bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scalable fine‐grained parallelization of plane‐wave–based ab initio molecular dynamics for large supercomputers
Authors: Vadali Ramkumar V. , Shi Yan , Kumar Sameer , Kale Laxmikant V. , Tuckerman Mark E. , Martyna Glenn J. 
Published: October 2004

AbstractMany systems of great importance in material science, chemistry, solid‐state physics, and biophysics require forces generated from an electronic structure calculation, as opposed to an empirically derived force law to describe their properties adequately. The use of such forces as input to Newton's equations of motion forms the basis of the ab initio molecular dynamics method, which is able to treat the dynamics of chemical bond‐breaking and ‐forming events. However, a very large number of electronic structure calculations must be performed to compute an ab initio molecular dynamics trajectory, making the efficiency as well as the accuracy of the electronic structure representation critical issues. One efficient and accurate electronic structure method is the generalized gradient approximation to the Kohn–Sham density functional theory implemented using a plane‐wave basis set and atomic pseudopotentials. The marriage of the gradient‐corrected density functional approach with molecular dynamics, as pioneered by Car and Parrinello (R. Car and M. Parrinello, Phys Rev Lett 1985, 55, 2471), has been demonstrated to be capable of elucidating the atomic scale structure and dynamics underlying many complex systems at finite temperature. However, despite the relative efficiency of this approach, it has not been possible to obtain parallel scaling of the technique beyond several hundred processors on moderately sized systems using standard approaches. Consequently, the time scales that can be accessed and the degree of phase space sampling are severely limited. To take advantage of next generation computer platforms with thousands of processors such as IBM's BlueGene, a novel scalable parallelization strategy for Car–Parrinello molecular dynamics is developed using the concept of processor virtualization as embodied by the Charm++ parallel programming system. Charm++ allows the diverse elements of a Car–Parrinello molecular dynamics calculation to be interleaved with low latency such that unprecedented scaling is achieved. As a benchmark, a system of 32 water molecules, a common system size employed in the study of the aqueous solvation and chemistry of small molecules, is shown to scale on more than 1500 processors, which is impossible to achieve using standard approaches. This degree of parallel scaling is expected to open new opportunities for scientific inquiry. © 2004 Wiley Periodicals, Inc. J Comput Chem 16: 2006–2022, 2004
Efficiency of the algorithms for the calculation of Slater molecular integrals in polyatomic molecules
Authors: Fernández Rico J. , López R. , Ema I. , Ramírez G. 
Published: October 2004

AbstractThe performances of the algorithms employed in a previously reported program for the calculation of integrals with Slater‐type orbitals are examined. The integrals are classified in types and the efficiency (in terms of the ratio accuracy/cost) of the algorithm selected for each type is analyzed. These algorithms yield all the one‐ and two‐center integrals (both one‐ and two‐electron) with an accuracy of at least 12 decimal places and an average computational time of very few microseconds per integral. The algorithms for three‐ and four‐center electron repulsion integrals, based on the discrete Gauss transform, have a computational cost that depends on the local symmetry of the molecule and the accuracy of the integrals, standard efficiency being in the range of eight decimal places in hundreds of microseconds. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1987–1994, 2004
Differentiation of sulfate and phosphate by H/D exchange mass spectrometry: application to isoflavone
Authors: Kanakubo Akira , Isobe Minoru 
Published: October 2004

