Student cluster competition: ParConnect reproducibility task report

Reproducibility is a desirable characteristic of any experimental work in computer science. In this paper, we reproduce the results in the paper, “A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications”, for verifying their claims on the speed and scalability of their algorithm. We first state the claims made in the original paper. Then, we describe our hardware and software setup used for the reproducibility task, followed by the steps taken to setup the proposed algorithm and profiling software. Lastly, we present the results obtained from our experiments and show that we are able to reproduce most of the claims made in the original paper.     

Load transfer of graphene/carbon nanotube/polyethylene hybrid nanocomposite by molecular dynamics simulation

Load transfer of the graphene/carbon nanotube (CNT)/polyethylene hybrid nanocomposite is studied here from molecular dynamics (MD) simulations. Simulations of this composite material under uniaxial tension were conducted by varying CNT’s position and diameter in the polymer matrix. The obtained results show that: (1) The peak strength of stress and strain evolution in the polymer matrix is lower than the peak strength of the graphene/graphene and graphene/polymer interfaces. Hence, the damage zone is always located in the polymer matrix. (2) Agglomerated two-layer graphenes do not possess an increased value in the peak strength compared with single-layer graphene-reinforced polymer nanocomposite (PNC), while two separate layers of graphene show slightly higher peak strength. (3) The largest peak strength is observed before CNT moves to the center of the polymer matrix. The damage location moves from the upper to the lower part of CNT when the CNT is located at the centre of polymer matrix. (4) The influence of the CNT diameter on the peak strength is not obvious, while the damage location and shape in the polymer matrix changes with respect to varying CNT diameters. In addition, the damage zone always falls outside the interphase zone.     

Effect of swaging on microstructure and mechanical properties of liquid-phase sintered 93W-4.9(Ni,Co)-2.1Fe alloy

The effect of swaging on the microstructure and mechanical properties of 93W-4.9Ni-2.1Fe alloy was investigated. The alloy was prepared by liquid-phase sintering under hydrogen atmosphere followed by vacuum heat treatment and swaging at 600 °C with different area reductions (ranging from 15.0% to 84.8%). The as-swaged alloy with area reduction 84.8% exhibits the highest ultimate tensile strength (about 1490 MPa) and the lowest elongation (about 2.5%), which has been attributed to higher fraction of tungsten cleavage. For the as-sintered alloys, the fracture modes are a combination of the ductile rupture of W-Ni-Fe-Co matrix, transgranular cleavage of the tungsten particles, W-W interfacial segregation and W-M interfacial debonding, whereas transgranular cleavage of the tungsten particles is the main characteristic in the as-swaged alloy. Transmission electron microscopy images indicate that tungsten grains and W-Ni-Fe-Co matrix phase are composed of high-density dislocations. Based on the results, when running the swaging of 93W-4.9(Ni, Co)-2.1Fe alloy at 600 °C, the strengthening mechanism can be mainly due to the working-hardening.     

Prediction of zonal and total discharges in smooth straight prismatic compound channels using regression modeling

Experimental results are presented concerning the zonal and total discharge distribution and characteristics in a compound channel cross-section comprising one rectangular main channel and two symmetrical floodplains. The discharges in the main channel, floodplains, and total compound channel are found to be highly correlated to several dimensionless parameters defined using the compound channel cross-section geometry. Multi-variable regression analysis was utilized for developing predictive models that can estimate the main channel, floodplains and total discharges as a function of four different dimensionless parameters. The developed models to predict the zonal and total discharges in compound channels are found to be highly significant according to several major statistics including the model standard error, coefficient of determination (R²), and F-statistic. The developed multi-variable regression-based models are also tested for validity using available experimental data. Several statistical tests applicable to the analysis of residuals have indicated the effectiveness of the developed predictive models.     

Resonance and it application to a vibratory mill

The dynamics of a driven oscillator, consisting of a cylindrical container suspended by springs and filled with a large number of freely moving balls, is investigated around the principal resonance frequency. The theoretical findings are applied to a cantilever resonance vibratory mill and allow for the experimental determination of the dynamical properties of the mill, estimation of the power input and its absorbed and dissipated fractions. The results are tested for the mechanical activation of quartz.     

