Testing multiple mapping conditioning mixing for Monte Carlo probability density function simulations

Mitarai [Phys. Fluids 17, 047101 (2005)] compared turbulent combustion models against homogeneous direct numerical simulations with extinction/recognition phenomena. The recently suggested multiple mapping conditioning (MMC) was not considered and is simulated here for the same case with favorable results. Implementation issues crucial for successful MMC simulations are also discussed.

On the inverse parabolicity of pdf equations in turbulent flows

The focus of the present work is the well-known feature of the probability density function (PDF) transport equations in turbulent flows-the inverse parabolicity of the equations. While it is quite common in fluid mechanics to interpret equations with direct (forward-time) parabolicity as diffusive (or as a combination of diffusion, convection and reaction), the possibility of a similar interpretation for equations with inverse parabolicity is not clear. According to Einstein's point of view, a diffusion process is associated with the random walk of some physical or imaginary particles, which can be modelled by a Markov diffusion process. In the present paper it is shown that the Markov diffusion process directly associated with the PDF equation represents a reasonable model for dealing with the PDFs of scalars but it significantly underestimates the diffusion rate required to simulate turbulent dispersion when the velocity components are considered.

Statistical tests of load-unload response ratio signals by lattice solid model: Implication to tidal triggering and earthquake prediction

Statistical tests of Load-Unload Response Ratio (LURR) signals are carried in order to verify statistical robustness of the previous studies using the Lattice Solid Model (MORA et al., 2002b). In each case 24 groups of samples with the same macroscopic parameters (tidal perturbation amplitude A, period T and tectonic loading rate k) but different particle arrangements are employed. Results of uni-axial compression experiments show that before the normalized time of catastrophic failure, the ensemble average LURR value rises significantly, in agreement with the observations of high LURR prior to the large earthquakes. In shearing tests, two parameters are found to control the correlation between earthquake occurrence and tidal stress. One is, A/(kT) controlling the phase shift between the peak seismicity rate and the peak amplitude of the perturbation stress. With an increase of this parameter, the phase shift is found to decrease. Another parameter, AT/k, controls the height of the probability density function (Pdf) of modeled seismicity. As this parameter increases, the Pdf becomes sharper and narrower, indicating a strong triggering. Statistical studies of LURR signals in shearing tests also suggest that except in strong triggering cases, where LURR cannot be calculated due to poor data in unloading cycles, the larger events are more likely to occur in higher LURR periods than the smaller ones, supporting the LURR hypothesis.

Mutational analysis of the large periplasmic loop 7-8 of the putrescine transporter PotE in Escherichia coli

The PotE protein is a putrescine-ornithine antiporter found in many gram-negative bacteria. It is a member of the APA family of transporters and has 12 predicted alpha-helical transmembrane spanning segments (TMS). While the substrate binding site has previously been mapped to a region near the surface of the cytoplasmic lipid layer, no structural feature within the periplasmic domains of PotE have been shown to be important for function. We examined the role of the only large outer loop, situated between transmembrane spanning segment 7 and 8, in putrescine uptake. Deletion of the highly conserved amino acids in the region closest to transmembrane spanning segment 7 produced a protein with little activity. Glycine-scanning mutagenesis of this region showed that Val(249) and Leu(254) were required for optimal transporter function. The V249G mutant transported putrescine at a lower maximal rate compared to wild-type (WT) but with the same substrate binding affinity. In contrast, the L254G mutant had a higher substrate affinity. A series of Val(249) mutants indicated that the hydrophobicity of this residue, which is located at or near the membrane surface, is important for PotE function. Secondary structure predictions of the large outer loop indicated the presence of a hydrophobic alpha-helix in the centre with a hydrophobic region at each end suggesting that the loop was not entirely exposed to the aqueous periplasmic space. The study shows that loop 7-8 is important for PotE function, possibly by forming a re-entrant loop in the channel of the transporter. (C) 2003 Elsevier Ltd. All rights reserved.

Exercise and the endothelial cell

Regular exercise is known to be effective in the prevention and treatment of cardiovascular disease. Among the cardioprotectant mechanisms influenced by exercise, the endothelium is becoming recognised as a major target. Preservation of endothelial cell structure is vital for frictionless blood flow, prevention of macrophage and lipid infiltration and, ultimately, optimal vascular function. Exercise causes various kinds of mechanical, chemical and thermal stresses, and repeated exposure to these stresses may precondition the endothelial cell to future stresses through a number of different mechanisms. This review discusses stress-induced changes in endothelial cell morphology, biochemistry and components of platelet activation and cell adhesion that impact on endothelial cell structure. An enhanced understanding of the effects of exercise on the endothelial cell will assist in directing future research into the prevention of cardiovascular disease. (c) 2004 Elsevier Ireland Ltd. All rights reserved.

