Characterizing the structures and folding of free proteins using 2-D gas-phase separations: observation of multiple unfolded conformers

Understanding the 3-D structure and dynamics of proteins and other biological macromolecules in various environments is among the central challenges of chemistry. Electrospray ionization can often transfer ions from solution to gas phase with only limited structural distortion, allowing their profiling using mass spectrometry and other gas-phase approaches. Ion mobility spectrometry (IMS) can separate and characterize macroion conformations with high sensitivity and speed. However, IMS separation power is generally insufficient for full resolution of major structural variants of protein ions and elucidation of their interconversion dynamics. Here we report characterization of macromolecular conformations using field asymmetric waveform IMS (FAIMS) coupled to conventional IMS in conjunction with mass spectrometry. The collisional heating of ions in the electrodynamic funnel trap between FAIMS and IMS stages enables investigating the structural evolution of particular isomeric precursors as a function of the intensity and duration of activation that can be varied over large ranges. These new capabilities are demonstrated for ubiquitin and cytochrome c, two common model proteins for structure and folding studies. For nearly all charge states, two-dimensional FAIMS/IMS separations distinguish many more conformations than either FAIMS or IMS alone, including some with very low abundance. For cytochrome c in high charge states, we find several abundant "unfolded" isomer series not distinguishable by IMS, possibly corresponding to different "string of beads" geometries. The unfolding of specific ubiquitin conformers selected by FAIMS has been studied by employing their heating in the FAIMS/IMS interface.     

Integrated configurable equipment selection and line balancing for mass production with serial–parallel machining systems

Solving equipment selection and line balancing problems together allows better line configurations to be reached and avoids local optimal solutions. This article considers jointly these two decision problems for mass production lines with serial–parallel workplaces. This study was motivated by the design of production lines based on machines with rotary or mobile tables. Nevertheless, the results are more general and can be applied to assembly and production lines with similar structures. The designers’ objectives and the constraints are studied in order to suggest a relevant mathematical model and an efficient optimization approach to solve it. A real case study is used to validate the model and the developed approach.     

A synthesis approach to distributed supervisory control design for manufacturing systems with Grafcet implementation

In supervisory control, computational complexity and implementation flexibility represent major challenges when a large number of local components compose a target system. To overcome these difficulties, we propose a formal approach to distributed control synthesis and implementation for automated manufacturing systems (AMS). We assume that the system is modelled with automata in a local modular fashion. Local control specifications are defined for each local subsystem by means of logical equations to construct local controllers (LCs). Then, global control specifications, stated as logical implications, are applied to the LCs, which allows synchronisation and cooperative interaction among the subsystems. This paper makes two contributions. First, it outlines a formal method for constructing minimally restrictive and deadlock-free distributed controllers (DCs). Second, it proposes a method for the interpretation of these DCs into Grafcet, which is a graphical modelling formalism widely used to design the controller’s dynamic behaviour for AMS. An experimental manufacturing system illustrates the approach.     

Launching propagating surface plasmon polaritons by a single carbon nanotube dipolar emitter

We report on the excitation of propagating surface plasmon polaritons in thin metal films by a single emitter. Upon excitation in the visible regime, individual semiconducting single-walled carbon nanotubes are shown to act as directional near-infrared point dipole sources launching propagating surface plasmons mainly along the direction of the nanotube axis. Plasmon excitation and propagation is monitored in Fourier and real space by leakage radiation microscopy and is modeled by rigorous theoretical calculations. Coupling to plasmons almost completely reshapes the emission of nanotubes both spatially and with respect to polarization as compared to photoluminescence on a dielectric substrate.     

Probing the nature of defects in graphene by Raman spectroscopy

Raman spectroscopy is able to probe disorder in graphene through defect-activated peaks. It is of great interest to link these features to the nature of disorder. Here we present a detailed analysis of the Raman spectra of graphene containing different type of defects. We found that the intensity ratio of the D and D' peak is maximum (～13) for sp(3)-defects, it decreases for vacancy-like defects (～7), and it reaches a minimum for boundaries in graphite (～3.5). This makes Raman Spectroscopy a powerful tool to fully characterize graphene.     

Effect of varying electric potential on surface-plasmon resonance sensing

The high sensitivity of surface-plasmon resonance (SPR) sensors allows measurements of small variations in surface potentials to be made. We studied the changes of the SPR angle when an oscillating electric potential was applied to a gold film on which surface plasmons were excited. The shifts of the SPR resonance angle were observed for various aqueous solutions as an adjacent medium. A model that takes into account the redistribution of charges at the double layer near the metal-liquid interface as well as the oxidation of the gold film was developed. It was found that a change in the electronic density at voltages below the oxidation potential and, in addition, the oxidation of the gold surface above this potential are the main mechanisms that account for the observed dependences. It was shown that relatively slow oxidation-reduction processes can explain the observed hysteresis effect. Application of these techniques to studies of dielectric properties and conformational changes of polar biomolecules, such as tubulin, are discussed.     