AbstractOften phosphorylation or sulfation is an important step which occurs in the signal transduction and cascade of metabolic pathways. Some natural products and metabolites contain one or more sulfate or phosphate groups. Isoflavone sulfate has been identified from high‐resolution mass spectrometry (HRMS) and enzymatic digestion by sulfatase. We previously reported the new water‐soluble isoflavone analogs, daidzein 7‐O‐phosphate and genistein 7‐O‐phosphate, which were surprisingly hydrolyzed by sulfatase. In this previous study, we could not determine the phosphate from the results of HRMS and enzymatic digestion, that is, HRMS and enzymatic digestion did not provide clear evidence. In this case, we drew conclusions from NMR analysis. HRMS has been ineffective with a regular fast atom bombardment (FAB) mass spectrometer to distinguish between phosphate and sulfate since the mass difference is only 0.009 mass units. There was, however, no conventional method of microanalysis to distinguish phosphate from sulfate owing to the same nominal mass. It is still very difficult to determine by negative FABMS [OP(O)(OH)2] = 80 and [OS(O)2OH] = 80. In this paper, we report a method to distinguish between these groups by using a popular low‐resolution mass instrument; thus, phosphate and sulfate were measured by H/D exchange mass spectrometry at the picomole level to differentiate [OP(O)(OD)2] = 82 and [OS(O)2OD] = 81, respectively. This method is applicable not only to the isoflavone, but also to other phospho and sulfo compounds. Copyright © 2004 John Wiley & Sons, Ltd.
Using collision‐induced dissociation with corrections for the ion number of degrees of freedom for quick comparisons of relative bonding strength
Authors: Vinokur Natalia , Ryzhov Victor 
Published: October 2004

AbstractThe number of degrees of freedom‐dependent stability of ions and ion–neutral non‐covalent complexes under collision‐induced dissociation (CID) conditions was studied in a quadrupole ion trap mass spectrometer. It was found that the stability of ions as probed by energy‐variable CID has a linear dependence on the total number of degrees of freedom for the ions (or ion–neutral complexes) with the same (or nearly the same) bonding energy. The slope of such a stability vs number of degrees of freedom dependence correlates with the binding energy. Proton‐bound amine dimers display the lowest slope as they have weak bonds. Breaking covalent bonds will result in much greater slopes. In addition to the binding energy, the vibrational frequencies of the ion also affect the stability vs number of degrees of freedom behavior. Studying such a dependence of the CID stability in a system paves the way for direct relative binding energy comparisons. The application of this approach is demonstrated by testing the relative heme affinities of anti‐malaria drugs and related compounds. Copyright © 2004 John Wiley & Sons, Ltd.
Fragmentation patterns of selected ergot alkaloids by electrospray ionization tandem quadrupole mass spectrometry
Authors: Lehner Andreas F. , Craig Morrie , Fannin Neil , Bush Lowell , Tobin Thomas 
Published: October 2004

AbstractTall fescue toxicosis and other maladies in livestock result from the ingestion of vasoconstrictive ergot alkaloids produced by fungal endophytes associated symbiotically with the grass. In order to facilitate future analyses of grass extracts considered responsible for outbreak of related livestock diseases, we examined the electrospray ionization mass spectra of specific ergot alkaloids under conditions that permit protonation. Our purposes were both to record the spectra with interpretation of mechanisms of fragmentation and to derive commonalities that would allow the prediction of mass spectra of related compounds for which standards were not readily available. With [M + H]+values in parentheses, water‐insoluble lysergic acid peptide ergot derivatives ergovaline (m/z534), ergotamine (m/z582), ergocornine (m/z562), ergocryptine (m/z576) and ergocrystine (m/z610) exhibited a consistent loss of water (−18 u) from the C‐12′ α‐hydroxy functionality. Of this group, ergovaline and ergotamine generated anm/z320 fragment deriving from cleavage of ring E amide and ether functions with retention of the peptide ring system methyl group. Ergocornine, ergocryptine and ergocrystine similarly formed anm/z348 fragment with retention of isopropyl. These assignments were supported by the lack of similar fragments from the water‐soluble ergot ergonovine, which lacks a peptide ring system. Clavine‐type ergot alkaloids lysergic acid and lysergol lack any substituents beyond simple ones directly on the C‐8 position and, similarly to ergonovine, lack significant fragments atm/z268, 251 and 225 shared by the peptide ergot alkaloids. Copyright © 2004 John Wiley & Sons, Ltd.
Determination of arginine and asymmetric dimethylarginine (ADMA) in human plasma by liquid chromatography/mass spectrometry with the isotope dilution technique
Authors: Martens‐Lobenhoffer Jens , Krug Olga , Bode‐Böger Stefanie M. 
Published: October 2004

