35 research outputs found
Quantum cosmology of a classically constrained nonsingular Universe
The quantum cosmological version of a nonsingular Universe presented by
Mukhanov and Brandenberger in the early nineties has been developed and the
Hamilton Jacobi equation has been found under semiclassical (WKB)
approximation. It has been pointed out that, parameterization of classical
trajectories with semiclassical time parameter, for such a classically
constrained system, is a nontrivial task and requires Lagrangian formulation
rather than the Hamiltonian formalism.Comment: 15 page
Entanglement entropy of black holes
The entanglement entropy is a fundamental quantity which characterizes the
correlations between sub-systems in a larger quantum-mechanical system. For two
sub-systems separated by a surface the entanglement entropy is proportional to
the area of the surface and depends on the UV cutoff which regulates the
short-distance correlations. The geometrical nature of the entanglement entropy
calculation is particularly intriguing when applied to black holes when the
entangling surface is the black hole horizon. I review a variety of aspects of
this calculation: the useful mathematical tools such as the geometry of spaces
with conical singularities and the heat kernel method, the UV divergences in
the entropy and their renormalization, the logarithmic terms in the
entanglement entropy in 4 and 6 dimensions and their relation to the conformal
anomalies. The focus in the review is on the systematic use of the conical
singularity method. The relations to other known approaches such as 't Hooft's
brick wall model and the Euclidean path integral in the optical metric are
discussed in detail. The puzzling behavior of the entanglement entropy due to
fields which non-minimally couple to gravity is emphasized. The holographic
description of the entanglement entropy of the black hole horizon is
illustrated on the two- and four-dimensional examples. Finally, I examine the
possibility to interpret the Bekenstein-Hawking entropy entirely as the
entanglement entropy.Comment: 89 pages; an invited review to be published in Living Reviews in
Relativit
Stochastic Gravity: Theory and Applications
Whereas semiclassical gravity is based on the semiclassical Einstein equation
with sources given by the expectation value of the stress-energy tensor of
quantum fields, stochastic semiclassical gravity is based on the
Einstein-Langevin equation, which has in addition sources due to the noise
kernel.In the first part, we describe the fundamentals of this new theory via
two approaches: the axiomatic and the functional. In the second part, we
describe three applications of stochastic gravity theory. First, we consider
metric perturbations in a Minkowski spacetime: we compute the two-point
correlation functions for the linearized Einstein tensor and for the metric
perturbations. Second, we discuss structure formation from the stochastic
gravity viewpoint. Third, we discuss the backreaction of Hawking radiation in
the gravitational background of a quasi-static black hole.Comment: 75 pages, no figures, submitted to Living Reviews in Relativit
Method of analysis of the spatial galaxy distribution at gigaparsec scales. I. Initial principles
Initial principles of a method of analysis of the luminous matter spatial
distribution with sizes about thousands Mpc are presented. The method is based
on an analysis of the photometric redshift distribution N(z) in the deep fields
with large redshift bins \Deltaz=0.1{\div}0.3. Number density fluctuations in
the bins are conditioned by the Poisson's noise, the correlated structures and
the systematic errors of the photo-z determination. The method includes
covering of a sufficiently large region on the sky by a net of the deep
multiband surveys with the sell size about 10^{\circ}x10^{\circ} where
individual deep fields have angular size about 10'x10' and may be observed at
telescopes having diameters 3-10 meters. The distributions of photo-z within
each deep field will give information about the radial extension of the super
large structures while a comparison of the individual radial distributions of
the net of the deep fields will give information on the tangential extension of
the super large structures. A necessary element of the method is an analysis of
possible distortion effects related to the methodic of the photo-z
determination.Comment: 12 page
Stochastic Gravity: Theory and Applications
Whereas semiclassical gravity is based on the semiclassical Einstein equation
with sources given by the expectation value of the stress-energy tensor of
quantum fields, stochastic semiclassical gravity is based on the
Einstein-Langevin equation, which has in addition sources due to the noise
