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Distance R (distance + r)
Selected AbstractsA fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2005David E. Shaw Abstract Classical molecular dynamics simulations of biological macromolecules in explicitly modeled solvent typically require the evaluation of interactions between all pairs of atoms separated by no more than some distance R, with more distant interactions handled using some less expensive method. Performing such simulations for periods on the order of a millisecond is likely to require the use of massive parallelism. The extent to which such simulations can be efficiently parallelized, however, has historically been limited by the time required for interprocessor communication. This article introduces a new method for the parallel evaluation of distance-limited pairwise particle interactions that significantly reduces the amount of data transferred between processors by comparison with traditional methods. Specifically, the amount of data transferred into and out of a given processor scales as O(R3/2p,1/2), where p is the number of processors, and with constant factors that should yield a substantial performance advantage in practice. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1318,1328, 2005 [source] Determining the character of motion in quiet and active galaxies with a satellite companionASTRONOMISCHE NACHRICHTEN, Issue 1 2009N.D. Caranicolas Abstract A galaxy model with a satellite companion is used to study the character of motion for stars moving in the x - y plane. It is observed that a large part of the phase plane is covered by chaotic orbits. The percentage of chaotic orbits increases when the galaxy has a dense nucleus of massMn. The presence of the dense nucleus also increases the stellar velocities near the center of the galaxy. For small values of the distance R between the two bodies, low energy stars display a chaotic region near the centre of the galaxy, when the dense nucleus is present, while for larger values of R the motion in active galaxies is regular for low energy stars. Our results suggest that in galaxies with a satellite companion, the chaotic character of motion is not only a result of galactic interaction but also a result caused by the dense nucleus. Theoretical arguments are used to support the numerical outcomes. We follow the evolution of the galaxy, as mass is transported adiabatically from the disk to the nucleus. Our numerical results are in satisfactory agreement with observational data from M51-type binary galaxies (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Comparison of Proximal Isovelocity Surface Area Method and Pressure Half Time Method for Evaluation of Mitral Valve Area in Patients Undergoing Balloon Mitral ValvotomyECHOCARDIOGRAPHY, Issue 9 2005Thottuvelil Narayanan Sunil Roy M.D. Background: The pressure half time (PHT) method is unreliable for measurement of mitral valve area (MVA) immediately after valvotomy. The proximal isovelocity surface area (PISA) method has been used to derive mitral valve area in patients with mitral stenosis. The aim of our study was to compare PISA method and PHT method in patients undergoing percutaneous balloon mitral valvotomy (BMV). Methods: The PISA was recorded from the apex and MVA was calculated using continuity equation by the formula 2,r2 Vr/Vm, where 2,r2 is the hemispheric isovelocity area, Vr is the velocity at the radial distance "r" from the orifice, and Vm is the peak velocity. A plain angle correction factor (,)/180 was used to correct the inlet angle subtended by leaflet tunnel as a result of leaflet doming. Results: MVA calculated using PISA method (r = 0.5217, P < 0.0001, SE = 0.016) and PHT (r = 0.6652, P < 0.0001, SE = 0.017) correlated well with 2D method in patients with mitral stenosis before BMV. After BMV, MVA by PISA method correlated well with 2D planimetry (r = 0.5803, P < 0.0001, SE = 0.053) but PHT showed poor correlation (r = 0.1334, P = 0.199, SE = 0.036). The variability of measurement of MVA was most marked with PHT method in the post-BMV period. Conclusion: The PISA method correlates well with 2D planimetry in patients with mitral stenosis before and after BMV and is superior to the PHT method in the post-BMV period where the latter may be unreliable. [source] Predator perches: a visual search perspectiveFUNCTIONAL ECOLOGY, Issue 2 2009Malte Andersson Summary 1Predators hunting by sight often search for prey from elevated perches or hovering positions above the prey habitat. Theory suggests that prey visibility depends strongly on predator perch height and distance, but their quantitative effects have not been experimentally tested in natural habitats. 2We estimate for the first time how prey visibility depends on predator perch height, distance and vegetation height in an open natural habitat, based on visibility measurements of two targets: a mounted bird and a graduated plate, from five perch heights (0·2,8 m) and six distances (5,120 m). 3For both targets, their proportion visible increases strongly with observer perch height and proximity. From the lowest perch, visibility of the target bird declines to < 5% beyond 20 m distance, but 40% of it remains visible from the highest perch even at 120 m. 4Models of predator search suggest that hunting success and predation rate depend strongly on the prey detection rate, which is expected to decline with distance r approximately as r,d. However, d, the distance decay parameter, has not previously been empirically estimated in natural predator habitats. For distance , prey visibility relationships similar to those observed here, we find a realistic estimate of d to be 2·1,2·4. 5The results demonstrate the crucial role of relative perch and vegetation height for prey visibility, which is of relevance for habitat management. The strong increase of prey visibility with predator search height suggests that removal of predator perches can improve the survival of endangered prey populations in open habitats. Conversely, perch preservation or addition can improve habitat suitability for some predator species where perches are rare or lacking. [source] Convergence radii of the polarization expansion of intermolecular potentialsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2009William H. Adams Abstract A new method is presented to evaluate convergence radii of the polarization expansion of interaction energies for pairs of atoms or molecules. The method is based on an analysis of the variation of the perturbed state vector as a function of the coupling constant , and does not require a calculation of perturbation corrections to high order. The convergence radii at infinite interatomic/intermolecular distances R, as well as a remarkably accurate representation of the R dependence of the convergence radii are obtained from simple calculations involving only monomer wave functions. For the interaction of the lithium and hydrogen atoms, the obtained convergence radii agree well with those obtained previously from the large-order calculations of Patkowski et al. (Patkowski et al., J Chem Phys, 2002, 117, 5124), but are expected to be considerably more accurate. Rigorous upper bounds and reasonable approximations to the convergence radii at R = , are obtained for the pairs of lithium, beryllium, boron, neon, and sodium atoms, as well as for the dimer consisting of two LiH molecules. For all the systems studied, the convergence radii are significantly smaller than the unity and rapidly decrease with the increase of the nuclear charge. It is hoped that the results of this investigation will help to analyze and eventually to compute the convergence radii of the symmetry-adapted perturbation theories which utilize the same partitioning of the Hamiltonian as the polarization expansion. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009 [source] The influence of experimental and model uncertainties on EXAFS resultsJOURNAL OF SYNCHROTRON RADIATION, Issue 2 2001Hermann Rossner We analyze EXAFS oscillations in k-space with the FEFF code to obtain main-shell distances R, and mean-square displacement parameters ,i2 for all single and multiple scattering paths i in the shells , up to a maximum shell radius Rmax. To quantify the uncertainty in the determination of these model parameters we take into account experimental errors and uncertainties connected with background subtraction, with the approximate handling of the electronic many-body problem in FEFF, and with the truncation of the multiple scattering series. The impact of these uncertainties on the R, and ,i2 is investigated in the framework of Bayesian methods. We introduce an a priori guess of these model parameters and consider two alternative strategies to control the weight of the a priori input relative to that of the experimental data. We can take a model parameter space of up to 250 dimensions. Optionally we can also fit the coordination numbers Nj (j,,) and the skewness of the distribution of the R, besides the R, and ,i2. The method is applied to 10K Cu K-edge and 300K Au L3 -edge data to obtain model parameters and their a posteriori error correlation matrices. [source] | ||||||||||