AbstractArginine (ARG) is a substrate for endogenous nitric oxide (NO) production whereas its metabolite, asymmetric dimethylarginine (ADMA), acts as an inhibitor. Sufficient NO production is essential for cardiovascular key functions, thus elevated concentration levels of ADMA are related to a range of cardiovascular diseases. Owing to the lack of reliable methods for the measurement of ARG and ADMA in human plasma, concentration values determined with these methods can differ considerably. We present here a simple and very robust liquid chromatographic/mass spectrometric method for the determination of ARG and ADMA utilizing isotope‐labeled internal standards. Sample preparation requires only protein precipitation; the analytes were derivatized with o‐phthalaldehyde–mercaptoethanol and separated on a reversed‐phase C18 column with gradient elution. The analytes were detected with an electrospray ionization ion trap instrument working in the full‐scan single mass spectrometry mode. Concentration values obtained with this method for healthy controls were ARG = 63.9 ± 23.9 µM and ADMA = 0.355 ± 0.066 µM, with a normal range for ADMA from 0.225 to 0.485 µM. The corresponding values for end‐stage chronic renal failure patients are ARG = 48.1 ± 18.5 µM, p < 0.01 and ADMA = 0.673 ± 0.134 M, p < 0.001. Copyright © 2004 John Wiley & Sons, Ltd.
Investigation into factors affecting precision in ion trap mass spectrometry using different scan directions and axial modulation potential amplitudes
Authors: Dobson G. , Murrell J. , Despeyroux D. , Wind F. , Tabet J.‐C. 
Published: October 2004

AbstractElectrospray ionization mass spectra obtained from different scan directions are observed to be dependent on the axial modulation potential amplitudes used for resonant ejection and on the positive deviation caused by higher even‐multipole fields present in most commercial ion traps. The axial modulation voltage influences the dissociation of ions during resonant ejection and the observed mass shifts. The higher even‐multipole fields in commercial ion traps are known to influence resonant ejection from the ion trap and can cause a loss in mass resolution for peaks in reverse scan mass spectra compared with that obtained by the forward scan. However, along with the dissociation of ions during resonant ejection causing a loss in resolution, the possibility of resolving an isotopic distribution is also shown to be influenced by the mass shifts caused by the space charge. These mass shifts differ depending on the scan direction employed. A significant loss in resolution can also result from resonant ejection using non‐optimal axial modulation voltages. We also present results showing the ejection of ions at $\beta_{z} = {1 \over 2}$ using the reverse scan mode without the axial modulation voltage. Ion ejection at $\beta_{z} = {1 \over 2}$ is uncommon in commercial (stretched ion traps) with the conventional analytical scan without the use of a frequency of the axial modulation voltage corresponding to this non‐linear resonance. Copyright © 2004 John Wiley & Sons, Ltd.
Changes in spring–summer cirrus cloud amount over Estonia, 1958–2003
Authors: Eerme Kalju 
Published: October 2004

AbstractThe data of hourly cloud detection during daytime at the Tartu–Tõravere meteorological station for the period 1958–2003 have been treated to find the monthly mean amounts of cirrus clouds (in tenths) for March–September and to study their variance. The highest mean value (4.1 tenths) was found in April and the lowest (three tenths) in July. The results of previous cloud‐type notation frequency‐based studies using no quantitative measure for cirrus cloud amount exhibit a maximum in June. The smoothed March–September cirrus cloud amount for 1958–2003 manifests alternation of relatively high and relatively low amounts with a period of approximately 20 years. The relative contribution of clear skies (cirrus amounts less than one tenth) has decreased, the lowest being during 1991–96. The cirrus cloud amount was weakly correlated with local characteristics of atmospheric moisture, such as precipitation, total cloud amount and low cloud amount. Low average cirrus amounts, however, were often recorded when the spring was dry. High cirrus amounts were observed when spring and most months were wet. Copyright © 2004 Royal Meteorological Society
The influence of atmospheric circulation on plant phenological phases in central and eastern Europe
Authors: Aasa Anto , Jaagus Jaak , Ahas Rein , Sepp Mait 
Published: October 2004