kernel. In the first part, we describe the fundamentals of this new theory via
two approaches: the axiomatic and the functional. In the second part, we
describe three applications of stochastic gravity theory. First, we consider
metric perturbations in a Minkowski spacetime, compute the two-point
correlation functions of these perturbations and prove that Minkowski spacetime
is a stable solution of semiclassical gravity. Second, we discuss structure
formation from the stochastic gravity viewpoint. Third, we discuss the
backreaction of Hawking radiation in the gravitational background of a black
hole and describe the metric fluctuations near the event horizon of an
evaporating black holeComment: 100 pages, no figures; an update of the 2003 review in Living Reviews
in Relativity gr-qc/0307032 ; it includes new sections on the Validity of
Semiclassical Gravity, the Stability of Minkowski Spacetime, and the Metric
Fluctuations of an Evaporating Black Hol
OneG: A Computational Tool for Predicting Cryptic Intermediates in the Unfolding Kinetics of Proteins under Native Conditions
Understanding the relationships between conformations of proteins and their stabilities is one key to address the protein folding paradigm. The free energy change (ΔG) of unfolding reactions of proteins is measured by traditional denaturation methods and native hydrogen-deuterium (H/D) exchange methods. However, the free energy of unfolding (ΔGU) and the free energy of exchange (ΔGHX) of proteins are not in good agreement, though the experimental conditions of both methods are well matching to each other. The anomaly is due to any one or combinations of the following reasons: (i) effects of cis-trans proline isomerisation under equilibrium unfolding reactions of proteins (ii) inappropriateness in accounting the baselines of melting curves (iii) presence of cryptic intermediates, which may elude the melting curve analysis and (iv) existence of higher energy metastable states in the H/D exchange reactions of proteins. Herein, we have developed a novel computational tool, OneG, which accounts the discrepancy between ΔGU and ΔGHX of proteins by systematically accounting all the four factors mentioned above. The program is fully automated and requires four inputs: three-dimensional structures of proteins, ΔGU, ΔGU* and residue-specific ΔGHX determined under EX2-exchange conditions in the absence of denaturants. The robustness of the program has been validated using experimental data available for proteins such as cytochrome c and apocytochrome b562 and the data analyses revealed that cryptic intermediates of the proteins detected by the experimental methods and the cryptic intermediates predicted by the OneG for those proteins were in good agreement. Furthermore, using OneG, we have shown possible existence of cryptic intermediates and metastable states in the unfolding pathways of cardiotoxin III and cobrotoxin, respectively, which are homologous proteins. The unique application of the program to map the unfolding pathways of proteins under native conditions have been brought into fore and the program is publicly available at http://sblab.sastra.edu/oneg.htm
PpiA, a Surface PPIase of the Cyclophilin Family in Lactococcus lactis
Background: Protein folding in the envelope is a crucial limiting step of protein export and secretion. In order to better understand this process in Lactococcus lactis, a lactic acid bacterium, genes encoding putative exported folding factors like Peptidyl Prolyl Isomerases (PPIases) were searched for in lactococcal genomes. Results: In L. lactis, a new putative membrane PPIase of the cyclophilin subfamily, PpiA, was identified and characterized. ppiA gene was found to be constitutively expressed under normal and stress (heat shock, H2O2) conditions. Under normal conditions, PpiA protein was synthesized and released from intact cells by an exogenously added protease, showing that it was exposed at the cell surface. No obvious phenotype could be associated to a ppiA mutant strain under several laboratory conditions including stress conditions, except a very low sensitivity to H2O2. Induction of a ppiA copy provided in trans had no effect i) on the thermosensitivity of an mutant strain deficient for the lactococcal surface protease HtrA and ii) on the secretion and stability on four exported proteins (a highly degraded hybrid protein and three heterologous secreted proteins) in an otherwise wild-type strain background. However, a recombinant soluble form of PpiA that had been produced and secreted in L. lactis and purified from a culture supernatant displayed both PPIase and chaperone activities. Conclusions: Although L. lactis PpiA, a protein produced and exposed at the cell surface under normal conditions, displaye