Designing amino acid sequences to fold with good hydrophobic cores

We present two methods for designing amino acid sequences ofproteins that will fold to have good hydrophobic cores. Giventhe coordinates of the desired target protein or polymer structure,the methods generate sequences of hydrophobic (H) and polar(P) monomers that are intended to fold to these structures.One method designs hydrophobic inside, polar outside; the otherminimizes an energy function in a sequence evolution process.The sequences generated by these methods agree at the levelof 60–80% of the sequence positions in 20 proteins inthe Protein Data Bank. A major challenge in protein design isto create sequences that can fold uniquely, i.e. to a singleconformation rather than to many. While an earlier lattice-basedsequence evolution method was shown not to design unique folders,our method generates unique folders in lattice model tests.These methods may also be useful in designing other types offoldable polymer not based on amino acids     

HDPE/LLDPE reactor blends with bimodal microstructures—part I: mechanical properties

Reactor blends of polyethylene/poly(ethylene-co-1-octene) resins with bimodal molecular weight and bimodal short chain branching distributions were synthesized in a two-step polymerization process. The compositions of these blends range from low molecular weight (LMW) homopolymer to high molecular weight (HMW) copolymer and, vice versa, HMW homopolymer to LMW copolymer. The physical properties of the blends were found to be consistent with the nature of the individual components. For the tensile properties, the stiffness decreases with increasing the fraction of the copolymer, regardless of the molecular weight of the homopolymer fraction. For these blends with bimodal microstructures, it was confirmed that the degree of crystallinity governs the stiffness of the polymer. However, the energy dampening properties of the polymers benefit from the presence of the copolymer. A balance of stiffness and toughness can be obtained by altering the composition of the blends. For some blends, the presence of HMW homopolymer can dominate the tensile properties, showing little variation in the stiffness with increased addition of copolymer. It was also demonstrated that the testing conditions and thermal treatment of the polymer greatly influence the resulting elastic and energy dampening properties. Depending on the desired application, annealing these polymers (especially very low density copolymers) not only increases the crystallinity and stiffness, but also changes the frequency response of the dynamic mechanical properties.     

Ellipsoidal neighbourhood outlier factor for distributed anomaly detection in resource constrained networks

Anomaly detection in resource constrained wireless networks is an important challenge for tasks such as intrusion detection, quality assurance and event monitoring applications. The challenge is to detect these interesting events or anomalies in a timely manner, while minimising energy consumption in the network. We propose a distributed anomaly detection architecture, which uses multiple hyperellipsoidal clusters to model the data at each sensor node, and identify global and local anomalies in the network. In particular, a novel anomaly scoring method is proposed to provide a score for each hyperellipsoidal model, based on how remote the ellipsoid is relative to their neighbours. We demonstrate using several synthetic and real datasets that our proposed scheme achieves a higher detection performance with a significant reduction in communication overhead in the network compared to centralised and existing schemes.     

Data collection in global software engineering research: learning from past experience

Global Software Engineering has become a standard in today’s software industry. Research in distributed software development poses severe challenges that are due to the spatial and temporal distribution of the actors, as well as to language, intercultural and organizational aspects. These challenges occur in addition to “traditional” challenges of the domain itself in large-scale software projects, like coordination and communication issues, requirements volatily, lack of domain knowledge, among others. While several authors have reported empirical studies of global software development projects, the methodological difficulties and challenges of this type of studies have not been sufficiently discussed. In this paper, we share our experiences of collecting and analysing qualitative data in the context of Global Software Engineering projects. We discuss strategies for gaining access to field sites, building trust and documenting distributed and complex work practices in the context of several research projects we have conducted in the past 9 years. The experiences described in this paper illustrate the need to deal with fundamental problems, such as understanding local languages and different cultures, observing synchronous interaction, or dealing with barriers imposed by political conflicts between the sites. Based on our findings, we discuss some practical implications and strategies that can be used by other researchers and provide some recommendations for future research in methodological aspects of Global Software Engineering.     

Scandinavian Thins on Top of Cake: New and Improved Algorithms for Stacking and Packing

We show how to compute the smallest rectangle that can enclose any polygon, from a given set of polygons, in nearly linear time; we also present a PTAS for the problem, as well as a linear-time algorithm for the case when the polygons are rectangles themselves. We prove that finding a smallest convex polygon that encloses any of the given polygons is NP-hard, and give a PTAS for minimizing the perimeter of the convex enclosure. We also give efficient algorithms to find the smallest rectangle simultaneously enclosing a given pair of convex polygons.     