AbstractThe objective of this study is to analyse relationships between the start dates of spring phenological phases and large‐scale atmospheric circulation patterns. The timing of phenological phases in temperate zones is driven by temperature, and temperature regime is generally determined by atmospheric circulation. The database analysed consists of the first dates of flowering of coltsfoot (Tussilago farfara L.), of birch (Betula pendula Roth.) leaf unfolding and of flowering of lilac (Syringa vulgaris L.); the North Atlantic oscillation (NAO) and the Arctic oscillation (AO) indices, frequencies of the circulation forms classified by Vangengeim and Girs, and of the groups of Grosswetterlagen presented by Hess and Brezowsky. The study area covers central and eastern Europe, and the period considered is 1951–98.The results show that the influence of the westerly airflow is more pronounced in the winter half‐year, and weakens and even disappears as spring advances. Phases have the highest correlation with NAO and AO indices during winter (December–March) and the first three months of the year (January–March), which have correlations stronger than −0.5 in the Baltic Sea region. Among the phenological phases, flowering of coltsfoot is the most strongly correlated with the NAO and AO indices, followed by leafing of birch and flowering of lilac. Airflow from the north and from the east has a greater influence in springtime, particularly in the northernmost and southernmost regions of the study area. Copyright © 2004 Royal Meteorological Society
Australian dust storms: temporal trends and relationships with synoptic pressure distributions (1960–99)
Authors: Ekström Marie , McTainsh Grant H. , Chappell Adrian 
Published: October 2004

AbstractMean‐sea‐level‐pressure patterns of the main atmospheric circulation for Australia were created using principal component analysis and non‐hierarchical cluster analysis. The patterns are related to dust storm occurrence from 95 meteorological stations across Australia during the period 1960–99. Dust storm stations were separated into two groups with distinct dust storm seasons: the spring–summer (September–February) dust storm group and the summer–autumn (December–May) dust storm group. Spring–summer dust storms are most likely controlled by the timing of non‐precipitation cold fronts over southern and central Australia and limited by summer precipitation. The summer–autumn dust storms are most likely controlled by the length of the driest period of the year. The stations of the first group are located mainly in the interior of the continent, and those of the second group are located mainly near the coastal regions of southern and western Australia. The location of the subtropical Indian Ocean high is shown here to influence dust storm occurrence during both seasons. A more westward displacement of this pressure centre in the Great Australian Bight allows cold fronts to enter the continent and increase the potential for dust storm activity. Copyright © 2004 Royal Meteorological Society
Hydro‐meteorological variability in the greater Ganges–Brahmaputra–Meghna basins
Authors: Chowdhury MD. Rashed , Ward Neil 
Published: October 2004

AbstractThe flows of the Ganges, Brahmaputra and Meghna (GBM) are highly seasonal, and heavily influenced by monsoon rainfall. As a result, these rivers swell to their banks and often overflow during the monsoon months. This is most pronounced in the downstream regions, particularly in Bangladesh, which is the lowest riparian country. The objective of this paper is to study this hydro‐meteorological variability in the greater GBM regions, including the headwater regions in India and their role in streamflows in Bangladesh, and explore the large‐scale oceanic factors affecting this hydro‐meteorological variability. Global precipitation data, Bangladesh rainfall and streamflow records have been analysed and related to large‐scale climate patterns, including upstream rainfall, regional atmospheric circulation and patterns of sea‐surface temperature.The findings have quantified how the streamflows of these rivers in Bangladesh are highly correlated with the rainfall in the upper catchments with typically a lag of about 1 month. Therefore, streamflows in Bangladesh could be reasonably estimated for 1 to 3 months in advance (especially for the Ganges and Brahmaputra rivers) by employing simple correlation, if rainfall data from countries further up are available on a real‐time and continuous basis. In the absence of rainfall data, streamflow forecasts are still possible from unusually warm or cold sea‐surface temperatures in the tropics. The study concludes that hydro‐meteorological information flow between Bangladesh and other neighbouring countries is essential for developing a knowledge base for evaluating the potential implications of seasonal streamflow forecast in the GBM basins in Bangladesh. Copyright © 2004 Royal Meteorological Society
Variability and trends in the duration and depth of snow cover in Poland in the 20th century
Authors: Falarz Małgorzata 
Published: October 2004

