Carbon K‐edge spectra of carbonate minerals

Carbon K‐edge X‐ray spectroscopy has been applied to the study of a wide range of organic samples, from polymers and coals to interstellar dust particles. Identification of carbonaceous materials within these samples is accomplished by the pattern of resonances in the 280–320 eV energy region. Carbonate minerals are often encountered in the study of natural samples, and have been identified by a distinctive resonance at 290.3 eV. Here C K‐edge and Ca L‐edge spectra from a range of carbonate minerals are presented. Although all carbonates exhibit a sharp 290 eV resonance, both the precise position of this resonance and the positions of other resonances vary among minerals. The relative strengths of the different carbonate resonances also vary with crystal orientation to the linearly polarized X‐ray beam. Intriguingly, several carbonate minerals also exhibit a strong 288.6 eV resonance, consistent with the position of a carbonyl resonance rather than carbonate. Calcite and aragonite, although indistinguishable spectrally at the C K‐edge, exhibited significantly different spectra at the Ca L‐edge. The distinctive spectral fingerprints of carbonates provide an identification tool, allowing for the examination of such processes as carbon sequestration in minerals, Mn substitution in marine calcium carbonates (dolomitization) and serpentinization of basalts.     

Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi

Due to the enormous importance of electrostatics in molecular biology, calculating the electrostatic potential and corresponding energies has become a standard computational approach for the study of biomolecules and nano‐objects immersed in water and salt phase or other media. However, the electrostatics of large macromolecules and macromolecular complexes, including nano‐objects, may not be obtainable via explicit methods and even the standard continuum electrostatics methods may not be applicable due to high computational time and memory requirements. Here, we report further development of the parallelization scheme reported in our previous work (Li, et al., J. Comput. Chem. 2012, 33, 1960) to include parallelization of the molecular surface and energy calculations components of the algorithm. The parallelization scheme utilizes different approaches such as space domain parallelization, algorithmic parallelization, multithreading, and task scheduling, depending on the quantity being calculated. This allows for efficient use of the computing resources of the corresponding computer cluster. The parallelization scheme is implemented in the popular software DelPhi and results in speedup of several folds. As a demonstration of the efficiency and capability of this methodology, the electrostatic potential, and electric field distributions are calculated for the bovine mitochondrial supercomplex illustrating their complex topology, which cannot be obtained by modeling the supercomplex components alone. © 2013 Wiley Periodicals, Inc.     

VinaMPI: Facilitating multiple receptor high‐throughput virtual docking on high‐performance computers

The program VinaMPI has been developed to enable massively large virtual drug screens on leadership‐class computing resources, using a large number of cores to decrease the time‐to‐completion of the screen. VinaMPI is a massively parallel Message Passing Interface (MPI) program based on the multithreaded virtual docking program AutodockVina, and is used to distribute tasks while multithreading is used to speed‐up individual docking tasks. VinaMPI uses a distribution scheme in which tasks are evenly distributed to the workers based on the complexity of each task, as defined by the number of rotatable bonds in each chemical compound investigated. VinaMPI efficiently handles multiple proteins in a ligand screen, allowing for high‐throughput inverse docking that presents new opportunities for improving the efficiency of the drug discovery pipeline. VinaMPI successfully ran on 84,672 cores with a continual decrease in job completion time with increasing core count. The ratio of the number of tasks in a screening to the number of workers should be at least around 100 in order to have a good load balance and an optimal job completion time. The code is freely available and downloadable. Instructions for downloading and using the code are provided in the Supporting Information. © 2013 Wiley Periodicals, Inc.     

PHI: A powerful new program for the analysis of anisotropic monomeric and exchange‐coupled polynuclear d‐ and f‐block complexes

A new program, PHI, with the ability to calculate the magnetic properties of large spin systems and complex orbitally degenerate systems, such as clusters of d‐block and f‐block ions, is presented. The program can intuitively fit experimental data from multiple sources, such as magnetic and spectroscopic data, simultaneously. PHI is extensively parallelized and can operate under the symmetric multiprocessing, single process multiple data, or GPU paradigms using a threaded, MPI or GPU model, respectively. For a given problem PHI is been shown to be almost 12 times faster than the well‐known program MAGPACK, limited only by available hardware. © 2013 Wiley Periodicals, Inc.     

