Parallel Assembly Research Articles

Oxorhenium‐Mediated Assembly of Noncyclic Selective Integrin Antagonists: A Combinatorial Approach

The parallel oxorhenium-mediated assembly of 288 noncyclic RGD analogues is reported. All complexes contain a NS(2) +S chelating motif that enables the unambiguous coordination of the oxorhenium and oxotechnetium cores. In this study, "modules S" contain a variety of pending guanidinium groups whereas the "NS(2) modules" are made of a series of N-acylated amino acids. Combination of sets of "NS(2) " and "S modules" together with tetrabutylammonium tetrachlorooxorhenate gave the corresponding oxorhenium complexes in good yields and satisfactory purities. Evaluation of these metalloconstructs towards integrins α(V) β(3) , α(IIb) β(3) , and α(V) β(5) led to the identification of micromolar and submicromolar antagonists of theses integrins. These compounds exhibit interesting selectivities and promise attractive applications for the molecular imaging of integrin-dependent pathologies.

Quantitative analysis of parallel nanowire array assembly by dielectrophoresis

We describe an assembly technique useful for generating ordered arrays of nanowires (NWs) between electrodes via dielectrophoresis (DEP) and an analysis technique useful for extracting quantitative information about the local electric fields and dielectrophoretic forces from video microscopy data. By tuning the magnitude of the applied electric fields such that the attractive forces on the NWs are of the same order of magnitude as the Brownian forces, and by taking advantage of the inter-NW repulsive forces during DEP, NWs can be assembled into parallel arrays with high reproducibility. By employing a particle-tracking code and analysis of NW motion, we demonstrate a method for quantitative mapping of the dielectrophoretic torques and NW-surface interactions as a function of position on the substrate, which allows a more complete understanding of the dynamics of the assembly and the ability to control these parameters for precise assembly.

A tabu search approach for mixed-model parallel assembly line balancing problem (type II)

There are two types of assembly line balancing problems (ALBPs), which have received a great attention in the literature during the past four decades: types I and II. Both versions of ALBP are NP-hard and cannot be solved by exact methods. This paper presents an efficient tabu search (TS) metaheuristic approach for allocating tasks to balance the mixed-model production through the parallel assembly lines. Firstly, an initial solution is determined by a heuristic algorithm. Secondly, an optimum cycle time for each line in the mixed-model parallel assembly line (MMPAL) is calculated through the TS. The developed methodology, tabu search mixed-model parallel assembly line balancing (TMMPALB) model, is tested on test problems producing three and four products. Computational experiments show that the TMMPALB produces good enough solutions in case of MMPALs. The results of the proposed procedure improve cycle times of 77 test problems out of 87.

Modelling, simulation and design constraints of electrostatic self-assembly of microparts

Self-assembly is a technique that involves the manipulation and alignment of microparts onto a substrate without additional machinery and makes it possible to assemble a large number of small devices in parallel. A novel concept for the self-alignment of microparts on a substrate by means of electrostatic attraction has been previously introduced and experimentally verified by the authors. In this paper FE modelling is used to determine the magnitude of the self-aligning force and from these findings, a semi-empirical, fitted force model is produced for circular, complementary electrodes between micropart and substrate. Based on this force model, constraints useful for the design and the prediction of the behaviour of microparts are proposed and dynamic simulations of the alignment procedure are presented. The results of these simulations and the previously conducted experiments, as well as the introduced design constraints are the first steps towards the modelling and the implementation of a parallel assembly approach of tiny parts and thereby integration of heterogeneous materials.

Evaluation of short read metagenomic assembly

BackgroundMetagenomic assembly is a challenging problem due to the presence of genetic material from multiple organisms. The problem becomes even more difficult when short reads produced by next generation sequencing technologies are used. Although whole genome assemblers are not designed to assemble metagenomic samples, they are being used for metagenomics due to the lack of assemblers capable of dealing with metagenomic samples. We present an evaluation of assembly of simulated short-read metagenomic samples using a state-of-art de Bruijn graph based assembler.ResultsWe assembled simulated metagenomic reads from datasets of various complexities using a state-of-art de Bruijn graph based parallel assembler. We have also studied the effect of k-mer size used in de Bruijn graph on metagenomic assembly and developed a clustering solution to pool the contigs obtained from different assembly runs, which allowed us to obtain longer contigs. We have also assessed the degree of chimericity of the assembled contigs using an entropy/impurity metric and compared the metagenomic assemblies to assemblies of isolated individual source genomes.ConclusionsOur results show that accuracy of the assembled contigs was better than expected for the metagenomic samples with a few dominant organisms and was especially poor in samples containing many closely related strains. Clustering contigs from different k-mer parameter of the de Bruijn graph allowed us to obtain longer contigs, however the clustering resulted in accumulation of erroneous contigs thus increasing the error rate in clustered contigs.

