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Search Results: 1 - 10 of 231410 matches for " Eric C. Martens "
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Influence of flux balance on the generalized chemical potential in mass transport models
Kirsten Martens,Eric Bertin
Statistics , 2011, DOI: 10.1088/1742-5468/2011/09/P09012
Abstract: In equilibrium systems, the conservation of the number of particles (or mass) leads to the equalization of the chemical potential throughout the system. Using a non-equilibrium generalization of the notion of chemical potential, we investigate the influence of disorder and of the balance of mass fluxes on the generalized chemical potential in the framework of stochastic mass transport models. We focus specifically on the issue of local mesurements of the chemical potential. We find that while local dynamical disorder does not affect the measurement process, the presence of large-scale geometrical heterogeneities (branching geometry) leads to unequal local measurement results in different points of the system. We interpret these results in terms of mass flux balance, and argue that the conditions for the global definition of the chemical potential still hold, but that local measurements fail to capture the global theoretical value.
Dependence of the fluctuation-dissipation temperature on the choice of observable
Kirsten Martens,Eric Bertin,Michel Droz
Physics , 2009, DOI: 10.1103/PhysRevLett.103.260602
Abstract: On general grounds, a nonequilibrium temperature can be consistently defined from generalized fluctuation-dissipation relations only if it is independent of the observable considered. We argue that the dependence on the choice of observable generically occurs when the phase-space probability distribution is non-uniform on constant energy shells. We relate quantitatively this observable dependence to a fundamental characteristics of nonequilibrium systems, namely the Shannon entropy difference with respect to the equilibrium state with the same energy. This relation is illustrated on a mean-field model in contact with two heat baths at different temperatures.
Entropy-based characterizations of the observable-dependence of the fluctuation-dissipation temperature
Kirsten Martens,Eric Bertin,Michel Droz
Physics , 2010, DOI: 10.1103/PhysRevE.81.061107
Abstract: The definition of a nonequilibrium temperature through generalized fluctuation-dissipation relations relies on the independence of the fluctuation-dissipation temperature from the observable considered. We argue that this observable independence is deeply related to the uniformity of the phase-space probability distribution on the hypersurfaces of constant energy. This property is shown explicitly on three different stochastic models, where observable-dependence of the fluctuation-dissipation temperature arises only when the uniformity of the phase-space distribution is broken. The first model is an energy transport model on a ring, with biased local transfer rules. In the second model, defined on a fully connected geometry, energy is exchanged with two heat baths at different temperatures, breaking the uniformity of the phase-space distribution. Finally, in the last model, the system is connected to a zero temperature reservoir, and preserves the uniformity of the phase-space distribution in the relaxation regime, leading to an observable-independent temperature.
Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts
Eric C. Martens,Elisabeth C. Lowe,Herbert Chiang,Nicholas A. Pudlo,Meng Wu,Nathan P. McNulty,D. Wade Abbott,Bernard Henrissat,Harry J. Gilbert,David N. Bolam,Jeffrey I. Gordon
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1001221
Abstract: Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in the adult gut, possess broad glycan-degrading abilities. These species use a series of membrane protein complexes, termed Sus-like systems, for catabolism of many complex carbohydrates. However, the role of these systems in degrading the chemically diverse repertoire of plant cell wall glycans remains unknown. Here we show that two closely related human gut Bacteroides, B. thetaiotaomicron and B. ovatus, are capable of utilizing nearly all of the major plant and host glycans, including rhamnogalacturonan II, a highly complex polymer thought to be recalcitrant to microbial degradation. Transcriptional profiling and gene inactivation experiments revealed the identity and specificity of the polysaccharide utilization loci (PULs) that encode individual Sus-like systems that target various plant polysaccharides. Comparative genomic analysis indicated that B. ovatus possesses several unique PULs that enable degradation of hemicellulosic polysaccharides, a phenotype absent from B. thetaiotaomicron. In contrast, the B. thetaiotaomicron genome has been shaped by increased numbers of PULs involved in metabolism of host mucin O-glycans, a phenotype that is undetectable in B. ovatus. Binding studies of the purified sensor domains of PUL-associated hybrid two-component systems in conjunction with transcriptional analyses demonstrate that complex oligosaccharides provide the regulatory cues that induce PUL activation and that each PUL is highly specific for a defined cell wall polymer. These results provide a view of how these species have diverged into different carbohydrate niches by evolving genes that target unique suites of available polysaccharides, a theme that likely applies to disparate bacteria from the gut and other habitats.
Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts
Eric C. Martens equal contributor ,Elisabeth C. Lowe equal contributor,Herbert Chiang,Nicholas A. Pudlo,Meng Wu,Nathan P. McNulty,D. Wade Abbott,Bernard Henrissat,Harry J. Gilbert,David N. Bolam ,Jeffrey I. Gordon
PLOS Biology , 2011, DOI: 10.1371/journal.pbio.1001221
Abstract: Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in the adult gut, possess broad glycan-degrading abilities. These species use a series of membrane protein complexes, termed Sus-like systems, for catabolism of many complex carbohydrates. However, the role of these systems in degrading the chemically diverse repertoire of plant cell wall glycans remains unknown. Here we show that two closely related human gut Bacteroides, B. thetaiotaomicron and B. ovatus, are capable of utilizing nearly all of the major plant and host glycans, including rhamnogalacturonan II, a highly complex polymer thought to be recalcitrant to microbial degradation. Transcriptional profiling and gene inactivation experiments revealed the identity and specificity of the polysaccharide utilization loci (PULs) that encode individual Sus-like systems that target various plant polysaccharides. Comparative genomic analysis indicated that B. ovatus possesses several unique PULs that enable degradation of hemicellulosic polysaccharides, a phenotype absent from B. thetaiotaomicron. In contrast, the B. thetaiotaomicron genome has been shaped by increased numbers of PULs involved in metabolism of host mucin O-glycans, a phenotype that is undetectable in B. ovatus. Binding studies of the purified sensor domains of PUL-associated hybrid two-component systems in conjunction with transcriptional analyses demonstrate that complex oligosaccharides provide the regulatory cues that induce PUL activation and that each PUL is highly specific for a defined cell wall polymer. These results provide a view of how these species have diverged into different carbohydrate niches by evolving genes that target unique suites of available polysaccharides, a theme that likely applies to disparate bacteria from the gut and other habitats.
Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome
Nathan P. McNulty,Meng Wu,Alison R. Erickson,Chongle Pan,Brian K. Erickson,Eric C. Martens,Nicholas A. Pudlo,Brian D. Muegge,Bernard Henrissat,Robert L. Hettich,Jeffrey I. Gordon
PLOS Biology , 2013, DOI: 10.1371/journal.pbio.1001637
Abstract: The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising >90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations at both a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of artificial communities.
Intensive thermodynamic parameters in nonequilibrium systems
Eric Bertin,Kirsten Martens,Olivier Dauchot,Michel Droz
Physics , 2006, DOI: 10.1103/PhysRevE.75.031120
Abstract: Considering a broad class of steady-state nonequilibrium systems for which some additive quantities are conserved by the dynamics, we introduce from a statistical approach intensive thermodynamic parameters (ITPs) conjugated to the conserved quantities. This definition does not require any detailed balance relation to be fulfilled. Rather, the system has to satisfy a general additivity property, which holds in most of the models usually considered in the literature, including those described by a matrix product ansatz with finite matrices. The main property of these ITPs is to take equal values in two subsystems, making them a powerful tool to describe nonequilibrium phase coexistence, as illustrated on different models. We finally discuss the issue of the equalization of ITPs when two different systems are put into contact. This issue is closely related to the possibility of measuring the ITPs using a small auxiliary system, in the same way as temperature is measured with a thermometer, and points at one of the major difficulties of nonequilibrium statistical mechanics. In addition, an efficient alternative determination, based on the measure of fluctuations, is also proposed and illustrated.
On the relevance of disorder in athermal amorphous materials under shear
Elisabeth Agoritsas,Eric Bertin,Kirsten Martens,Jean-Louis Barrat
Physics , 2015, DOI: 10.1140/epje/i2015-15071-x
Abstract: We show that, at least at a mean-field level, the effect of structural disorder in sheared amorphous media is very dissimilar depending on the thermal or athermal nature of their underlying dynamics. We first introduce a toy model, including explicitly two types of noise (thermal versus athermal). Within this interpretation framework, we argue that mean-field athermal dynamics can be accounted for by the so-called H{\'e}braud-Lequeux (HL) model, in which the mechanical noise stems explicitly from the plastic activity in the sheared medium. Then, we show that the inclusion of structural disorder, by means of a distribution of yield energy barriers, has no qualitative effect in the HL model, while such a disorder is known to be one of the key ingredients leading kinematically to a finite macroscopic yield stress in other mean-field descriptions, such as the Soft-Glassy-Rheology model. We conclude that the statistical mechanisms at play in the emergence of a macroscopic yield stress, and a complex stationary dynamics at low shear rate, are different in thermal and athermal amorphous systems.
Iceman Survived due to Cooling Device
M. Roser,F. Martens,C. Storm
ISRN Cardiology , 2011, DOI: 10.5402/2011/617912
Abstract:
An approximate self-consistent theory of the magnetic field of fluted penumbrae
T. Neukirch,P. C. H. Martens
Physics , 1997,
Abstract: A self-consistent mathematical description of the magnetic field of fluted sunspot penumbrae is presented. This description is based on an expansion of the nonlinear force-free magnetohydrostatic equations written in cylindrical coordinates. The lowest order solutions are mathematically equivalent to laminated force-free equilibria in Cartesian geometry. The lowest order solutions have no toroidal component of the magnetic field and the magnetic pressure does not vary with azimuth but the solutions allow arbitrary variations of the magnetic field components with azimuth. Explicit solutions are presented which have a realistic radial profile of the magnetic field strength and reproduce the basic features of the observations.
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