Matching conditional moments in PDF modelling of nonpremixed combustion

The rate of generation of fluctuations with respect to the scalar values conditioned on the mixture fraction, which significantly affects turbulent nonpremixed combustion processes, is examined. Simulation of the rate in a major mixing model is investigated and the derived equations can assist in selecting the model parameters so that the level of conditional fluctuations is better reproduced by the models. A more general formulation of the multiple mapping conditioning (MMC) model that distinguishes the reference and conditioning variables is suggested. This formulation can be viewed as a methodology of enforcing certain desired conditional properties onto conventional mixing models. Examples of constructing consistent MMC models with dissipation and velocity conditioning as well as of combining MMC with large eddy simulations (LES) are also provided. (c) 2005 The Combustion Institute. Published by Elsevier Inc. All rights reserved.

Structure and dynamics of ASC2, a pyrin domain-only protein that regulates inflammatory signaling

Pyrin domain (PYD)-containing proteins are key components of pathways that regulate inflammation, apoptosis, and cytokine processing. Their importance is further evidenced by the consequences of mutations in these proteins that give rise to autoimmune and hyperinflammatory syndromes. PYDs, like other members of the death domain ( DD) superfamily, are postulated to mediate homotypic interactions that assemble and regulate the activity of signaling complexes. However, PYDs are presently the least well characterized of all four DD subfamilies. Here we report the three-dimensional structure and dynamic properties of ASC2, a PYD-only protein that functions as a modulator of multidomain PYD-containing proteins involved in NF-KB and caspase-1 activation. ASC2 adopts a six-helix bundle structure with a prominent loop, comprising 13 amino acid residues, between helices two and three. This loop represents a divergent feature of PYDs from other domains with the DD fold. Detailed analysis of backbone N-15 NMR relaxation data using both the Lipari-Szabo model-free and reduced spectral density function formalisms revealed no evidence of contiguous stretches of polypeptide chain with dramatically increased internal motion, except at the extreme N and C termini. Some mobility in the fast, picosecond to nanosecond timescale, was seen in helix 3 and the preceding alpha 2-alpha 3 loop, in stark contrast to the complete disorder seen in the corresponding region of the NALP1 PYD. Our results suggest that extensive conformational flexibility in helix 3 and the alpha 2-alpha 3 loop is not a general feature of pyrin domains. Further, a transition from complete disorder to order of the alpha 2-alpha 3 loop upon binding, as suggested for NALP1, is unlikely to be a common attribute of pyrin domain interactions.

No relationship between low-density lipoproteins and endothelial function in hemodialysis patients

Background: Relationships between low-density lipoprotein cholesterol and endothelial function in hemodialysis patients have yet to be investigated. Furthermore, current reporting of endothelial function data using flow-mediated dilatation has recognised limitations. The aims of the study were to determine the relationship between low-density lipoproteins and endothelial function in hemodialysis patients and to investigate the validity of determining the area under the curve for data collected during the flow-mediated dilatation technique. Methods: Brachial artery responses to reactive hyperemia (endothelial-dependent) and glyceryl trinitrate (endothelial-independent) were assessed in 19 hemodialysis patients using high-resolution ultrasound. Lipid profiles and other factors known to effect brachial artery reactivity were also measured prior to the flow-mediated dilatation technique. Results: There were no significant relationships between serum low-density lipoproteins and endothelial-dependent or -independent vasodilation using absolute change (mm), relative change (%), time to peak change (s) or area under the curve (mm(.)s). In hemodialysis patients with atherosclerosis, area under the curve analysis showed a significantly (p < 0.05) decreased endothelial-dependent response (mean +/- S.D.: 19.2 +/- 17.4) compared to non-atherosclerotic patients (42.3 +/- 28.6). However, when analysing these data using absolute change, relative change or time to peak dilatation, there were no significant differences between the two groups. Conclusions: In summary, there was no relationship between low-density lipoproteins and endothelial function in hemodialysis patients. In addition, area under the curve analysis of flow-mediated vasodilatation data may be a useful method of determining the temporal vascular response during the procedure. (c) 2004 Elsevier Ireland Ltd. All rights reserved.