Aspects of (2+1) dimensional gravity: AdS3 asymptotic dynamics in the framework of Fefferman-Graham-Lee theorems

Using the Chern-Simon formulation of (2+1) gravity, we derive, for the general asymptotic metrics given by the Fefferman-Graham-Lee theorems, the emergence of the Liouville mode associated to the boundary degrees of freedom of (2+1) dimensional anti de Sitter geometries.Comment: 6 pages, Latex, presented at the Journees Relativistes 99, Weimar, September 12-17, 1999; revised version with minor modifications and 1 reference adde

Stochastic noise reduction upon complexification: positively correlated birth-death type systems

Cell systems consist of a huge number of various molecules that display specific patterns of interactions, which have a determining influence on the cell's functioning. In general, such complexity is seen to increase with the complexity of the organism, with a concomitant increase of the accuracy and specificity of the cellular processes. The question thus arises how the complexification of systems - modeled here by simple interacting birth-death type processes - can lead to a reduction of the noise - described by the variance of the number of molecules. To gain understanding of this issue, we investigated the difference between a single system containing molecules that are produced and degraded, and the same system - with the same average number of molecules - connected to a buffer. We modeled these systems using Ito stochastic differential equations in discrete time, as they allow straightforward analytical developments. In general, when the molecules in the system and the buffer are positively correlated, the variance on the number of molecules in the system is found to decrease compared to the equivalent system without a buffer. Only buffers that are too noisy by themselves tend to increase the noise in the main system. We tested this result on two model cases, in which the system and the buffer contain proteins in their active and inactive state, or protein monomers and homodimers. We found that in the second test case, where the interconversion terms are non-linear in the number of molecules, the noise reduction is much more pronounced; it reaches up to 20% reduction of the Fano factor with the parameter values tested in numerical simulations on an unperturbed birth-death model. We extended our analysis to two arbitrary interconnected systems.Comment: 38 pages, 5 figures, to appear in J. Theor. Bio

Optimality of the genetic code with respect to protein stability and amino acid frequencies

How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same amino acid or for a similar one in terms of its biochemical properties, so the structure and function of the coded protein remain relatively unaltered. Previous studies have attempted to address this question more quantitatively, namely by statistically estimating the fraction of randomly generated codes that do better than the genetic code regarding its overall robustness. In this paper, we extend these results by investigating the role of amino acid frequencies in the optimality of the genetic code. When measuring the relative fitness of the natural code with respect to a random code, it is indeed natural to assume that a translation error affecting a frequent amino acid is less favorable than that of a rare one, at equal mutation cost. We find that taking the amino acid frequency into account accordingly decreases the fraction of random codes that beat the natural code, making the latter comparatively even more robust. This effect is particularly pronounced when more refined measures of the amino acid substitution cost are used than hydrophobicity. To show this, we devise a new cost function by evaluating with computer experiments the change in folding free energy caused by all possible single-site mutations in a set of known protein structures. With this cost function, we estimate that of the order of one random code out of 100 millions is more fit than the natural code when taking amino acid frequencies into account. The genetic code seems therefore structured so as to minimize the consequences of translation errors on the 3D structure and stability of proteins.Comment: 31 pages, 2 figures, postscript fil

Noncommutative Locally Anti-de Sitter Black Holes

We give a review of our joint work on strict deformation of BHTZ 2+1 black holes \cite{BRS02,BDHRS03}. However some results presented here are not published elsewhere, and an effort is made for enlightening the instrinsical aspect of the constructions. This shows in particular that the three dimensional case treated here could be generalized to an anti-de Sitter space of arbitrary dimension provided one disposes of a universal deformation formula for the actions of a parabolic subgroup of its isometry group.Comment: 10 pages, based on a talk given by P.B., to appear in the proceedings of the workshop `Noncommutative Geometry and Physics 2004' (Feb. 2004, Keio University, Japan) (World Scientific