Molecular dynamics simulations of mutated Mycobacterium tuberculosis l-alanine dehydrogenase to illuminate the role of key residues

l-Alanine dehydrogenase from Mycobacterium tuberculosis (l-MtAlaDH) catalyzes the NADH-dependent interconversion of l-alanine and pyruvate, and it is considered to be a potential target for the treatment of tuberculosis. The experiment has verified that amino acid replacement of the conserved active-site residues which have strong stability and no great changes in biological evolutionary process, such as His96 and Asp270, could lead to inactive mutants [Ågren et al., J. Mol. Biol. 377 (2008) 1161–1173]. However, the role of these conserved residues in catalytic reaction still remains unclear. Based on the crystal structures, a series of mutant structures were constructed to investigate the role of the conserved residues in enzymatic reaction by using molecular dynamics simulations. The results show that whatever the conserved residues were mutated, the protein can still convert its conformation from open state to closed state as long as NADH is present in active site. Asp270 maintains the stability of nicotinamide ring and ribose of NADH through hydrogen bond interactions, and His96 is helpful to convert the protein conformation by interactions with Gln271, whereas, they would lead to the structural rearrangement in active site and lose the catalytic activity when they were mutated. Additionally, we deduce that Met301 plays a major role in catalytic reaction due to fixing the nicotinamide ring of NADH to prevent its rotation, and we propose that Met301 would be mutated to the hydrophobic residue with large steric hindrance in side chain to test the activity of the protein in future experiment.     

Studies on pore blocking mechanism and technical feasibility of a hybrid PAC-MF process for reclamation of irrigation water from biotreated POME

An integrated low-cost adsorption (with powdered activated carbon, PAC) and cross-flow membrane filtration (with microfiltration membranes of 0.1 and 0.2 μm pore sizes) process was employed for the treatment of biotreated palm oil mill effluent (POME) to produce irrigation water that is fully benchmarked with water-quality standards. The permeate quality was within the recommended standard for irrigation water, as the concentrations of all critical constituents were well below their recommended values. Sustainability of the process integration was further confirmed with the domination of cake filtration over other blocking mechanisms with higher R² values at all trans-membrane pressures. Suitable extended usage of permeate was found for toilet/urinal flushing.     

Reduction of primary tar vapor from biomass by hot char particles in fixed bed gasification

This study investigated the reduction of primary tar vapor from biomass pyrolysis over a bed of hot char particles, focusing on the effect of different operating conditions and char properties. The char samples were prepared from wood, paddy straw, palm kernel shell, and activated carbon. The primary tar was produced from fir wood by pyrolysis at 500 °C and passed through a reactor filled with char particles with different lengths and temperatures.The tar cracking reactions became active above 700 °C, and the presence of hot char particles promoted more tar reduction compared with thermal cracking alone. The mass yield of the primary tar was reduced from 24.8% by pyrolysis to 13.7% by thermal cracking at 800 °C, and further to 7.7% by hot char particles in a reactor volume of 1.48 cm³/g_wood. In terms of carbon yield, these values correspond to 32.1%, 19.9% and 11.8%, respectively. The tar with smaller molecular weights was quickly decomposed to gases, whereas the heavy tar was resistant to cracking, even when the reactor volume was increased to 6.90 cm³/g_wood. The tar cracking behaviors were similar for four char types despite differences in microscopic surface areas, pore-size distributions, and inorganic contents. The results suggest that creating a tar-cracking zone using char particles situated between the pyrolysis and gasification zones could be helpful in converting the primary tar vapor in a downdraft fixed-bed gasifier, but the degree of conversion is not high enough to eliminate tar issues completely.     

The Relational Economy of Informality: Spatial Dimensions of Street Trading in Ivory Park,South Africa

The paper seeks to contribute towards an understanding of the spatial ordering of the neighbourhood economy of marginalised urban communities where informal businesses predominate. In doing so, we examine the spatial economy of informality in which contestations and agreements over space exert an organising dynamic. These social-spatial processes are examined through a case study in Ivory Park, Johannesburg, wherein we focus on the consumption and organisation of space, the infrastructural and architectural strategies that entrepreneurs utilise in responding to market impulses, risks and pressure and the unseen organisational logics as well as social processes in which the use of space is contested. The analysis is based on primary data collected through a business census and a social-spatial examination of the street market environment, including infrastructure and business forms. The research highlights three aspects of this relational economy that are insightful for the process of thinking about how cities should respond to economic informality. First, the case illustrates the flexible agility of businesses, witnessed in the responsiveness of business activities to space and place dynamics. Second, it illuminates some of the unseen organisational logics that accommodate different business and non-business needs (traders versus pedestrians; small businesses versus large) but also uphold power dynamics. Third, it reveals the social processes that facilitate inclusivity, from surveillance, to the acceptance of ‘outsiders’ and the sociability afforded by the publicness of interactions within the street space. Taken together, these aspects demonstrate the importance of reimagining current approaches to managing neighbourhood economies in ways that are sensitive to the complex systems that spatial informalities can generate.