Anodic stripping voltammetry of antimony at unmodified carbon electrodes

Antimony is an element of significant environmental concern, yet has been neglected relative to other heavy metals in electroanalysis. As such very little research has been reported on the electroanalytical determination of antimony at unmodified carbon electrodes. In this paper we report the electrochemical determination of Sb(III) in HCl solutions using unmodified carbon substrates, with focus on non-classical carbon materials namely edge plane pyrolytic graphite (EPPG), boron doped diamond (BDD) and screen-printed electrodes (SPE). Using differential pulse anodic stripping voltammetry, EPPG was found to give a considerably greater response towards antimony than other unmodified carbon electrodes, allowing highly linear ranges in nanomolar concentrations and a detection limit of 3.9?nM in 0.25?M HCl. Furthermore, the sensitivity of the response from EPPG was 100 times greater than for glassy carbon (GC). Unmodified GC gave a comparable response to previous results using the bare substrate, and BDD gave an improved, yet still very high limit of detection of 320?nM compared to previous analysis using an iridium oxide modified BDD electrode. SPEs gave a very poor response to antimony, even at high concentrations, observing no linearity from standard additions, as well as a major interference from the ink intrinsic to the working electrode carbon material. Owing to its superior performance relative to other carbon electrodes, the EPPG electrode was subjected to further analytical testing with antimony. The response of the electrode for a 40?nM concentration of Sb(III) was reproducible with a mean peak current of 1.07?µA and variation of 8.4% (n?=?8). The effect of metals copper, bismuth and arsenic were investigated at the electrode, as they are common interferences for stripping analysis of antimony.     

文化框架下多群智能优化算法的云作业调度

作业调度是一种云计算核心技术,为了获得更优的云计算作业调度方案,提出一种文化框架下多群智能优化算法的云作业调度方法。首先构建云作业调度问题的数学模型,然后借助文化算法模型,粒子群算法组成信仰空间,人工鱼群算法组成群体空间,两者之间并行演化,相互促进,对云计算作业调度数学模型进行求解,最后通过仿真实验测试算法的性能。结果表明,本文加快了算法的收敛速度,获得了更优的云计算作业调度方案,大幅度缩短少云计算作业完成时间,具有一定的实用价值。     

Biocomputing Based on DNA Strand Displacement Reactions

The high sequence specificity and precise base complementary pairing principle of DNA provides a rich orthogonal molecular library for molecular programming, making it one of the most promising materials for developing bio-compatible intelligence. In recent years, DNA has been extensively studied and applied in the field of biological computing. Among them, the toehold-mediated strand displacement reaction (SDR) with properties including enzyme free, flexible design and precise control, have been extensively used to construct biological computing circuits. This review provides a systemic overview of SDR design principles and the applications. Strategies for designing DNA-only, enzymes-assisted, other molecules-involved and external stimuli-controlled SDRs are described. The recently realized computing functions and the application of DNA computing in other fields are introduced. Finally, the advantages and challenges of SDR-based computing are discussed.     

Multiple mobility edges in a 1D Aubry chain with Hubbard interaction in presence of electric field: Controlled electron transport

Electronic behavior of a 1D Aubry chain with Hubbard interaction is critically analyzed in presence of electric field. Multiple energy bands are generated as a result of Hubbard correlation and Aubry potential, and, within these bands localized states are developed under the application of electric field. Within a tight-binding framework we compute electronic transmission probability and average density of states using Green's function approach where the interaction parameter is treated under Hartree–Fock mean field scheme. From our analysis we find that selective transmission can be obtained by tuning injecting electron energy, and thus, the present model can be utilized as a controlled switching device.     

Investigations of silicone breast implants with the NMR-MOUSE

Silicone breast implants are used for breast augmentation and breast reconstruction. The issues of concern associated with such implants are: (a) the quality control of each implant before implantation, and (b) the detection of implant bleeding after implantation. We have studied the use of the Nuclear Magnetic Resonance-MObile Universal Surface Explorer (NMR-MOUSE) for the nondestructive testing of (a) the quality of implant shells, and (b) changes in implant gel due to leakage of body fluid into the implant. Depth profiles measured nondestructively through implant shells at different positions of each implant by the Profile NMR-MOUSE assured good reproducibility of the quality and thickness of different shell layers. The leakage of implants upon rupture was mimicked by observing changes in the transverse NMR relaxation time of the implant gel upon ingress of physiological saline solution and safflower oil through the rupture. Results demonstrate that nondestructive testing with unilateral NMR is a potential method for use in the quality control of implants and for the screening of implants for rupture after implantation.