Insights into the relation between noise and biological complexity

Understanding under which conditions the increase of systems complexity is evolutionary advantageous, and how this trend is related to the modulation of the intrinsic noise, are fascinating issues of utmost importance for synthetic and systems biology. To get insights into these matters, we analyzed chemical reaction networks with different topologies and degrees of complexity, interacting or not with the environment. We showed that the global level of fluctuations at the steady state, as measured by the sum of the Fano factors of the number of molecules of all species, is directly related to the topology of the network. For systems with zero deficiency, this sum is constant and equal to the rank of the network. For higher deficiencies, we observed an increase or decrease of the fluctuation levels according to the values of the reaction fluxes that link internal species, multiplied by the associated stoichiometry. We showed that the noise is reduced when the fluxes all flow towards the species of higher complexity, whereas it is amplified when the fluxes are directed towards lower complexity species.Comment: 5 pages, 3 figure

BTZ black holes, WZW models and noncommutative geometry

This note is based on a talk given by one of the authors (S. D.) at the "Rencontres Math\'ematiques de Glanon", held in Glanon in July 2004. We will first introduce the BTZ black hole, solution of Einstein's gravity in 2+1 dimensions, and emphasize some remarkable properties of its geometry. We will essentially pay attention to the non-rotating black hole, whose structure is significantly different to the generic case. We will then turn the some aspects of string theory, namely the emergence of non-commutative geometry and the embedding of the BTZ black hole as an exact string background using the Wess-Zumino-Witten (WZW) model. We will show the existence of winding symmetric WZW D1-branes in this space-time from the geometrical properties of the non-rotating black hole. Finally, we will introduce strict deformations of these spaces, yielding an example of non-commutative lorentzian non-compact space, with non-trivial causal structure.Comment: 22pp, 16pp text, 10 figures, to appear in the prooceedings of the "Rencontres math\'ematiques de Glanon", July 200

Star products on extended massive non-rotating BTZ black holes

$AdS_3$ space-time admits a foliation by two-dimensional twisted conjugacy classes, stable under the identification subgroup yielding the non-rotating massive BTZ black hole. Each leaf constitutes a classical solution of the space-time Dirac-Born-Infeld action, describing an open D-string in $AdS_3$ or a D-string winding around the black hole. We first describe two nonequivalent maximal extensions of the non-rotating massive BTZ space-time and observe that in one of them, each D-string worldsheet admits an action of a two-parameter subgroup (\ca \cn) of \SL. We then construct non-formal, \ca \cn-invariant, star products that deform the classical algebra of functions on the D-string worldsheets and on their embedding space-times. We end by giving the first elements towards the definition of a Connes spectral triple on non-commutative $AdS$ space-times.Comment: 25 pages, 1 figur

Uniqueness of the asymptotic AdS3 geometry

We explicitly show that in (2+1) dimensions the general solution of the Einstein equations with negative cosmological constant on a neigbourhood of timelike spatial infinity can be obtained from BTZ metrics by coordinate transformations corresponding geometrically to deformations of their spatial infinity surface. Thus, whatever the topology and geometry of the bulk, the metric on the timelike extremities is BTZ.Comment: LaTeX, 8 pages, no figures, version that will appear in Class. Quant. Gra

The first peptides: the evolutionary transition between prebiotic amino acids and early proteins

The issues we attempt to tackle here are what the first peptides did look like when they emerged on the primitive earth, and what simple catalytic activities they fulfilled. We conjecture that the early functional peptides were short (3 to 8 amino acids long), were made of those amino acids, Gly, Ala, Val and Asp, that are abundantly produced in many prebiotic synthesis experiments and observed in meteorites, and that the neutralization of Asp's negative charge is achieved by metal ions. We further assume that some traces of these prebiotic peptides still exist, in the form of active sites in present-day proteins. Searching these proteins for prebiotic peptide candidates led us to identify three main classes of motifs, bound mainly to Mg^{2+} ions: D(F/Y)DGD corresponding to the active site in RNA polymerases, DGD(G/A)D present in some kinds of mutases, and DAKVGDGD in dihydroxyacetone kinase. All three motifs contain a DGD submotif, which is suggested to be the common ancestor of all active peptides. Moreover, all three manipulate phosphate groups, which was probably a very important biological function in the very first stages of life. The statistical significance of our results is supported by the frequency of these motifs in today's proteins, which is three times higher than expected by chance, with a P-value of 3 10^{-2}. The implications of our findings in the context of the appearance of life and the possibility of an experimental validation are discussed.Comment: 22 pages, 2 figures, J. Theor. Biol. (2009) in pres