Multiple-colony ant algorithm for parallel assembly line balancing problem

Assembly lines are designed as flow oriented production systems which perform operations on standardized products in a serial manner. Balancing of assembly lines is one of the most important problems among the other problems of assembly lines like designing and managing. In today's highly competitive manufacturing environment increasing system flexibility, reducing failure sensitivity, improving system balance and productivity are crucial. Parallel assembly lines provide some opportunities in improving these objectives especially when the capacity of production system is insufficient. Unlike the traditional assembly lines there are a few studies on balancing parallel assembly lines in the present literature. Parallel assembly line balancing is a NP-hard problem similar to other assembly lines. In this paper, a novel multiple-colony ant algorithm is developed for balancing bi-objective parallel assembly lines. The proposed algorithm is also one of the first attempts in modeling and solving the present problem with swarm intelligence based meta-heuristics. The proposed approach is extensively tested on the benchmark problems and performance of the approach is compared with existing algorithms. It is shown that the proposed approach is very effective.

Self-assembly of dies through electrostatic attraction: modelling of alignment forces and kinematics

A variety of self-assembly procedures have been introduced. An interesting and prospective application of this technology is the manufacturing of heterogeneously integrated electronic circuits. The two main approaches are top-down and bottom-up self-assembly. Top-down self-assembly is a massively parallel approach for assembly and alignment of small but highly functional parts onto a substrate without using additional machinery. This paper discusses a concept where electrostatic forces are used to achieve top-down self-alignment of parts in the micro- and milli scale. This approach is also concievable to accomplish accurate alignment of pre-positioned dies, for example electronic integrated circuits. For this approach complementary and electrically conductive micro-structured patterns serve as alignment structures. Experimental results have verified that it is feasible to accomplish self-assembly and accurate alignment of single micro-structured parts. The alignment forces and kinematics for parts in the range of a few hundred micrometers have been modelled and computed, respectively. Simulations have been performed in Matlab/Simulink. The presented simulation tool along with the experimental results is the first steps towards the modelling and the realisation of a massively parallel assembly approach of dies.

Parallel genome assembly from pre-biotic split-genes: A solution for the mosaic genome conundrum

AbstractThe classical concept that all complex life evolved from a simple bacterium-like life form has been questioned by comparative genomics and proteomics. Several discoveries, including the occurrence of entirely new genes in unexpected life forms without any precursors, and the random mosaic distribution of genes across organisms in higher taxa undermine the principal assertions of this theory. We present a new model of the pre-biotic parallel evolution of eukaryotic genomes starting with the structurally complex split genes, which are far more probable of supporting biological information and of occurring in random DNA sequences than contiguous genes. By comparing the mosaic patterns of simulated genomes and extant genomes, we show that genomes arising from simulated assembly of random split genes form the same gene distribution patterns observed in extant eukaryotes. This parallel genome origin model eliminates the post-genomic and classical conundrums faced by the linear branching evolution model.

Parallel microassembly with a robotic manipulation system

This paper proposes a methodology to assemble multiple micro-components simultaneously with a robotic manipulator using a parallel assembly method. Through manipulating and assembling the micro-components, intricate, out-of-plane, three-dimensional micro-devices can now be fabricated. Use of a parallel microassembly process rather that a serial approach can significantly increase the productivity and reduce the cost of assembling micro-devices. The parallel microassembly operation proposed in this work was developed and implemented on a 6-DOF robot manipulator to attain considerable manufacturing flexibility. In this study, three passive microgrippers were bonded in parallel to the end-effector of the manipulator. Three microparts were then grasped by the grippers from the worktable of the manipulator, rotated 90°, and assembled onto the base substrate simultaneously. During the parallel microassembly operation, the visual image may not be able to monitor all three gripper-part pairs simultaneously due to the limited field of view of the microscope. Through the use of an alignment-calibration algorithm with only one gripper-part set, the remaining two sets were successfully manipulated and inserted onto the desired assembly location.

