Effects of spatial dispersion in near-field radiative heat transfer between two parallel metallic surfaces

We study the heat transfer between two parallel metallic semi-infinite media with a gap in the nanometer-scale range. We show that the near-field radiative heat flux saturates at distances smaller than the metal skin depth when using a local dielectric constant and investigate the origin of this effect. The effect of non-local corrections is analysed using the Lindhard-Mermin and Boltzmann-Mermin models. We find that local and non-local models yield the same heat fluxes for gaps larger than 2 nm. Finally, we explain the saturation observed in a recent experiment as a manifestation of the skin depth and show that heat is mainly dissipated by eddy currents in metallic bodies.Comment: Version without figures (8 figures in the complete version

Observation of mesoscopic crystalline structures in a two-dimensional Rydberg gas

The ability to control and tune interactions in ultracold atomic gases has paved the way towards the realization of new phases of matter. Whereas experiments have so far achieved a high degree of control over short-ranged interactions, the realization of long-range interactions would open up a whole new realm of many-body physics and has become a central focus of research. Rydberg atoms are very well-suited to achieve this goal, as the van der Waals forces between them are many orders of magnitude larger than for ground state atoms. Consequently, the mere laser excitation of ultracold gases can cause strongly correlated many-body states to emerge directly when atoms are transferred to Rydberg states. A key example are quantum crystals, composed of coherent superpositions of different spatially ordered configurations of collective excitations. Here we report on the direct measurement of strong correlations in a laser excited two-dimensional atomic Mott insulator using high-resolution, in-situ Rydberg atom imaging. The observations reveal the emergence of spatially ordered excitation patterns in the high-density components of the prepared many-body state. They have random orientation, but well defined geometry, forming mesoscopic crystals of collective excitations delocalised throughout the gas. Our experiment demonstrates the potential of Rydberg gases to realise exotic phases of matter, thereby laying the basis for quantum simulations of long-range interacting quantum magnets.Comment: 10 pages, 7 figure

Nonequilibrium effective field theory for absorbing state phase transitions in driven open quantum spin systems

Phase transitions to absorbing states are among the simplest examples of critical phenomena out of equilibrium. The characteristic feature of these models is the presence of a fluctuationless configuration which the dynamics cannot leave, which has proved a rather stringent requirement in experiments. Recently, a proposal to seek such transitions in highly tuneable systems of cold atomic gases offers to probe this physics and, at the same time, to investigate the robustness of these transitions to quantum coherent effects. Here we specifically focus on the interplay between classical and quantum fluctuations in a simple driven open quantum model which, in the classical limit, reproduces a contact process, which is known to undergo a continuous transition in the "directed percolation" universality class. We derive an effective long-wavelength field theory for the present class of open spin systems and show that, due to quantum fluctuations, the nature of the transition changes from second to first order, passing through a bicritical point which appears to belong instead to the "tricritical directed percolation" class

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

A systems biology approach to analyse leaf carbohydrate metabolism in Arabidopsis thaliana.

Plant carbohydrate metabolism comprises numerous metabolite interconversions, some of which form cycles of metabolite degradation and re-synthesis and are thus referred to as futile cycles. In this study, we present a systems biology approach to analyse any possible regulatory principle that operates such futile cycles based on experimental data for sucrose (Scr) cycling in photosynthetically active leaves of the model plant Arabidopsis thaliana. Kinetic parameters of enzymatic steps in Scr cycling were identified by fitting model simulations to experimental data. A statistical analysis of the kinetic parameters and calculated flux rates allowed for estimation of the variability and supported the predictability of the model. A principal component analysis of the parameter results revealed the identifiability of the model parameters. We investigated the stability properties of Scr cycling and found that feedback inhibition of enzymes catalysing metabolite interconversions at different steps of the cycle have differential influence on stability. Applying this observation to futile cycling of Scr in leaf cells points to the enzyme hexokinase as an important regulator, while the step of Scr degradation by invertases appears subordinate

Basic Regulatory Principles of Escherichia coli's Electron Transport Chain for Varying Oxygen Conditions.

For adaptation between anaerobic, micro-aerobic and aerobic conditions Escherichia coli's metabolism and in particular its electron transport chain (ETC) is highly regulated. Although it is known that the global transcriptional regulators FNR and ArcA are involved in oxygen response it is unclear how they interplay in the regulation of ETC enzymes under micro-aerobic chemostat conditions. Also, there are diverse results which and how quinones (oxidised/reduced, ubiquinone/other quinones) are controlling the ArcBA two-component system. In the following a mathematical model of the E. coli ETC linked to basic modules for substrate uptake, fermentation product excretion and biomass formation is introduced. The kinetic modelling focusses on regulatory principles of the ETC for varying oxygen conditions in glucose-limited continuous cultures. The model is based on the balance of electron donation (glucose) and acceptance (oxygen or other acceptors). Also, it is able to account for different chemostat conditions due to changed substrate concentrations and dilution rates. The parameter identification process is divided into an estimation and a validation step based on previously published and new experimental data. The model shows that experimentally observed, qualitatively different behaviour of the ubiquinone redox state and the ArcA activity profile in the micro-aerobic range for different experimental conditions can emerge from a single network structure. The network structure features a strong feed-forward effect from the FNR regulatory system to the ArcBA regulatory system via a common control of the dehydrogenases of the ETC. The model supports the hypothesis that ubiquinone but not ubiquinol plays a key role in determining the activity of ArcBA in a glucose-limited chemostat at micro-aerobic conditions

Model-guided identification of a therapeutic strategy to reduce hyperammonemia in liver diseases

Background & Aims: Recently, spatial-temporal/metabolic mathematical models have been established that allow the simulation of metabolic processes in tissues. We applied these models to decipher ammonia detoxification mechanisms in the liver. Methods: An integrated metabolic-spatial-temporal model was used to generate hypotheses of ammonia metabolism. Predicted mechanisms were validated using time-resolved analyses of nitrogen metabolism, activity analyses, immunostaining and gene expression after induction of liver damage in mice. Moreover, blood from the portal vein, liver vein and mixed venous blood was analyzed in a time dependent manner. Results: Modeling revealed an underestimation of ammonia consumption after liver damage when only the currently established mechanisms of ammonia detoxification were simulated. By iterative cycles of modeling and experiments, the reductive amidation of alpha-ketoglutarate (alpha-KG) via glutamate dehydrogenase (GDH) was identified as the lacking component. GDH is released from damaged hepatocytes into the blood where it consumes ammonia to generate glutamate, thereby providing systemic protection against hyperammonemia. This mechanism was exploited therapeutically in a mouse model of hyperammonemia by injecting GDH together with optimized doses of cofactors. Intravenous injection of GDH (720 U/kg), alpha-KG (280 mg/kg) and NADPH (180 mg/kg) reduced the elevated blood ammonia concentrations (>200 mu M) to levels close to normal within only 15 min. Conclusion: If successfully translated to patients the GDH-based therapy might provide a less aggressive therapeutic alternative for patients with severe hyperammonemia. (C) 2015 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved

Transcription factor activity <i>R</i>_Act (e.g. FNR) in dependence on the respective metabolic signal <i>x</i> (e.g. O₂).

<p>As modelled in equations (11a) and (11b), small changes of the metabolite in the range around <i>K</i>_A lead to a hypersensitive large change in the regulator activity.</p