kmos: A lattice kinetic Monte Carlo framework

Kinetic Monte Carlo (kMC) simulations have emerged as a key tool for microkinetic modeling in heterogeneous catalysis and other materials applications. Systems, where site-specificity of all elementary reactions allows a mapping onto a lattice of discrete active sites, can be addressed within the particularly efficient lattice kMC approach. To this end we describe the versatile kmos software package, which offers a most user-friendly implementation, execution, and evaluation of lattice kMC models of arbitrary complexity in one- to three-dimensional lattice systems, involving multiple active sites in periodic or aperiodic arrangements, as well as site-resolved pairwise and higher-order lateral interactions. Conceptually, kmos achieves a maximum runtime performance which is essentially independent of lattice size by generating code for the efficiency-determining local update of available events that is optimized for a defined kMC model. For this model definition and the control of all runtime and evaluation aspects kmos offers a high-level application programming interface. Usage proceeds interactively, via scripts, or a graphical user interface, which visualizes the model geometry, the lattice occupations and rates of selected elementary reactions, while allowing on-the-fly changes of simulation parameters. We demonstrate the performance and scaling of kmos with the application to kMC models for surface catalytic processes, where for given operation conditions (temperature and partial pressures of all reactants) central simulation outcomes are catalytic activity and selectivities, surface composition, and mechanistic insight into the occurrence of individual elementary processes in the reaction network.Comment: 21 pages, 12 figure

The state space of short-range Ising spin glasses: the density of states

The state space of finite square and cubic Ising spin glass models is analysed in terms of the global and the local density of states. Systems with uniform and gaussian probability distribution of interactions are compared. Different measures for the local state density are presented and discussed. In particular the question whether the local density of states grows exponentially or not is considered. The direct comparison of global and local densities leads to consequences for the structure of the state space.Comment: 18 pages (including 6 figures); submitted to Z.f.Physik

Reweighting towards the chiral limit

We propose to perform fully dynamical simulations at small quark masses by reweighting in the quark mass. This approach avoids some of the technical difficulties associated with direct simulations at very small quark masses. We calculate the weight factors stochastically, using determinant breakup and low mode projection to reduce the statistical fluctuations. We find that the weight factors fluctuate only moderately on nHYP smeared dynamical Wilson-clover ensembles, and we could successfully reweight 16^4, (1.85fm)^4 volume configurations from m_q = 20MeV to m_q = 5MeV quark masses, reaching the epsilon-regime. We illustrate the strength of the method by calculating the low energy constant F from the epsilon-regime pseudo-scalar correlator.Comment: 17 pages, 8 figure

Differential regulation of Ota and Otb, two primary glycine betaine transporters in the methanogenic archaeon Methanosarcina mazei go1

Methanogenic archaea accumulate glycine betaine in response to hypersalinity, but the regulation of proteins involved, their mechanism of activation and regulation of the corresponding genes are largely unknown. Methanosarcina mazei differs from most other methanoarchaea in having two gene clusters both encoding a potential glycine betaine transporter, Ota and Otb. Western blot as well as quantitative real-time PCR revealed that Otb is not regulated by osmolarity. On the other hand, cellular levels of Ota increased with increasing salt concentrations. A maximum was reached at 300-500 m M NaCl. Ota concentrations reached a maximum 4 h after an osmotic upshock. Hyperosmolarity also caused an increase in cellular Ota concentrations. In addition to osmolarity Ota expression was regulated by the growth phase. Expression of Ota as well as transport of betaine was downregulated in the presence of glycine betaine. Copyright (c) 2007 S. Karger AG, Basel

Detecting solar chameleons through radiation pressure

Light scalar fields can drive the accelerated expansion of the universe. Hence, they are obvious dark energy candidates. To make such models compatible with tests of General Relativity in the solar system and "fifth force" searches on Earth, one needs to screen them. One possibility is the so-called "chameleon" mechanism, which renders an effective mass depending on the local matter density. If chameleon particles exist, they can be produced in the sun and detected on Earth exploiting the equivalent of a radiation pressure. Since their effective mass scales with the local matter density, chameleons can be reflected by a dense medium if their effective mass becomes greater than their total energy. Thus, under appropriate conditions, a flux of solar chameleons may be sensed by detecting the total instantaneous momentum transferred to a suitable opto-mechanical force/pressure sensor. We calculate the solar chameleon spectrum and the reach in the chameleon parameter space of an experiment using the preliminary results from a force/pressure sensor, currently under development at INFN Trieste, to be mounted in the focal plane of one of the X-Ray telescopes of the CAST experiment at CERN. We show, that such an experiment signifies a pioneering effort probing uncharted chameleon parameter space.Comment: revised versio

KCNK5 is Functionally Down-Regulated Upon Long-Term Hypotonicity in Ehrlich Ascites Tumor Cells

Background/Aims: Regulatory volume decrease (RVD) in response to acute cell swelling is well described and KCNK5 (also known as TASK-2 or K2P5.1) has been shown to be the volume sensitive K+ channel in Ehrlich cells. Very little is, on the other hand, known about the effects of long-term hypotonicity on expression and function of KCNK5, thus we have investigated the effect of long-term hypotonicity (24h - 48h) on KCNK5 in Ehrlich cells on the mRNA, protein and physiological levels. Methods: Physiological effects of long-term hypotonicity were measured using patch-clamp and Coulter counter techniques. Expression patterns of KCNK5 on mRNA and protein levels were established using real-time qPCR and western blotting respectively. Results: The maximum swelling-activated current through KCNK5 was significantly decreased upon 48h of hypotonicity and likewise the RVD response was significantly impaired after both 24 and 48h of hypotonic stimulation. No significant differences in the KCNK5 mRNA expression patterns between control and stimulated cells were observed, but a significant decrease in the KCNK5 protein level 48h after stimulation was found. Conclusion: The data suggest that the strong physiological impairment of KCNK5 in Ehrlich cells after long-term hypotonic stimulation is predominantly due to down-regulation of the KCNK5 protein synthesis

Efficiency of a thermodynamic motor at maximum power

Several recent theories address the efficiency of a macroscopic thermodynamic motor at maximum power and question the so-called "Curzon-Ahlborn (CA) efficiency." Considering the entropy exchanges and productions in an n-sources motor, we study the maximization of its power and show that the controversies are partly due to some imprecision in the maximization variables. When power is maximized with respect to the system temperatures, these temperatures are proportional to the square root of the corresponding source temperatures, which leads to the CA formula for a bi-thermal motor. On the other hand, when power is maximized with respect to the transitions durations, the Carnot efficiency of a bi-thermal motor admits the CA efficiency as a lower bound, which is attained if the duration of the adiabatic transitions can be neglected. Additionally, we compute the energetic efficiency, or "sustainable efficiency," which can be defined for n sources, and we show that it has no other universal upper bound than 1, but that in certain situations, favorable for power production, it does not exceed 1/2