Dioxythiophene-Based Polymer Electrodes for Supercapacitor Modules

We report on the electrochemical and capacitive behaviors of poly(2,2-dimethyl-3,4-propylene-dioxythipohene) (PProDOT-Me2) films as polymeric electrodes in Type I electrochemical supercapacitors. The supercapacitor device displays robust capacitive charging/discharging behaviors with specific capacitance of 55 F/g, based on 60 μg of PProDOT-Me2 per electrode, that retains over 85% of its storage capacity after 32 000 redox cycles at 78% depth of discharge. Moreover, an appreciable average energy density of 6 Wh/kg has been calculated for the device, along with well-behaved and rapid capacitive responses to 1.0 V between 5 to 500 mV s(-1). Tandem electrochemical supercapacitors were assembled in series, in parallel, and in combinations of the two to widen the operating voltage window and to increase the capacitive currents. Four supercapacitors coupled in series exhibited a 4.0 V charging/discharging window, whereas assembly in parallel displayed a 4-fold increase in capacitance. Combinations of both serial and parallel assembly with six supercapacitors resulted in the extension of voltage to 3 V and a 2-fold increase in capacitive currents. Utilization of bipolar electrodes facilitated the encapsulation of tandem supercapacitors as individual, flexible, and lightweight supercapacitor modules.

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

An accurate genome sequence of a desired species is now a pre-requisite for genome research. An important step in obtaining a high-quality genome sequence is to correctly assemble short reads into longer sequences accurately representing contiguous genomic regions. Current sequencing technologies continue to offer increases in throughput, and corresponding reductions in cost and time. Unfortunately, the benefit of obtaining a large number of reads is complicated by sequencing errors, with different biases being observed with each platform. Although software are available to assemble reads for each individual system, no procedure has been proposed for high-quality simultaneous assembly based on reads from a mix of different technologies. In this paper, we describe a parallel short-read assembler, called Ray, which has been developed to assemble reads obtained from a combination of sequencing platforms. We compared its performance to other assemblers on simulated and real datasets. We used a combination of Roche/454 and Illumina reads to assemble three different genomes. We showed that mixing sequencing technologies systematically reduces the number of contigs and the number of errors. Because of its open nature, this new tool will hopefully serve as a basis to develop an assembler that can be of universal utilization (availability: http://deNovoAssembler.sf.Net/). For online Supplementary Material , see www.liebertonline.com.

Upregulation of paxillin and focal adhesion signaling follows Dystroglycan Complex deletions and promotes a hypertensive state of differentiation

Anchorage to matrix is mediated for many cells not only by integrin-based focal adhesions but also by a parallel assembly of integral and peripheral membrane proteins known as the Dystroglycan Complex. Deficiencies in either dystrophin (mdx mice) or γ-sarcoglycan (γSG−/− mice) components of the Dystroglycan Complex lead to upregulation of numerous focal adhesion proteins, and the phosphoprotein paxillin proves to be among the most prominent. In mdx muscle, paxillin-Y31 and Y118 are both hyper-phosphorylated as are key sites in focal adhesion kinase (FAK) and the stretch-stimulatable pro-survival MAPK pathway, whereas γSG−/− muscle exhibits more erratic hyper-phosphorylation. In cultured myotubes, cell tension generated by myosin-II appears required for localization of paxillin to adhesions while vinculin appears more stably integrated. Overexpression of wild-type (WT) paxillin has no obvious effect on focal adhesion density or the physical strength of adhesion, but WT and a Y118F mutant promote contractile sarcomere formation whereas a Y31F mutant shows no effect, implicating Y31 in striation. Self-peeling of cells as well as Atomic Force Microscopy (AFM) probing of cells with or without myosin-II inhibition indicate an increase in cell tension within paxillin-overexpressing cells. However, prednisolone, a first-line glucocorticoid for muscular dystrophies, decreases cell tension without affecting paxillin at adhesions, suggesting a non-linear relationship between paxillin and cell tension. Hypertension that results from upregulation of integrin adhesions is thus a natural and treatable outcome of Dystroglycan Complex down-regulation.