Engineering microfluidic papers: effect of fiber source and paper sheet properties on capillary-driven fluid flow

In the present study, we introduce a novel approach to control and modulate fluid transport inside microfluidic papers using lab-engineered paper sheets. Lab-sheets consisting of different fiber sources (eucalyptus sulfate and cotton linters pulp) and varying porosities were designed and further modified with small millimeter-scaled channels using hydrophobic barriers consisting of fiber-attached, hydrophobic polymers. The capillary-driven transport of an aqueous solution was monitored visually, and the influence of parameters such as fiber source, paper grammage, and channel width on the flow rates through the channel was investigated. The experimental results were compared with those obtained with commercially available filter papers. Our findings suggest that accurate control of fluid transport processes with standard filter papers is complex. Additionally, if the channel width is smaller than the mean fiber length, flow rates become dependent on the geometric parameters of the channel because of the formation of dead-end pores at the hydrophobic barriers. Finally, control of the paper sheets porosity, by varying the fiber density of the lab-made paper, affords the fabrication of chemically identical sheets whereby capillary flow is largely influenced and can be modulated accordingly by simple papermaking processes.     

Algorithms for Quantum Branching Programs Based on Fingerprinting

In the paper, we develop a method for constructing quantum algorithms for computing Boolean functions by quantum ordered read-once branching programs (quantum OBDDs). Our method is based on ˉngerprinting technique and representation of Boolean functions by their characteristic polynomials. We use circuit notation for branching programs for desired algorithms presentation. For several known functions our approach provides optimal QOBDDs. Namely we consider such functions as MODm, EQn, Palindromen, and PERMn (testing whether given Boolean matrix is the Permutation Matrix). We also propose a generalization of our method and apply it to the Boolean variant of the Hidden Subgroup Problem.     

Oxidation of pyrite in coal to magnetite

When bituminous coal is heated in an inert atmosphere (He) containing small amounts of oxygen at 393–455 °C, pyrite (FeS₂) in coal is partially converted to magnetite (Fe₃0₄). The maximum amount of Fe₃0₄ formed during the time of heating corresponds to 5–20% of the total pyrite present, depending on the coal sample. The magnetite forms as an outer crust on the pyrite grains. The fact that the magnetic properties of the pyrite grains are substantially increased by the magnetite crust suggests that pyrite can be separated from coal by use of a low magnetic field. In a laboratory test, 75% removal is obtained by means of a 500 Oe magnet on three samples, and 60% on a fourth sample.     

Control policies for an industrial acetylene hydrogenation reactor

This paper addresses the problem of finding optimal operational policies for an acetylene reactor for day to day operation. A lumped parameter model based on four main reactions is developed and used to examine the effects of the reactor manipulated variables on key reaction parameters. An optimal and a sub-optimal operational policy which minimize the ethylene loss over time are formulated and the solution techniques are presented. The results indicate that the reactor model is in good agreement with industrial plant data. The performance of the optimal control policy is very similar to the performance of the sub-optimal control policy. However, the sub-optimal formulation, while retaining the dominant features of the optimal response, reduces the computational requirements. Finally, some issues concerning the real-time implementation of an advanced acetylene reactor control scheme are presented. These include the estimation of the optimum regeneration cycle, a recursive model update algorithm, the process optimizer and their overall coordination. A preliminary analysis of the benefits associated with the advanced control scheme suggests a considerable reduction in the yearly ethylene loss.     

An electrochemical impedance spectroscopy and scanning electron microscopy study of the influence of positive plate compression on the electrochemical behaviour of lead-acid batteries

This study has developed an electrochemical impedance spectroscopy (EIS) method for the in situ investigation of the influence of positive plate compression on the electrochemical behaviour of lead-acid batteries during charge/discharge cycling. The EIS data for a fully charged and fully discharged battery are internally consistent with the expected kinetics of a battery in the opposite states of charge, and demonstrate that EIS measurements may be recorded with a high level of reproducibility. Furthermore, this study has necessitated the development of a special cell incorporating horizontally orientated battery plates that can be subjected to elevated pressure through the stacking of lead bricks on top of the cell, as well as a physically robust reference electrode system that can withstand the application of pressure. For this purpose, a platinum-wire pseudo-reference electrode has been developed, and has been shown to exhibit sufficient electrode stability over the period of an EIS recording, enabling the measurement of reproducible and meaningful EIS data. Additionally, the influence of positive plate compression on the behaviour of the lead-acid battery has been investigated by using scanning electron microscopy (SEM). Clearly, the experimental data show that plate compression enhances significantly the kinetics and concomitant performance of the lead-acid battery, and this is related to the enhanced reactivity of the active material, as rationalized by using the agglomeration-of-spheres (AOS) model.