Full configuration interaction algorithm on a massively parallel architecture: Direct-list implementation

A parallel full configuration interaction (FCI) code, implemented on a distributed memory MPP computer, has been modified in order to use a direct algorithm to compute the lists of mono- and biexcitations each time they are needed. We were able to perform FCI calculations on the ground state of the acetylene molecule with two different basis sets, corresponding to more than 2.5 and 5 billion Slater determinants, respectively. The calculations were performed on a Cray-T3D and a Cray-T3E, both machines having 128 processors. Performance and comparison between the two computers are reported and discussed. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 658–672, 1998     

Molecular dynamics for proteins: Performance evaluation on massively parallel computers based on mesh networks using a space decomposition approach

Parallel computing seems to be the solution for molecular dynamics of large atomic systems, such as proteins in water environments, but the simulation time critically depends on the processor allocation strategy. A study of the optimal processor allocation based on a space decomposition algorithm for single instruction multiple data flow mesh computers is presented. A particular effort has been made to identify the best criterion according to which the atoms can be allocated to the processors using a spatial decomposition approach. The computing time depends on the granularity of the space decomposition among processing elements and on the ratio between the computation power of processing elements and the communication speed of the interprocessor network. © 1996 by John Wiley & Sons, Inc.     

Identification of methylated regions with peak search based on Poisson model from massively parallel methylated DNA immunoprecipitation-sequencing data

DNA methylation is one of the most important epigenetic modification types, which plays a critical role in gene expression. High efficient surveying of whole genome DNA methylation has been aims of many researchers for long. Recently, the rapidly developed massively parallel DNA‐sequencing technologies open the floodgates to vast volumes of sequence data, enabling a paradigm shift in profiling the whole genome methylation. Here, we describe a strategy, combining methylated DNA immunoprecipitation sequencing with peak search to identify methylated regions on a whole‐genome scale. Massively parallel methylated DNA immunoprecipitation sequencing combined with methylation DNA immunoprecipitation was adopted to obtain methylated DNA sequence data from human leukemia cell line K562, and the methylated regions were identified by peak search based on Poison model. From our result, 140 958 non‐overlapping methylated regions have been identified in the whole genome. Also, the credibility of result has been proved by its strong correlation with bisulfite‐sequencing data (Pearson R²=0.92). It suggests that this method provides a reliable and high‐throughput strategy for whole genome methylation identification.     

Integrated massively parallel sequencing of 15 autosomal STRs and Amelogenin using a simplified library preparation approach

Massively parallel sequencing (MPS) technologies, also termed as next‐generation sequencing (NGS), are becoming increasingly popular in study of short tandem repeats (STR). However, current library preparation methods are usually based on ligation or two‐round PCR that requires more steps, making it time‐consuming (about 2 days), laborious and expensive. In this study, a 16‐plex STR typing system was designed with fusion primer strategy based on the Ion Torrent S5 XL platform which could effectively resolve the above challenges for forensic DNA database‐type samples (bloodstains, saliva stains, etc.). The efficiency of this system was tested in 253 Han Chinese participants. The libraries were prepared without DNA isolation and adapter ligation, and the whole process only required approximately 5 h. The proportion of thoroughly genotyped samples in which all the 16 loci were successfully genotyped was 86% (220/256). Of the samples, 99.7% showed 100% concordance between NGS‐based STR typing and capillary electrophoresis (CE)‐based STR typing. The inconsistency might have been caused by off‐ladder alleles and mutations in primer binding sites. Overall, this panel enabled the large‐scale genotyping of the DNA samples with controlled quality and quantity because it is a simple, operation‐friendly process flow that saves labor, time and costs.     