Massive Parallel Assembly of Microbeads for Fabrication of Microtools Having Spherical Structure and Powerful Manipulation by Optical Tweezers

Production of functional microtools having an arbitrary shape by self-assembly of microparticles and heat treatment above the glass transition temperature of the microparticles was developed. Polystyrene microbeads were used as a material of the microtool. A solution including microparticles was dispersed onto the silicon substrate having microtool patterns fabricated by photolithography and etching. Dispersed particles were introduced to the pattern by gravity force. Microparticles in the pattern aggregate autonomously by surface tension through evaporation of the solution. Aggregated microparticles were fused by heating above the glass transition temperature (100°C). Fused microparticles were detached from the pattern by ultrasonic treatment and used as microtools. Produced microtool has spherical part since the microtool is made of microparticles. Spherical part is suitable for trapping point of optical tweezers. We demonstrated production of microtools using self-assembly and manipulation of the fabricated microtool on a chip.

Selective Parallel Integration of Individual Metallic Single-Walled Carbon Nanotubes from Heterogeneous Solutions

The dielectrophoretic separation of individual metallic single-walled carbon nanotubes (SWNTs) from heterogeneous solutions and their simultaneous deposition between electrodes is achieved and confirmed by direct electric transport measurements. Out-of-solution guided parallel assembly of individual SWNTs was investigated for electric field frequencies between 1 and 200 MHz. At 200 MHz, 19 of the 22 deposited SWNTs (86%) displayed metallic behavior, whereas at lower frequencies the expected random growth distribution of 1/3 metallic SWNTs prevailed. A threshold separation frequency of 188 MHz is extracted from a surface-conductivity model, and a conductivity weighting factor is introduced to elucidate the separation frequency dependence. Low-frequency experiments and numerical simulations show that long-range nanotube transport is governed by hydrodynamic effects whereas local trapping is dominated by dielectrophoretic forces. The electrokinetic framework of dielectrophoresis in low-concentration solutions is thus provided and allows a deeper understanding of the underlying mechanisms in dielectrophoretic deposition processes for long and large-diameter SWNT-based low-resistance device integration.

Scheduling algorithms for an air conditioner manufacturing system composed of multiple parallel assembly lines

This paper focuses on a scheduling problem in a manufacturing system composed of multiple parallel assembly lines. There are multiple orders to be processed in this system, and each order is specified by the product type, the number of products to be processed, and the due date. Each product is composed of two types of subassemblies, one unit of an external subassembly and one or more units of an internal subassembly. In the system, the parallel assembly lines are not identical, and certain lines are designated for certain product types. We present heuristic algorithms for the scheduling problem with the objective of minimizing total tardiness of orders. For an evaluation of the performance of the suggested algorithms, computational experiments are performed on a number of problem instances and results show that the suggested algorithms work better than the method used in a real manufacturing system.

In-Fusion BioBrick assembly and re-engineering.

Genetic circuits can be assembled from standardized biological parts called BioBricks. Examples of BioBricks include promoters, ribosome-binding sites, coding sequences and transcriptional terminators. Standard BioBrick assembly normally involves restriction enzyme digestion and ligation of two BioBricks at a time. The method described here is an alternative assembly strategy that allows for two or more PCR-amplified BioBricks to be quickly assembled and re-engineered using the Clontech In-Fusion PCR Cloning Kit. This method allows for a large number of parallel assemblies to be performed and is a flexible way to mix and match BioBricks. In-Fusion assembly can be semi-standardized by the use of simple primer design rules that minimize the time involved in planning assembly reactions. We describe the success rate and mutation rate of In-Fusion assembled genetic circuits using various homology and primer lengths. We also demonstrate the success and flexibility of this method with six specific examples of BioBrick assembly and re-engineering. These examples include assembly of two basic parts, part swapping, a deletion, an insertion, and three-way In-Fusion assemblies.