AbstractThis study investigates the changes and variability of the number of days with snow cover of ≥1 cm depth and the seasonal maximum snow cover depth at 66 meteorological stations throughout Poland, spanning a period of 50 (1948–49 to 1997–98) to 108 (1895–96 to 2002–03) winter seasons. A slight decreasing trend was observed with snow cover characteristics in most of Poland during the second half of the 20th century, but no change was distinguished for the longer periods. The snow cover changes are related to circulation changes, and particularly to the increased frequency of western advection over Poland. However, the scale of the snow cover change is not proportional to the air temperature changes, which have been found in many previous studies to display an increasing statistically significant trend in winter. An increasing trend of snow cover in the last 50 winter seasons is observed in areas with abundant snow cover only, i.e. in northeastern Poland (snow cover depth) and in the mountains (snow cover duration). In lowland areas of Poland the snow cover duration indicates an 8 year periodicity. The year‐to‐year variability of snow cover has been increasing, particularly during the second half of the 20th century. Copyright © 2004 Royal Meteorological Society
Super‐resolution image reconstruction using multisensors
Authors: Ching Wai‐Ki , Ng Michael K. , Sze Kenton N. , Yau Andy C. 
Published: October 2004

AbstractSuper‐resolution image reconstruction refers to obtaining an image at a resolution higher than that of a camera (sensor) used in recording the image. In this paper, we present a new joint minimization model in which an objective function is set up consisting of three terms: the data fitting term, the regularization terms for the reconstructed image and the observed low‐resolution images. An alternating minimization iterative algorithm is proposed and developed to reconstruct the image. We give a convergence analysis of the alternating minimization iterative algorithm and show that it converges forH1‐norm regularization functional. Numerical examples are given to illustrate the effectiveness of the joint minimization model and the efficiency of the algorithm. Copyright © 2004 John Wiley & Sons, Ltd.
Numerical behaviour of multigrid methods for symmetric Sinc–Galerkin systems
Authors: Ng Michael K. , Serra‐Capizzano Stefano , Tablino‐Possio Cristina 
Published: October 2004

AbstractThe symmetric Sinc–Galerkin method developed by Lund (Math. Comput. 1986; 47:571–588), when applied to second‐order self‐adjoint boundary value problems on d dimensional rectangular domains, gives rise to an N × N positive definite coefficient matrix which can be viewed as the sum of d Kronecker products among d − 1 real diagonal matrices and one symmetric Toeplitz‐plus‐diagonal matrix. Thus, the resulting coefficient matrix has a strong structure so that it can be advantageously used in solving the discrete system. The main contribution of this paper is to present and analyse a multigrid method for these Sinc–Galerkin systems. In particular, we show by numerical examples that the solution of a discrete symmetric Sinc–Galerkin system can be obtained in an optimal way only using O(N log N) arithmetic operations. Numerical examples concerning one‐ and two‐dimensional problems show that the multigrid method is practical and efficient for solving the above symmetric Sinc–Galerkin linear system. Copyright © 2004 John Wiley & Sons, Ltd.
Global optimization of minimum weight truss topology problems with stress, displacement, and local buckling constraints using branch‐and‐bound
Authors: Stolpe M. 
Published: October 2004

AbstractWe present a convergent continuous branch‐and‐bound algorithm for global optimization of minimum weight truss topology problems with displacement, stress, and local buckling constraints. Valid inequalities which strengthen the problem formulation are derived. The inequalities are generated by solving well‐defined convex optimization problems. Computational results are reported on a large collection of problems taken from the literature. Most of these problems are, for the first time, solved with a proof of global optimality. Copyright © 2004 John Wiley & Sons, Ltd.