A massively parallel electrochemical approach to the miniaturization of organic micro- and nanostructures on surfaces

This paper describes a simple and convenient strategy for reducing the dimensions of organic micro-and nanostructures on metal surfaces. By varying electrochemical desorption conditions, features patterned by dip-pen nanolithography or micro contact printing and made of linear alkanethiols or selenols can be gradually desorbed in a controlled fashion. The process is referred to as electrochemical whittling because the adsorbate desorption is initiated at the exterior of the feature and moves inward as a function of time. The whittling process and adsorbate desorption were studied as a function of substrate morphology, adsorbate head and tail groups, and electrolyte solvent and salt. Importantly, one can independently address different nanostructures made of different adsorbates and effect their miniaturization based upon ajudicious selection of adsorbate, applied potential, and supporting electrolyte. Some of the physical and chemical origins of these observations have been elucidated.     

Hybrid heterojunction solar cell based on organic-inorganic silicon nanowire array architecture

Silicon nanowire arrays (SiNWs) on a planar silicon wafer can be fabricated by a simple metal-assisted wet chemical etching method. They can offer an excellent light harvesting capability through light scattering and trapping. In this work, we demonstrated that the organic-inorganic solar cell based on hybrid composites of conjugated molecules and SiNWs on a planar substrate yielded an excellent power conversion efficiency (PCE) of 9.70%. The high efficiency was ascribed to two aspects: one was the improvement of the light absorption by SiNWs structure on the planar components; the other was the enhancement of charge extraction efficiency, resulting from the novel top contact by forming a thin organic layer shell around the individual silicon nanowire. On the contrary, the sole planar junction solar cell only exhibited a PCE of 6.01%, due to the lower light trapping capability and the less hole extraction efficiency. It indicated that both the SiNWs structure and the thin organic layer top contact were critical to achieve a high performance organic/silicon solar cell.     

MOVIPAC: Vibrational spectroscopy with a robust meta‐program for massively parallel standard and inverse calculations

We present the software package MO VI PAC for calculations of vibrational spectra, namely infrared, Raman, and Raman Optical Activity (ROA) spectra, in a massively parallelized fashion. MO VI PAC unites the latest versions of the programs SNF and AKIRA alongside with a range of helpful add‐ons to analyze and interpret the data obtained in the calculations. With its efficient parallelization and meta‐program design, MO VI PAC focuses in particular on the calculation of vibrational spectra of very large molecules containing on the order of a hundred atoms. For this purpose, it also offers different subsystem approaches such as Mode‐ and Intensity‐Tracking to selectively calculate specific features of the full spectrum. Furthermore, an approximation to the entire spectrum can be obtained using the Cartesian Tensor Transfer Method. We illustrate these capabilities using the example of a large π‐helix consisting of 20 (S)‐alanine residues. In particular, we investigate the ROA spectrum of this structure and compare it to the spectra of α‐ and 3₁₀‐helical analogs. © 2012 Wiley Periodicals, Inc.     

Microfluidic array cytometer based on refractive optical tweezers for parallel trapping, imaging and sorting of individual cells

Analysis of genetic and functional variability in populations of living cells requires experimental techniques capable of monitoring cellular processes such as cell signaling of many single cells in parallel while offering the possibility to sort interesting cell phenotypes for further investigations. Although flow cytometry is able to sequentially probe and sort thousands of cells per second, dynamic processes cannot be experimentally accessed on single cells due to the sub-second sampling time. Cellular dynamics can be measured by image cytometry of surface-immobilized cells, however, cell sorting is complicated under these conditions due to cell attachment. We here developed a cytometric tool based on refractive multiple optical tweezers combined with microfluidics and optical microscopy. We demonstrate contact-free immobilization of more than 200 yeast cells into a high-density array of optical traps in a microfluidic chip. The cell array could be moved to specific locations of the chip enabling us to expose in a controlled manner the cells to reagents and to analyze the responses of individual cells in a highly parallel format using fluorescence microscopy. We further established a method to sort single cells within the microfluidic device using an additional steerable optical trap. Ratiometric fluorescence imaging of intracellular pH of trapped yeast cells allowed us on the one hand to measure the effect of the trapping laser on the cells' viability and on the other hand to probe the dynamic response of the cells upon glucose sensing.     

