A comparison between parallelization approaches in molecular dynamics simulations on GPUs

We test the relative performances of two different approaches to the computation of forces for molecular dynamics simulations on graphics processing units. A “vertex‐based” approach, where a computing thread is started per particle, is compared to an “edge‐based” approach, where a thread is started per each potentially non‐zero interaction. We find that the former is more efficient for systems with many simple interactions per particle while the latter is more efficient if the system has more complicated interactions or fewer of them. By comparing computation times on more and less recent graphics processing unit technology, we predict that, if the current trend of increasing the number of processing cores—as opposed to their computing power—remains, the “edge‐based” approach will gradually become the most efficient choice in an increasing number of cases. © 2014 Wiley Periodicals, Inc.     

Building up key segments of N-glycans in the gas phase: intrinsic structural preferences of the alpha(1,3) and alpha(1,6) dimannosides

The intrinsic conformer specific vibrational spectra of two important subunits of the core pentasaccharide of N-linked glycans, the alpha(1,3) and alpha(1,6) dimannosides, have been recorded in the gas phase. Coupling these measurements with a computational exploration of their conformational landscapes has enabled their conformational assignment and has identified characteristic vibrational signatures associated with particular conformational families-including those that do or do not display inter-ring hydrogen bonding across the glycosidic linkage. In addition, the IR spectra of the monosaccharide moieties provide benchmarks, through which the conformational assignments can be refined. This introduces a general concept of modularity and secondary structure in oligosaccharides--essential for the success of similar studies on larger oligosaccharides in the future.     

He I photoelectron spectra and valence synchrotron photoionization for XC(O)SCl (X = F, Cl) compounds

Small penta-atomic molecules like FC(O)SCl and ClC(O)SCl have been analyzed by using both photoelectron spectroscopy (PES) and results derived from the use of synchrotron radiation in the same energy range. For this second experiment total ion yield (TIY), photoelectron photoion coincidence (PEPICO), and partial ion yield (PIY) spectra have been recorded. This set of data together with results obtained by computational chemistry allow us to study electronic properties and the ionization channels of both species. Thus, whereas the photodissociation behavior of FC(O)SCl can be divided into three well-defined energy regions, the fragmentation dynamics of ClC(O)SCl seems to be more complex. Nevertheless, simultaneous evaluation of the PES and valence synchrotron photoionization studies helps to clarify the molecular ionization processes.     

Excess Molar Volumes of (Methyl Ethanoate + 1-Chlorooctane + an n-Alkane) Ternary Mixtures and Their Constituent Binaries at 25°C

Excess molar volumes, at the temperature 25°C and atmospheric pressure over the whole composition range, are reported for the following binary mixtures: methyl ethanoate + (n-octane, n-decane); methyl ethanoate + 1-chlorooctane; 1-chlorooctane + (n-heptane, n-octane, n-nonane, n-decane); and for the ternary mixtures methyl ethanoate + 1-chlorooctane + (n-heptane, n-octane, n-nonane, n-decane). The values of excess molar volumes were calculated from density and composition results. The excess volumes were utilized to test the multiproperty group-contribution model of Nitta et al. using parameter sets available in the literature. Experimental results from ternary mixtures have also been compared to predictions from several empirical and semiempirical models, which utilize, exclusively, results from binary mixtures.     

A new algorithm for NMR spectral normalization.

There is increasing use of high-resolution NMR spectroscopy to examine variations in cell metabolism and/or structure in response to numerous physical, chemical, and biological agents. In these types of studies, in order to obtain relative quantitative information, a comparison between signal intensities of control samples and treated or exposed ones is often conducted. The methods thus far developed for this purpose are not directly related to the overall intrinsic properties of the samples, but rather to the addition of external substances of known concentrations or to indirect measurement of internal substances. In this paper, a new method for quantitatively comparing the spectra of cell samples is presented. It depends on a normalization algorithm which takes into consideration all cell metabolites present in the sample. In particular, the algorithm is based on maximizing, by an opportune sign variable measure, the spectral region in which the two spectra are superimposed. The algorithm was tested by Monte Carlo simulations as well as experimentally by comparing two samples of known contents with the new method and with an older method using a standard. At the end, the algorithm was applied to real spectra of cell samples to show how it could be used to obtain qualitative and quantitative biological information.     

4-Dimensional Frobenius manifolds and Painleve’ VI

A Frobenius manifold has tri-Hamiltonian structure if it is even-dimensional and its spectrum is maximally degenerate. We study the case of the lowest nontrivial dimension \(n=4\) and show that, under the assumption of semisimplicity, the corresponding isomonodromic Fuchsian system is described by the Painlevé \(\hbox {VI}\mu \) equation. Since the solutions of this equation are known to parametrize semisimple Frobenius manifolds of dimension \(n=3\) , this leads to an explicit procedure mapping 3-dimensional Frobenius structures of 4-dimensional ones, and giving all tri-Hamiltonian structures in four dimensions. We illustrate the construction by computing two examples in the framework of Frobenius structures on Hurwitz spaces.     

Mercury(II) dibromo-bis-(3-amino-5-mercapto-1,2,4-triazole): synthesis,crystal structure,and infrared characterization

The title compound C₄H₈N₈S₂HgBr₂ was prepared and characterized by means of X-ray crystallography, and i.r. measurements. The crystals are orthorhombic, space group Pbcn (no. 60) witha=9.707(2),b=8.609(1),c=16.128(2) Å, andZ=4. The compound exhibits discrete monometallic units with the 1,2,4-triazole molecule acting as a monodentate ligand. The structure consists of units in which the mercury atom is coordinated in a distorted tetrahedral geometry by two sulfur and two bromine atoms. The NH and NH₂ group of the 3-amino-5-mercapto-1,2,4-triazole unit are involved in intermolecular hydrogen bonds. Infrared bands are diagnostic of the coordination environment around the metal atoms.     

ADP晶体的全方位生长方法研究

采用一种全新的ADP晶体生长方法,使晶体首先恢复其理想外形,实现晶体的全方位生长,从而提高晶体的生长速度.并对所得晶体进行了透过率,激光散射,摇摆曲线测试及热重差热分析,与常规生长方法比较并分析了全方位生长方法的优势.