Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

We describe an algorithm for computing nonbonded interactions with cutoffs on a graphics processing unit. We have incorporated it into OpenMM, a library for performing molecular simulations on high‐performance computer architectures. We benchmark it on a variety of systems including boxes of water molecules, proteins in explicit solvent, a lipid bilayer, and proteins with implicit solvent. The results demonstrate that its performance scales linearly with the number of atoms over a wide range of system sizes, while being significantly faster than other published algorithms. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

PAPER—Accelerating parallel evaluations of ROCS

Modern graphics processing units (GPUs) are flexibly programmable and have peak computational throughput significantly faster than conventional CPUs. Herein, we describe the design and implementation of PAPER, an open‐source implementation of Gaussian molecular shape overlay for NVIDIA GPUs. We demonstrate one to two order‐of‐magnitude speedups on high‐end commodity GPU hardware relative to a reference CPU implementation of the shape overlay algorithm and speedups of over one order of magnitude relative to the commercial OpenEye ROCS package. In addition, we describe errors incurred by approximations used in common implementations of the algorithm. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

Complexometric titration of copper(II) using nitrosochromotropic acid as a new metal indicator

Summary Nitrosochromotropic acid gives a violet coloured soluble complex with Cu^II in ammonium chloride-ammonium hydroxide buffer solution, which is less stable than Cu^II-EDTA complex. When microquantities of Cu^II solution containing 1 or 2 drops of nitrosochromotropic acid in the ph range 7.25 to 8.00, are titrated with EDTA, a sharp colour change from violet to orange occurs at the end point. The method of titration can be carried out from 20° to 40° C, but the copper complex dissociates at higher temperature and gives low results. The separation of Zn²⁺, Cd²⁺, Co²⁺, Ni²⁺, Pb²⁺ and alkaline earths, is necessary as they interfere in the titrations with EDTA.

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Zusammenfassung Nitrosochromotropsäure bildet mit Kupfer(II) in Ammoniumchlorid-Ammoniak-Pufferlösung einen violett gefärbten löslichen Komplex, der weniger stabil ist als der Kupfer(II)-ÄDTA-Komplex. Mikromengen Kupfer(II) können imph-Bereich von 7,25–8,00 unter Zusatz von 1–2 Tropfen Nitrosochromotropsäurelösung als Indicator mit ÄDTA-Lösung titriert werden, wobei am Endpunkt ein scharfer Umschlag von Violett nach Orange erfolgt. Die Temperatur der Lösung soll 20–40° C betragen; bei höherer Temperatur erhält man zu niedrige Werte, da der Kupferkomplex dann dissoziiert. Zn²⁺, Cd²⁺, Co²⁺, Ni²⁺, Pb²⁺ und Erdalkalien müssen vor der Titration abgetrennt werden.

     

Thermal conduction through loose and granular two-phase materials at normal pressure

The integrated theory derived for the lattice-type dispersions is modified and extended to estimate the effective thermal conductivity of loose and granular two-phase materials at normal pressure assuming an effective continuous media approximation. A comparison of calculated values ofλ _e with the reported experimental results over a wide range of loose and granular two-phase materials shows a good agreement.     

Microdetermination of indoles with N-bromoacetamide in acetic acid medium

Summary A titrimetric method for the microdetermination of indole and its derivatives withN-bromoacetamide is described. It has been observed thatN-bromoacetamide brominates the compound containing indole nucleus in the presence of acetic acid. The usual reaction time is 15 minutes and the reaction is carried out at room temperature. The relative errors are less than ±1.5% at the mg level.

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Zusammenfassung Die maßanalytische Bestimmung von Indol und seinen Derivaten mitN-Bromacetamid wurde beschrieben. Dieses Reagens bromiert in Gegenwart von Essigsäure indolhältige Verbindungen innerhalb 15 min bei Zimmertemperatur. Der rel. Fehler ist geringer als ±1,5%.

     

Micro determination of olefinic unsaturation. Reaction of N-bromosuccinimide with olefins in polar medium

Summary A micro method for the determination of olefinic unsaturation in organic compounds has been developed. 2–10 mg sample dissolved in acetic acid is reacted with a known excess of N-bromosuccinimide at room temperature and the excess reagent is back titrated iodometrically. The maximum deviation in the results is ±2%. The compounds containing electron withdrawing groups close to the C=C site are not reactive and hence could not be determined by this procedure.