Formation and recovery of a cell sheet by a particle monolayer with the surface roughness

We studied the topographical effect of roughness displayed by a closely packed particle monolayer on formation of a cell monolayer (cell sheet). Particle monolayers were prepared by Langmuir-Blodgett deposition using particles, which were 527nm (SA053) and 1270nm (SA127) in diameter. Human umbilical vein endothelial cells (HUVECs) were seeded at a high density (2.0 x10(5)cells/cm(2)) onto particle monolayers. It was found that cells gradually became into contact with adjacent cells on the SA053 monolayer and the formed cell sheet could be readily detached from the particle monolayer by gentle pipetting. On the other hand, cells adhering onto the tissue culture polystyrene (TCPS) and the SA127 particle monolayer were difficult to peel off. At a low cell seeding density (5.0x10(4)cells/cm(2)), pre-coating with bovine plasma fibronectin (FN) allowed cell growth on an SA053 particle monolayer, and a confluent monolayer was able to be peeled as a cell sheet from the particle monolayer just by pipetting. By immunostaining of human fibronectin, we found that fibronectin was secreted and concentrated onto the substrate side of a cell sheet. The obtained cell sheet adhered and grew on the TCPS again within 20min.     

Time‐dependent molecular fields created by the interaction of an external electromagnetic field with a molecular system

When an external, time‐dependent field interacts with a molecular system various phenomena may take place. However, concentrating on a region close enough to a point of conical intersection, we find that this external field builds up a field similar to an electromagnetic field formed on the one hand by Field‐Dressed nonadiabatic coupling terms which are reminiscent of the Maxwell–Lorentz Vector potentials, and on the other hand via a scalar potential formed by the dipole‐interaction with an external field. In this article, we show that this new field, to be termed Molecular Field, is characterized by several spatial and space‐time Field‐Dressed Curl equations and one, single, space‐time Field‐Dressed Divergence equation. These equations are then shown to yield, just as in the general theory of electromagnetism, the corresponding Field‐Dressed Wave Equations. This achievement could be materialized employing the (1,2) antisymmetric matrix elements of any of the 2×2 dimensional Field‐Dressed nonadiabatic coupling matrices. © 2014 Wiley Periodicals, Inc.     

Microfluidic system for dielectrophoretic separation based on a trapezoidal electrode array

This paper presents a novel microfluidic device for dielectrophoretic separation based on a trapezoidal electrode array (TEA). In this method, particles with different dielectric properties are separated by the device composed of the TEA for the dielectrophoretic deflection of particles under negative dielectrophoresis (DEP) and poly(dimethylsiloxane)(PDMS) microfluidic channel with a sinuous and expanded region. Polystyrene microparticles are exposed to an electric field generated from the TEA in the microfluidic channel and are dielectrophoretically focused to make all of them line up to one sidewall. When these particles arrive at the region of another TEA for dielectrophoretic separation, they are separated having different positions along the perpendicular direction to the fluid flow due to their different dielectrophoretic velocities. To evaluate the separation process and performance, both the effect of the flow rate on dielectrophoretic focusing and the influence of the number of trapezoidal electrodes on dielectrophoretic separation are investigated. Now that this method utilizes the TEA as a source of negative DEP, non-specific particle adhering to the electrode surface can be prevented; conventional separation approaches depending on the positive DEP force suffer from this problem. In addition, since various particle types are continuously separated, this method can be easily applicable to the separation and analysis of various dielectric particles with high particle recovery and selectivity.     

Construction and evaluation of a capillary array DNA sequencer based on a micromachined sheath-flow cuvette

A capillary array electrophoresis DNA sequencer is reported based on a micromachined sheath-flow cuvette as the detection chamber. This cuvette is equipped with a set of micromachined features that hold the capillaries in precise registration to ensure uniform spacing between the capillaries, in order to generate uniform hydrodynamic flow in the cuvette. A laser beam excites all of the samples simultaneously, and a microscope objective images fluorescence onto a set of avalanche photodiodes, which operate in the analog mode. A high-gain transimpedance amplifier is used for each photodiode, providing high duty-cycle detection of fluorescence.     