Positionally Isomeric Organic Gelators: Structure–Gelation Study, Racemic versus Enantiomeric Gelators, and Solvation Effects

Low molecular weight gelator molecules consisting of aliphatic acid, amino acid (phenylglycine), and omega-aminoaliphatic acid units have been designed. By varying the number of methylene units in the aliphatic and omega-aminoaliphatic acid chains, as defined by descriptors m and n, respectively, a series of positionally isomeric gelators having different positions of the peptidic hydrogen-bonding unit within the gelator molecule has been obtained. The gelation properties of the positional isomers have been determined in relation to a defined set of twenty solvents of different structure and polarity and analyzed in terms of gelator versatility (G(ver)) and effectiveness (G(eff)). The results of gelation tests have shown that simple synthetic optimizations of a "lead gelator molecule" by variation of m and n, end-group polarity (carboxylic acid versus sodium carboxylate), and stereochemistry (racemate versus optically pure form) allowed the identification of gelators with tremendously improved versatility (G(ver)) and effectiveness (G(eff)). Dramatic differences in G(eff) values of up to 70 times could be observed between pure racemate/enantiomer pairs of some gelators, which were manifested even in the gelation of very similar solvents such as isomeric xylenes. The combined results of spectroscopic ((1)H NMR, FTIR), electron microscopy (TEM), and X-ray diffraction studies suggest similar organization of the positionally isomeric gelators at the molecular level, comprising parallel beta-sheet hydrogen-bonded primary assemblies that form inversed bilayers at a higher organizational level. Differential scanning calorimetry (DSC) studies of selected enantiomer/racemate gelator pairs and their o- and p-xylene gels revealed the simultaneous presence of different polymorphs in the racemate gels. The increased gelation effectiveness of the racemate compared to that of the single enantiomer is most likely a consequence of its spontaneous resolution into enantiomeric bilayers and their subsequent organization into polymorphic aggregates of different energy. The latter determine the gel fiber thickness and solvent immobilization capacity of the formed gel network.

Determination of constitutive and morphological parameters of columnar thin films by inverse homogenization

A dielectric columnar thin film (CTF), characterized macroscopically by a relative permittivity dyadic, was investigated theoretically. The CTF was assumed, on the nanoscale, to be an assembly of parallel, identical, elongated ellipsoidal inclusions made of an isotropic dielectric material that has a different refractive index from the bulk material that was evaporated to fabricate the CTF. The inverse Bruggeman homogenization formalism was developed in order to estimate the refractive index of the deposited material, one of the two shape factors of the ellipsoidal inclusions, and the volume fraction occupied by the deposited material, from a knowledge of relative permittivity dyadic of the CTF. A modified Newton-Raphson technique was implemented to solve the inverse Bruggeman equations. Numerical studies revealed how the three nanoscale parameters of CTFs vary as functions of the vapor incidence angle.

Dielectrophoretic integration of single- and few-layer graphenes

The dielectrophoretic integration of single- and few-layered graphenes from three distinct graphene suspensions is presented, enabling the parallel assembly of individual two-dimensional nanostructures at predefined locations. The first suspension is an aqueous solution of graphene oxide, the second is ultrasonically exfoliated pristine graphene in N-methyl-pyrrolidone (NMP), and the third is exfoliated graphene in surfactant-stabilized 1 wt % aqueous SDBS solutions. The most crucial aspect for the successful thin flake deposition is the solution quality of the exfoliated graphene. After dielectrophoresis, single-layer graphene oxide is placed between the electrodes, which, while initially insulating, recovers its electrical conductivity following thermal reduction. From the chemically unmodified graphene-NMP solutions, the directed assembly of electrically active few-layer graphene flakes is realized, with flake thicknesses in the range 8–30 nm. Liquid phase exfoliation in water-surfactant solutions yields significantly thicker flake dimensions from 50 to several 100 nm due to the higher enthalpy of mixing in the dispersion. To achieve single-layer pristine graphene dielectrophoretic deposition, higher solution qualities must be available, consisting largely of single-layer graphene sheets. The reported research provides an important framework for parallel fabrication approaches of graphene-based devices.

High-performance finite-element simulations of seismic wave propagation in three-dimensional nonlinear inelastic geological media

We present finite-element numerical simulations of seismic wave propagation in non linear inelastic geological media. We demonstrate the feasibility of large-scale modeling based on an implicit numerical scheme and a nonlinear constitutive model. We illustrate our methodology with an application to regional scale modeling in the French Riviera, which is prone to earthquakes. The PaStiX direct solver is used to handle large matrix numerical factorizations based on hybrid parallelism to reduce memory overhead. A specific methodology is introduced for the parallel assembly in the context of soil nonlinearity. We analyse the scaling of the parallel algorithms on large-scale configurations and we discuss the physical results.