Dynamic Load Balancing in a Geophysics Application Using STAPL

Seismic wavefront simulation is a common method to understand the composition of earth below the surface, especially for hydrocarbon exploration. One of these simulation methods is the wavefront construction algorithm. In this thesis, we reduced the load imbalance in a parallel implementation of the wavefront construction algorithm. We added a generic redistribution framework for data structures in the C++ parallel library STAPL. We present a redistribution algorithm for the parallel wavefront construction application which uses the recursive coordinate bisection method to find a near-optimal data distribution of the data. This algorithm leveraged the added redistribution features in STAPL to improve the running time of our application. We compared the run time of the application with and without redistribution on different geophysics models. We show that the proposed redistribution provides up to 9.45x speedup on a Cray XE6m cluster and 11.85x speedup on an IBM BlueGene/Q cluster

Characterization and control of proton-ATPase along the nephron.

International audienceSince it is now well established that the Na-H exchanger accounts for only part of tubular proton secretion, we attempted to characterize the molecular processes responsible for the remaining moiety. In particular, we evaluated the possible roles of proton pumps in urinary acidification. For this purpose, we characterized ATPase activities associated with the electrogenic H pump, on the one hand, and with H-K-ATPase, on the other. In order to circumvent the axial heterogeneity of nephron, this study was carried out on microdissected segments of nephron. The present report summarized experiments which aimed: (1) at characterizing H-ATPase and H-K-ATPase on kinetic and pharmacologic bases in the successive segments of mammalian nephrons; (2) at evaluating the ionic transport mediated by these two ATPases; and (3) at determining the factors which control the activity of these pumps

Difference in the Na affinity of Na(+)-K(+)-ATPase along the rabbit nephron: modulation by K

International audienceThe sensitivity of Na(+)-K(+)-ATPase to Na was determined in single segments of rabbit nephron isolated by microdissection. In the cortical collecting tubule (CCT), Na(+)-K(+)-ATPase was threefold more sensitive to Na (apparent K0.5 approximately 3 mM) than in proximal convoluted tubule and cortical thick ascending limb (apparent K0.5 approximately 10 mM). Furthermore, increasing K concentration from 5 to greater than 100 mM markedly reduced the affinity of the pump for Na in all three nephron segments. In fact, the main shift in Na affinity occurred when K changed from 100 to 120 mM; in the CCT, increasing K concentration from 100 to 120 mM while maintaining Na concentration at 10 mM reduced Na(+)-K(+)-ATPase activity by greater than 35%. These findings confirm that, in kidney cells as in other cells, intracellular Na limits the rate of Na(+)-K(+)-ATPase. Thus any alteration of intracellular Na concentration modifies the pump activity in a way that contributes to the restoration of intracellular Na homeostasis. This adaptive property is particularly efficient in the collecting tubule in which the apparent K0.5 of the pump for Na is close to normal intracellular Na concentration. Furthermore, changes in intracellular K concentration, which usually accompany those of Na so as to maintain the total cation concentration constant, potentiate the regulatory role of Na through modifications of its affinity for the pump

Effect of metabolic acidosis and alkalosis on NEM-sensitive ATPase in rat nephron segments

International audienceAn N-ethylmaleimide (NEM)-sensitive adenosinetriphosphatase (ATPase) displaying the kinetic and pharmacological properties of an electrogenic proton pump has been described in the different segments of rat nephron, where it mediates part of the active tubular proton secretion. This study was therefore designed to evaluate whether changes in urinary acidification observed during metabolic acidosis or alkalosis were associated with alterations of the activity of tubular NEM-sensitive ATPase, and if so, to localize the nephron segments responsible for these changes. Within 1 wk after the onset of ammonium chloride treatment, rats developed a metabolic acidosis, and NEM-sensitive ATPase activity was markedly increased in the medullary thick ascending limb of Henle's loop and outer medullary collecting tubule, and slightly increased in the cortical collecting tubule. Conversely, treatment with sodium bicarbonate induced a metabolic alkalosis that was accompanied by decreased NEM-sensitive ATPase activity in medullary thick ascending limb and outer medullary collecting tubule. NEM-sensitive ATPase activity was not altered in any other nephron segment tested in alkalotic and acidotic rats, i.e., the proximal tubule and the cortical thick ascending limb of Henle's loop. Changes qualitatively similar were observed as soon as 3 h after the onset of NaHCO3 or NH4Cl-loading. In the medullary collecting tubule, alterations of NEM-sensitive ATPase activity are in part due to hyperaldosteronism observed in both acidotic and alkalotic rats.(ABSTRACT TRUNCATED AT 250 WORDS