A simple mix design method for structural lightweight aggregate concrete

Current design methods for structural lightweight aggregate concrete (SLWAC) are usually only valid for a limited range of concrete compositions that have previously been subjected to trial tests. The SLWAC mix design is more complex than that of normal weight concrete as more parameters need to be determined. Taking this into account, a simplified design method is proposed for SLWAC made with natural sand. The major advantages of the proposed method are that it is easy to apply and it can be generalized to any type of lightweight aggregate (LWA). For this, three additional design parameters are needed: the strength of LWA in concrete; the limit strength; the SLWAC potential strength. At most, two experimental mixtures are needed to determine these parameters. A biphasic model to estimate the strength of SLWAC is evaluated and high correlations are obtained. The good performance of the suggested method is demonstrated by examples of practical application and by the comparison with experimental results reported by the authors and other investigators.     

Research and partnership in studies of sugarcane using molecular markers: a scientometric approach

In this study, we applied scientometric methods and performed a science mapping analysis to investigate and describe the application of molecular markers in genetic studies for sugarcane. We analyzed 344 papers retrieved from Web of Science Thomson Reuters database, considering the time frame from 1974 to 2017, allowing the analysis of the produced scientific knowledge, temporal trends and research partnership in the subject. To our knowledge, a scientometric evaluation of the use of molecular markers for genetic studies in sugarcane has not yet been reported. Our main finding shows that dominant markers are more commonly used than co-dominant markers, and that when co-dominant markers are applied, most of the retrieved information is underexploited, due to lack of knowledge for the use of dosage information. Our results also show that despite the development of high-throughput sequencing technologies, for sugarcane only 13.33% of the studies reported the use of more than 1000 markers. We also found connectivity among researchers and institutions publishing worldwide, but only few authors represented a bridge between different research groups. Thus, the international research partnership is still low. Our findings show dominance in country publication. Six countries (India, Brazil, USA, Australia, China, and France) were responsible for 80% of the published papers and received most citations. We suggest special reinforcement in building international partnership, since collaborations occur mostly within countries. International collaboration can improve research performance and eventually lead to a better exploitation and more development of knowledge for sugarcane.

     

Using common weights and efficiency invariance principles for resource allocation and target setting

Data envelopment analysis (DEA) has proven to be a useful technique for evaluating the relative performance of comparable and homogeneous decision-making units (DMUs). In recent years, DEA-based resource allocation and target setting approaches have gained more and more attention from both practitioners and academic researchers. In this paper, we propose a new mechanism to simultaneously adopt the principles of common weights and efficiency invariance in allocating multiple resources and setting multiple targets among DMUs. To obtain the final plan, we minimise the deviation between the possible plan based on common weights and another feasible plan emphasising efficiency invariance. If the minimum deviation equals zero, one optimal plan will be determined. In general situations, however, the proposed approach will present two plans that have a non-zero deviation. One is generated using a common set of weights for all DMUs in such a way that the change of efficiencies is minimised, while the other is generated by strictly keeping efficiency scores unchanged yet having similar or even identical weights on input–output measures for each DMU to the utmost extent. The efficacy and usefulness of the proposed approach are demonstrated using a numerical example from previous literature and an empirical application to an urban bus company in China.     

A conservative embedded boundary method for an inviscid compressible flow coupled with a fragmenting structure

We present an embedded boundary method for the interaction between an inviscid compressible flow and a fragmenting structure. The fluid is discretized using a finite volume method combining Lax–Friedrichs fluxes near the opening fractures, where the density and pressure can be very low, with high‐order monotonicity‐preserving fluxes elsewhere. The fragmenting structure is discretized using a discrete element method based on particles, and fragmentation results from breaking the links between particles. The fluid‐solid coupling is achieved by an embedded boundary method using a cut‐cell finite volume method that ensures exact conservation of mass, momentum, and energy in the fluid. A time explicit approach is used for the computation of the energy and momentum transfer between the solid and the fluid. The embedded boundary method ensures that the exchange of fluid and solid momentum and energy is balanced. Numerical results are presented for two‐dimensional and three‐dimensional fragmenting structures interacting with shocked flows. Copyright © 2015 John Wiley & Sons, Ltd.