VIII chromosome (about 25%)
On gravitational fluctuations and the semiclassical limit in minisuperspace models
No full textAn attempt is made to go beyond the semiclassical approximation for gravity in the Born-Oppenheimer decomposition of the wave-function in minisuperspace. New terms are included which correspond to quantum gravitational fluctuations on the background metric. They induce a back-reaction on the semiclassical background and can lead to the avoidance of the singularities the classical theory predicts in cosmology and in the gravitational collapse of compact objects
On time evolution of quantum black holes
No full textThe time evolution of black holes involves both the canonical equations of quantum gravity and the statistical mechanics of Hawking radiation, neither of which contains a time variable. In order to introduce the time, we apply the semiclassical approximation to the Hamiltonian constraint on the apparent horizon and show that, when the backreaction is included, it suggests the existence of a long-living remnant, similarly to what is obtained in the microcanonical picture for the Hawking radiation. © 2001 Elsevier Science B.V
Gravitational tests of the generalized uncertainty principle
Full text linkWe compute the corrections to the Schwarzschild metric necessary to reproduce the Hawking temperature derived from a generalized uncertainty principle (GUP), so that the GUP deformation parameter is directly linked to the deformation of the metric. Using this modified Schwarzschild metric, we compute corrections to the standard general relativistic predictions for the light deflection and perihelion precession, both for planets in the solar system and for binary pulsars. This analysis allows us to set bounds for the GUP deformation parameter from well-known astronomical measurements
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