Simultaneous evaluation of toxicities using a mammalian cell array chip prepared by photocatalytic lithography

A prototype of a mammalian cell array chip was developed on a flat glass surface. A superhydrophilic (water contact angle = 5°)/highly hydrophobic (120°) pattern was prepared on a fluorinated polymer-coated glass surface by means of photocatalytic lithography, and A549 (a human alveolar epithelial cell line), Hep G2 (a human hepatoma cell line) and mouse fibroblast 3T3 cells were inoculated onto the superhydrophilic regions. The cell populations were confined in the superhydrophilic regions for at least 24 h and separated from each other for at least one week. Organ-specific toxicity of aflatoxin B₁ and non-specific toxicity of adriamycin were successfully detected by using the cell array chip.     

Towards a force field based on density fitting

Total intermolecular interaction energies are determined with a first version of the Gaussian electrostatic model (GEM-0), a force field based on a density fitting approach using s-type Gaussian functions. The total interaction energy is computed in the spirit of the sum of interacting fragment ab initio (SIBFA) force field by separately evaluating each one of its components: electrostatic (Coulomb), exchange repulsion, polarization, and charge transfer intermolecular interaction energies, in order to reproduce reference constrained space orbital variation (CSOV) energy decomposition calculations at the B3LYP/aug-cc-pVTZ level. The use of an auxiliary basis set restricted to spherical Gaussian functions facilitates the rotation of the fitted densities of rigid fragments and enables a fast and accurate density fitting evaluation of Coulomb and exchange-repulsion energy, the latter using the overlap model introduced by Wheatley and Price [Mol. Phys. 69, 50718 (1990)]. The SIBFA energy scheme for polarization and charge transfer has been implemented using the electric fields and electrostatic potentials generated by the fitted densities. GEM-0 has been tested on ten stationary points of the water dimer potential energy surface and on three water clusters (n = 16,20,64). The results show very good agreement with density functional theory calculations, reproducing the individual CSOV energy contributions for a given interaction as well as the B3LYP total interaction energies with errors below kBT at room temperature. Preliminary results for Coulomb and exchange-repulsion energies of metal cation complexes and coupled cluster singles doubles electron densities are discussed.     

A new solid-phase extraction disk based on a sheet of single-walled carbon nanotubes

A new kind of solid-phase extraction disk based on a sheet of single-walled carbon nanotubes (SWCNTs) is developed in this study. The properties of such disks are tested, and different disks showed satisfactory reproducibility. One liter of aqueous solution can pass through the disk within 10–100 min while still allowing good recoveries. Two disks (DD-disk) can be stacked to enrich phthalate esters, bisphenol A (BPA), 4-n-nonylphenol (4-NP), 4-tert-octylphenol (4-OP) and chlorophenols from various volumes of solution. The results show that SWCNT disks have high extraction ability for all analytes. The SWCNT disk can extract polar chlorophenols more efficiently than a C₁₈ disk from water solution. Unlike the activated carbon disk, analytes adsorbed by the new disks can be eluted completely with 8–15 mL of methanol or acetonitrile. Finally, the DD-disk system is used to pretreat 1000-mL real-world water samples spiked with BPA, 4-OP and 4-NP. Detection limits of 7, 25, and 38 ng L⁻¹ for BPA, 4-OP, and 4-NP, respectively, were achieved under optimized conditions. The advantages of this new disk include its strong adsorption ability, its high flow rate and its easy preparation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Synthesis and characterization of thermoreversible biopolymer microgels based on hydrogen bonded nucleobase pairing

We describe the synthesis and characterization of a thermoreversibly cross-linked biopolymer microgel based on protein, DNA, and peptide nucleic acid (PNA) components. The DNA assembles into a trifunctional three-way junction (TWJ) with single-stranded overhangs. PNA oligomers complementary to these overhangs and bearing terminal biotin groups hybridize to the DNA TWJ and simultaneously bind to the tetrafunctional protein avidin, leading to a cross-linked system. Dynamic light scattering experiments reveal that micron-sized particles are formed. Static light scattering was used to characterize the internal structure of these microgels, which were found to have a fractal dimension of 1.85, indicative of a loose network structure. Heating disrupts the weakest component in the system, namely the PNA-DNA hybrid, resulting in dissolution of the microgel, while cooling restores the hydrogen bonding leading to reassembly of the microgel. Variation of the nucleotide sequence permits tuning of the gelation temperature with fine control.     

