A hybrid model for chaotic front dynamics: From semiconductors to water tanks

We present a general method for studying front propagation in nonlinear systems with a global constraint in the language of hybrid tank models. The method is illustrated in the case of semiconductor superlattices, where the dynamics of the electron accumulation and depletion fronts shows complex spatio-temporal patterns, including chaos. We show that this behavior may be elegantly explained by a tank model, for which analytical results on the emergence of chaos are available. In particular, for the case of three tanks the bifurcation scenario is characterized by a modified version of the one-dimensional iterated tent-map.Comment: 4 pages, 4 figure

Bubble and Dew Point Calculations in Multicomponent and Multireactive Mixtures

Bubble and dew point calculations are useful in chemical engineering and play an important role in the study of separation equipments for non-reactive and reactive mixtures. To the best of the authors’s knowledge, few methods have been proposed for these calculations in systems with several chemical reactions. The objective of this paper is to introduce new conditions for performing bubble and dew point calculations in reactive mixtures. We have developed these conditions based on the application of transformed variables of Ung and Doherty (1995). Using these transformed variables, the solution space is restricted to compositions that are already at chemical equilibrium and by consequence the problem dimension is also reduced. The reliability and efficiency of three equation-solving methods are tested and compared using our equilibrium conditions: a) a simultaneous equation-solving approach using Newton method (SESN), b) an equation-decoupling approach using successive substitution method (EDSS) and c) an optimization approach using the stochastic optimization method Simulated Annealing(OSA). Our results indicated that even for simple reactive systems, bubble and dew point calculations are challenging for classical equation-solving methods and require robust strategies. We conclude that OSA and EDSS methods are reliable to locate bubble and dew points in reactive systems. EDSS is more efficient than OSA; however, OSA does not need initial guesses and is more suitable for difficult problems

Determination of asphalt contents in bituminous pavements by neutron scattering

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Gibbs Energy Minimization Using Simulated Annealing for Two-phase Equilibrium Calculations in Reactive Systems

Phase equilibrium calculations in systems subject to chemical reactions are involved in the design, synthesis and optimization of reactive separation processes. Until now, several methods have been developed to perform simultaneously physical and chemical equilibrium calculations. However, published methods may face numerical difficulties such as variable initialization dependence, divergence and convergence to trivial solutions or unstable equilibrium states. Besides, these methods generally use conventional composition variables and reactions extents as unknowns which directly affect the numerical implementation, reliability and efficiency of solving strategies. The objective of this work is to introduce and test an alternative approach to perform Gibbs energy minimization in phase equilibrium problems for reactive systems. Specifically, we have employed the transformed composition variables of Ung and Doherty and the stochastic optimization method Simulated Annealing for two-phase equilibrium calculations in reacting systems. Performance of this strategy has been tested using several benchmark problems and results show that proposed approach is generally suitable for the global minimization of transformed Gibbs energy in reactive systems with two-phase equilibrium

Experimental Critical Current Patterns in Josephson Junction Ladders

We present an experimental and theoretical study of the magnetic field dependence of the critical current of Josephson junction ladders. At variance with the well-known case of a one-dimensional (1D) parallel array of Josephson junctions the magnetic field patterns display a single minimum even for very low values of the self-inductance parameter $\beta_{\rm L}$. Experiments performed changing both the geometrical value of the inductance and the critical current of the junctions show a good agreement with numerical simulations. We argue that the observed magnetic field patterns are due to a peculiar mapping between the isotropic Josephson ladder and the 1D parallel array with the self-inductance parameter $\beta_{\rm L}^{\rm eff}=\beta_{\rm L}+2$.Comment: 4 pages, 4 picture

Classical wave experiments on chaotic scattering

We review recent research on the transport properties of classical waves through chaotic systems with special emphasis on microwaves and sound waves. Inasmuch as these experiments use antennas or transducers to couple waves into or out of the systems, scattering theory has to be applied for a quantitative interpretation of the measurements. Most experiments concentrate on tests of predictions from random matrix theory and the random plane wave approximation. In all studied examples a quantitative agreement between experiment and theory is achieved. To this end it is necessary, however, to take absorption and imperfect coupling into account, concepts that were ignored in most previous theoretical investigations. Classical phase space signatures of scattering are being examined in a small number of experiments.Comment: 33 pages, 13 figures; invited review for the Special Issue of J. Phys. A: Math. Gen. on "Trends in Quantum Chaotic Scattering

An essential thioredoxin-type protein of Trypanosoma brucei acts as redox-regulated mitochondrial chaperone