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Mikrobestimmung der Ungesättigtheit von Olefinen. Reaktion von N-Bromsuccinimid mit Olefinen in polarem Medium

Zusammenfassung 2–10mg der Probe werden in Essigsäure gelöst, mit überschüssigem Reagens versetzt und der Überschuß jodometrisch zurücktitriert. Der maximale Fehler der Ergebnisse beträgt ±2%. Verbindungen, die benachbart zur C=C-Doppelbindung elektronenentziehende Gruppen enthalten, können nicht analysiert werden.

     

Analysis of poly(amidoamine) dendrimer structure by UV-vis spectroscopy

We report a UV-vis spectroscopic study of four different types of poly(amidoamine) dendrimers. The results indicate that the degree of protonation of the interior tertiary amines of these dendrimers correlates directly to an absorption band with λ(max) in the range of 280-285 nm. Specifically, at low pH, the tertiary amines are protonated and the 280-285 nm band is absent. However, at elevated pH, when these groups are deprotonated, this band appears. Similar results were obtained for a simple model compound. The dependence of the 280-285 nm band on the chemical state of the tertiary amines of the dendrimers was confirmed by complexing them with Pd(2+) and Pt(2+). In this case the band disappears, and it only reappears when the metal ions are decomplexed following reduction with BH(4)(-). Finally, filtration experiments showed that the absorption band between 280-285 nm arises exclusively from intact, or nearly intact, dendrimers rather than low-molecular-weight fragments.     

A study of iso- and alio-valent cation doped Ag2SO4 solid electrolyte

2 SO₄. The solid solubility limits up to x≤3 mole% for monovalent, x≤5.27 mole% for divalent and x≤3.63 mole% for trivalent cation doped Ag₂SO₄ are set with XRD, SEM, IR and DSC techniques. A predominant dependence of conductivity on the ionic size of iso- and alio-valent cations is observed. In particular, the conductivity enhances in both α and β phases, despite having a lower ionic-size dopant cation (relative to that of Ag⁺) in the transition element cation doped Ag₂SO₄. Ca²⁺, Ba²⁺, Y³⁺ and Dy³⁺ doped samples show depature from the regular behaviour in the β-phase. The conductivity behaviour is discussed considering ionic size, valence and electronic structure of the guest cations. Received: 3 February 1997/Accepted: 27 May 1997     

Influence of protonation on physico-chemical properties of metal extractants

Summary The protonation constants of several metal extractants, especially hydroxamic acids have been determined by a solvent extraction method. The influence of the acidity on the solubility and the distribution ratio has been studied. A plot correlates the protonation behaviour of these metal extractants with the Hammett Acidity Function, H_o. The protonation constant is useful to explain the acid catalysed hydrolysis rate of these metal extractants and to determine the extraction coefficients of their metal chelates.     

Preliminary design studies of a 100 MeV H−/H+ LINAC as injector for SNS synchrotron/ADS LINAC

It is proposed to construct a spallation neutron source (SNS) at Centre for Advanced Technology (CAT) based on a 1 GeV proton synchrotron with 100 MeV H⁻ LINAC as injector. Additionally, the LINAC can form the first 100 MeV part of a 1 GeV proton LINAC to be built in future for accelerator driven system (ADS) applications. We are exploring a configuration of the 100 MeV LINAC which will consist of an H⁻ ion source, a 4–6 MeV RFQ followed either by a 20 MeV drift tube LINAC (DTL) and 100 MeV separated function drift tube LINAC (SDTL) or a coupled cavity drift tube LINAC (CCDTL) structure. In this paper, we present the results of our preliminary physics design studies of the RFQ-SDTL, RFQ-CCDTL and RFQ-DTL-SDTL configurations. The design of the 4.5 MeV RFQ is discussed along with the matching sections between the RFQ-SDTL/DTL and RFQ-CCDTL. The choice of the accelerator configuration and that of various parameters of the individual accelerator structures under consideration are discussed. The design objectives are to arrive at a configuration which eases heat removal for CW operation and which is less prone to halo formation in order to reduce the beam loss at higher energies.