The logic of metabolism and its fuzzy consequences

Intermediary metabolism molecules are orchestrated into logical pathways stemming from history (L-amino acids, D-sugars) and dynamic constraints (hydrolysis of pyrophosphate or amide groups is the driving force of anabolism). Beside essential metabolites, numerous variants derive from programmed or accidental changes. Broken down, variants enter standard pathways, producing further variants. Macromolecule modification alters enzyme reactions specificity. Metabolism conform thermodynamic laws, precluding strict accuracy. Hence, for each regular pathway, a wealth of variants inputs and produces metabolites that are similar to but not the exact replicas of core metabolites. As corollary, a shadow, paralogous metabolism, is associated to standard metabolism. We focus on a logic of paralogous metabolism based on diversion of the core metabolic mimics into pathways where they are modified to minimize their input in the core pathways where they create havoc. We propose that a significant proportion of paralogues of well-characterized enzymes have evolved as the natural way to cope with paralogous metabolites. A second type of denouement uses a process where protecting/deprotecting unwanted metabolites - conceptually similar to the procedure used in the laboratory of an organic chemist - is used to enter a completely new catabolic pathway

Existence of global strong solutions in critical spaces for barotropic viscous fluids

This paper is dedicated to the study of viscous compressible barotropic fluids in dimension $N\geq2$. We address the question of the global existence of strong solutions for initial data close from a constant state having critical Besov regularity. In a first time, this article show the recent results of \cite{CD} and \cite{CMZ} with a new proof. Our result relies on a new a priori estimate for the velocity, where we introduce a new structure to \textit{kill} the coupling between the density and the velocity as in \cite{H2}. We study so a new variable that we call effective velocity. In a second time we improve the results of \cite{CD} and \cite{CMZ} by adding some regularity on the initial data in particular $\rho_{0}$ is in $H^{1}$. In this case we obtain global strong solutions for a class of large initial data on the density and the velocity which in particular improve the results of D. Hoff in \cite{5H4}. We conclude by generalizing these results for general viscosity coefficients

On the global well-posedness for the Boussinesq system with horizontal dissipation

In this paper, we investigate the Cauchy problem for the tridimensional Boussinesq equations with horizontal dissipation. Under the assumption that the initial data is an axisymmetric without swirl, we prove the global well-posedness for this system. In the absence of vertical dissipation, there is no smoothing effect on the vertical derivatives. To make up this shortcoming, we first establish a magic relationship between $\frac{u^{r}}{r}$ and $\frac{\omega_\theta}{r}$ by taking full advantage of the structure of the axisymmetric fluid without swirl and some tricks in harmonic analysis. This together with the structure of the coupling of \eqref{eq1.1} entails the desired regularity.Comment: 32page

The metIC operon involved in methionine biosynthesis in Bacillus subtilis is controlled by transcription antitermination

There are two major pathways for methionine biosynthesis in micro-organisms. Little is known about these pathways in Bacillus subtilis. The authors assigned a function to the metI (formerly yjcI) and metC (formerly yjcJ) genes of B. subtilis by complementing Escherichia coli metB and metC mutants, analysing the phenotype of B. subtilis metI and metC mutants, and carrying out enzyme activity assays. These genes encode polypeptides belonging to the cystathionine -synthase family of proteins. Interestingly, the MetI protein has both cystathionine -synthase and O-acetylhomoserine thiolyase activities, whereas the MetC protein is a cystathionine ß-lyase. In B. subtilis, the transsulfuration and the thiolation pathways are functional in vivo. Due to its dual activity, the MetI protein participates in both pathways. The metI and metC genes form an operon, the expression of which is subject to sulfur-dependent regulation. When the sulfur source is sulfate or cysteine the transcription of this operon is high. Conversely, when the sulfur source is methionine its transcription is low. An S-box sequence, which is located upstream of the metI gene, is involved in the regulation of the metIC operon. Northern blot experiments demonstrated the existence of two transcripts: a small transcript corresponding to the premature transcription termination at the terminator present in the S-box and a large one corresponding to transcription of the complete metIC operon. When methionine levels were limiting, the amount of the full-length transcript increased. These results substantiate a model of regulation by transcription antitermination.published_or_final_versio

On the global well-posedness of a class of Boussinesq- Navier-Stokes systems

In this paper we consider the following 2D Boussinesq-Navier-Stokes systems \partial_{t}u+u\cdot\nabla u+\nabla p+ |D|^{\alpha}u &= \theta e_{2} \partial_{t}\theta+u\cdot\nabla \theta+ |D|^{\beta}\theta &=0 \quad with $\textrm{div} u=0$ and $0<\beta<\alpha<1$. When $\frac{6-\sqrt{6}}{4}<\alpha< 1$, $1-\alpha<\beta\leq f(\alpha)$, where $f(\alpha)$ is an explicit function as a technical bound, we prove global well-posedness results for rough initial data.Comment: 23page

On the Cauchy problem for a nonlinearly dispersive wave equation

We establish the local well-posedness for a new nonlinearly dispersive wave equation and we show that the equation has solutions that exist for indefinite times as well as solutions which blowup in finite times. Furthermore, we derive an explosion criterion for the equation and we give a sharp estimate from below for the existence time of solutions with smooth initial data.Comment: arxiv version is already officia

From Analog to Digital Computing: Is Homo sapiens’ Brain on Its Way to Become a Turing Machine?

The abstract basis of modern computation is the formal description of a finite state machine, the Universal Turing Machine, based on manipulation of integers and logic symbols. In this contribution to the discourse on the computer-brain analogy, we discuss the extent to which analog computing, as performed by the mammalian brain, is like and unlike the digital computing of Universal Turing Machines. We begin with ordinary reality being a permanent dialog between continuous and discontinuous worlds. So it is with computing, which can be analog or digital, and is often mixed. The theory behind computers is essentially digital, but efficient simulations of phenomena can be performed by analog devices; indeed, any physical calculation requires implementation in the physical world and is therefore analog to some extent, despite being based on abstract logic and arithmetic. The mammalian brain, comprised of neuronal networks, functions as an analog device and has given rise to artificial neural networks that are implemented as digital algorithms but function as analog models would. Analog constructs compute with the implementation of a variety of feedback and feedforward loops. In contrast, digital algorithms allow the implementation of recursive processes that enable them to generate unparalleled emergent properties. We briefly illustrate how the cortical organization of neurons can integrate signals and make predictions analogically. While we conclude that brains are not digital computers, we speculate on the recent implementation of human writing in the brain as a possible digital path that slowly evolves the brain into a genuine (slow) Turing machine