Most known thioredoxin-type proteins (Trx) participate in redox pathways, using two highly conserved cysteine residues to catalyze thiol-disulfide exchange reactions. Here we demonstrate that the so far unexplored Trx2 from African trypanosomes (Trypanosoma brucei) lacks protein disulfide reductase activity but functions as an effective temperature-activated and redox-regulated chaperone. Immunofluorescence microscopy and fractionated cell lysis revealed that Trx2 is located in the mitochondrion of the parasite. RNA-interference and gene knock-out approaches showed that depletion of Trx2 impairs growth of both mammalian bloodstream and insect stage procyclic parasites. Procyclic cells lacking Trx2 stop proliferation under standard culture conditions at 27°C and are unable to survive prolonged exposure to 37°C, indicating that Trx2 plays a vital role that becomes augmented under heat stress. Moreover, we found that Trx2 contributes to the in vivo infectivity of T. brucei. Remarkably, a Trx2 version, in which all five cysteines were replaced by serine residues, complements for the wildtype protein in conditional knock-out cells and confers parasite infectivity in the mouse model. Characterization of the recombinant protein revealed that Trx2 can coordinate an iron sulfur cluster and is highly sensitive towards spontaneous oxidation. Moreover, we discovered that both wildtype and mutant Trx2 protect other proteins against thermal aggregation and preserve their ability to refold upon return to non-stress conditions. Activation of the chaperone function of Trx2 appears to be triggered by temperature-mediated structural changes and inhibited by oxidative disulfide bond formation. Our studies indicate that Trx2 acts as a novel chaperone in the unique single mitochondrion of T. brucei and reveal a new perspective regarding the physiological function of thioredoxin-type proteins in trypanosomes

Molecular crowding defines a common origin for the Warburg effect in proliferating cells and the lactate threshold in muscle physiology

Aerobic glycolysis is a seemingly wasteful mode of ATP production that is seen both in rapidly proliferating mammalian cells and highly active contracting muscles, but whether there is a common origin for its presence in these widely different systems is unknown. To study this issue, here we develop a model of human central metabolism that incorporates a solvent capacity constraint of metabolic enzymes and mitochondria, accounting for their occupied volume densities, while assuming glucose and/or fatty acid utilization. The model demonstrates that activation of aerobic glycolysis is favored above a threshold metabolic rate in both rapidly proliferating cells and heavily contracting muscles, because it provides higher ATP yield per volume density than mitochondrial oxidative phosphorylation. In the case of muscle physiology, the model also predicts that before the lactate switch, fatty acid oxidation increases, reaches a maximum, and then decreases to zero with concomitant increase in glucose utilization, in agreement with the empirical evidence. These results are further corroborated by a larger scale model, including biosynthesis of major cell biomass components. The larger scale model also predicts that in proliferating cells the lactate switch is accompanied by activation of glutaminolysis, another distinctive feature of the Warburg effect. In conclusion, intracellular molecular crowding is a fundamental constraint for cell metabolism in both rapidly proliferating- and non-proliferating cells with high metabolic demand. Addition of this constraint to metabolic flux balance models can explain several observations of mammalian cell metabolism under steady state conditions

Genome-Wide Studies of Histone Demethylation Catalysed by the Fission Yeast Homologues of Mammalian LSD1

In order to gain a more global view of the activity of histone demethylases, we report here genome-wide studies of the fission yeast SWIRM and polyamine oxidase (PAO) domain homologues of mammalian LSD1. Consistent with previous work we find that the two S. pombe proteins, which we name Swm1 and Swm2 (after SWIRM1 and SWIRM2), associate together in a complex. However, we find that this complex specifically demethylates lysine 9 in histone H3 (H3K9) and both up- and down-regulates expression of different groups of genes. Using chromatin-immunoprecipitation, to isolate fragments of chromatin containing either H3K4me2 or H3K9me2, and DNA microarray analysis (ChIP-chip), we have studied genome-wide changes in patterns of histone methylation, and their correlation with gene expression, upon deletion of the swm1+ gene. Using hyper-geometric probability comparisons we uncover genetic links between lysine-specific demethylases, the histone deacetylase Clr6, and the chromatin remodeller Hrp1. The data presented here demonstrate that in fission yeast the SWIRM/PAO domain proteins Swm1 and Swm2 are associated in complexes that can remove methyl groups from lysine 9 methylated histone H3. In vitro, we show that bacterially expressed Swm1 also possesses lysine 9 demethylase activity. In vivo, loss of Swm1 increases the global levels of both H3K9me2 and H3K4me2. A significant accumulation of H3K4me2 is observed at genes that are up-regulated in a swm1 deletion strain. In addition, H3K9me2 accumulates at some genes known to be direct Swm1/2 targets that are down-regulated in the swm1¿ strain. The in vivo data indicate that Swm1 acts in concert with the HDAC Clr6 and the chromatin remodeller Hrp1 to repress gene expression. In addition, our in vitro analyses suggest that the H3K9 demethylase activity requires an unidentified post-translational modification to allow it to act. Thus, our results highlight complex interactions between histone demethylase, deacetylase and chromatin remodelling activities in the regulation of gene expression