Temperature‐sensitive chitosan membranes as a substrate for cell adhesion and cell sheet detachment

A series of temperature‐sensitive poly(CSA‐co‐NIPAAm) membranes that were suitable for cell culture and confluent cell sheets detachment were prepared. The membranes with thermo‐responsive surface properties were synthesized by the copolymerization of acrylic acid‐derivatized chitosan (CSA) and N‐isopropylacrylamide (NIPAAm) in aqueous solution. Characterization of the membranes were carried out by means of the Fourier transform infrared (FTIR), X‐ray photoelectron spectroscopy (XPS), scanning electron microscope (SEM), and water contact‐angle (WCA) measurements. The adhesion and detachment of mouse fibroblast (L929) cells on these membranes have been investigated. The study showed that poly(CSA‐co‐NIPAAm) membranes could not only enhance fibroblasts attachment but also harvest confluent cell sheets by simply lowering the temperature. Furthermore, the detached cells retained high viability and could proliferate again after transferred to a new culture surface. Copyright © 2011 John Wiley & Sons, Ltd.     

Investigation of the effects of graphite flake alignment on thermal emissivity by applying a magnetic field during coating of an aluminum sheet

In this study we investigated the effects of graphite flake alignment on thermal emissivity by applying a magnetic field during coating of aluminum sheets with graphite. The coating paste was prepared by ball milling graphite flakes with an organic binder. The graphite flake content was 9.1, 13.0, 16.7, 20.0, or 23.1 wt.%. After coating of aluminum sheets with the paste by dipping, a magnetic field was applied vertically to the coated aluminum sheet by use of neodymium magnets. It was observed that the graphite flakes were aligned at an angle to the surface by application of the magnetic field. In contrast, in the absence of the magnetic field the graphite flakes were aligned horizontally on the aluminum sheets. The surface roughness of specimens prepared by use of a magnetic field (MF; R _a = 10.172–14.654 μm) was more than twofold that of specimens for which no magnetic field was applied (NMF; R _a = 4.564 μm). The thermal emissivity of MF9 (9.1 wt.% graphite; ε = 0.80) was higher than that of NMF9 (9.1 wt.% graphite; ε = 0.77). The thermal emissivity of MF20 (20.0 wt.% graphite) was 0.91, the highest in this study. It was shown that flakes aligned at an angle to the surface contribute to enhanced thermal emissivity. Well aligned graphite flakes are therefore expected to enable high thermal dissipation from electronic components.     

An automated method for in vitro anticancer drug efficacy monitoring based on cell viability measurement using a portable photodiode array chip

An integrated circuit (IC) bipolar semiconductor photodiode array (PDA) microchip system coupled with light emitting diodes (LEDs) was used for rapid, automated cell viability measurements and high-throughput drug efficacy monitoring. Using the absorption property of trypan blue dye against the red light emitted by LEDs, we determined the effect of three anticancer drugs, viz., camptothecin (CAM), sodium salicylate (Na-Sal) and naringenin (Nar) on the cell viability of human promyelocytic leukemia cells (HL-60) and human embryonic kidney cells (HEK-293). Cell viabilities were measured based on the relative reduction in the photo responses of the photodiodes, covered with known concentration of trypan blue-stained cells. The developed method offers greater sensitivity and hence an excellent estimation of cell viability, but without all the hassle of conventional methods. Flow cytometric measurement and confocal microscopy were applied as complementary techniques for further validation of the results. The work presented here has important implications with regard to high-throughput measurement of optimal concentrations of different drugs against different cell lines in vitro.