Control of spatiotemporal chaos in catalytic CO oxidation by laser-induced pacemakers

Control of spatiotemporal chaos is achieved in the catalytic oxidation of CO on Pt(110) by localized modification of the kinetic properties of the surface chemical reaction. In the experiment, a small temperature heterogeneity is created on the surface by a focused laser beam. This heterogeneity constitutes a pacemaker and starts to emit target waves. These waves slowly entrain the medium and suppress the spatiotemporal chaos that is present in the absence of control. We compare this experimental result with a numerical study of the Krischer-Eiswirth-Ertl model for CO oxidation on Pt(110). We confirm the experimental findings and identify regimes where complete and partial controls are possible.

Fiber bragg gratings:advances in fabrication process and tools

Successful commercialization of a technology such as Fiber Bragg Gratings requires the ability to manufacture devices repeatably, quickly and at low cost. Although the first report of photorefractive gratings was in 1978 it was not until 1993, when phase mask fabrication was demonstrated, that this became feasible. More recently, draw tower fabrication on a production level and grating writing through the polymer jacket have been realized; both important developments since they preserve the intrinsic strength of the fiber. Potentially the most significant recent development has been femtosecond laser inscription of gratings. Although not yet a commercial technology, it provides the means of writing multiple gratings in the optical core providing directional sensing capability in a single fiber. Femtosecond processing can also be used to machine the fiber to produce micronscale slots and holes enhancing the interaction between the light in the core and the surrounding medium. © 2011 Bentham Science Publishers Ltd. All rights reserved.

High-throughput manufacturing of size-tuned liposomes by a new microfluidics method using enhanced statistical tools for characterization

Microfluidics has recently emerged as a new method of manufacturing liposomes, which allows for reproducible mixing in miliseconds on the nanoliter scale. Here we investigate microfluidics-based manufacturing of liposomes. The aim of these studies was to assess the parameters in a microfluidic process by varying the total flow rate (TFR) and the flow rate ratio (FRR) of the solvent and aqueous phases. Design of experiment and multivariate data analysis were used for increased process understanding and development of predictive and correlative models. High FRR lead to the bottom-up synthesis of liposomes, with a strong correlation with vesicle size, demonstrating the ability to in-process control liposomes size; the resulting liposome size correlated with the FRR in the microfluidics process, with liposomes of 50 nm being reproducibly manufactured. Furthermore, we demonstrate the potential of a high throughput manufacturing of liposomes using microfluidics with a four-fold increase in the volumetric flow rate, maintaining liposome characteristics. The efficacy of these liposomes was demonstrated in transfection studies and was modelled using predictive modeling. Mathematical modelling identified FRR as the key variable in the microfluidic process, with the highest impact on liposome size, polydispersity and transfection efficiency. This study demonstrates microfluidics as a robust and high-throughput method for the scalable and highly reproducible manufacture of size-controlled liposomes. Furthermore, the application of statistically based process control increases understanding and allows for the generation of a design-space for controlled particle characteristics.

Control of the properties of micro-structured waveguides in LiNbO3 fabricated by direct femtosecond laser inscription

This paper reports on buried waveguides fabricated in lithium niobate (LN) by the method of direct femtosecond (fs) laser inscription. 5% MgO doped LiNbO3 was chosen as the host material because of its high quality and damage threshold, as well as relatively low cost. Direct fs inscription by astigmatically shaped beam in crystals usually produces multiple 'smooth' tracks (with reduced refractive index), which encircle the light guiding 'core', thus creating a depressed cladding WG. A high-repetition rate fs laser system was used for inscription at a depth of approximately 500 μm. Using numerical modelling, it was demonstrated that the properties of fs-written WGs can be controlled by the WG geometry. Buried, depressed-cladding WGs in LN host with circular cross-section were also demonstrated. Combining control over the WG dispersion with quasi-phase matching will allow various ultralow-pump-power, highly-efficient, nonlinear light-guiding devices - all in an integrated optics format.

Editorial overview:new protein production tools for structural biology

Full text: The idea of producing proteins from recombinant DNA hatched almost half a century ago. In his PhD thesis, Peter Lobban foresaw the prospect of inserting foreign DNA (from any source, including mammalian cells) into the genome of a λ phage in order to detect and recover protein products from Escherichia coli [ 1 and 2]. Only a few years later, in 1977, Herbert Boyer and his colleagues succeeded in the first ever expression of a peptide-coding gene in E. coli — they produced recombinant somatostatin [ 3] followed shortly after by human insulin. The field has advanced enormously since those early days and today recombinant proteins have become indispensable in advancing research and development in all fields of the life sciences. Structural biology, in particular, has benefitted tremendously from recombinant protein biotechnology, and an overwhelming proportion of the entries in the Protein Data Bank (PDB) are based on heterologously expressed proteins. Nonetheless, synthesizing, purifying and stabilizing recombinant proteins can still be thoroughly challenging. For example, the soluble proteome is organized to a large part into multicomponent complexes (in humans often comprising ten or more subunits), posing critical challenges for recombinant production. A third of all proteins in cells are located in the membrane, and pose special challenges that require a more bespoke approach. Recent advances may now mean that even these most recalcitrant of proteins could become tenable structural biology targets on a more routine basis. In this special issue, we examine progress in key areas that suggests this is indeed the case. Our first contribution examines the importance of understanding quality control in the host cell during recombinant protein production, and pays particular attention to the synthesis of recombinant membrane proteins. A major challenge faced by any host cell factory is the balance it must strike between its own requirements for growth and the fact that its cellular machinery has essentially been hijacked by an expression construct. In this context, Bill and von der Haar examine emerging insights into the role of the dependent pathways of translation and protein folding in defining high-yielding recombinant membrane protein production experiments for the common prokaryotic and eukaryotic expression hosts. Rather than acting as isolated entities, many membrane proteins form complexes to carry out their functions. To understand their biological mechanisms, it is essential to study the molecular structure of the intact membrane protein assemblies. Recombinant production of membrane protein complexes is still a formidable, at times insurmountable, challenge. In these cases, extraction from natural sources is the only option to prepare samples for structural and functional studies. Zorman and co-workers, in our second contribution, provide an overview of recent advances in the production of multi-subunit membrane protein complexes and highlight recent achievements in membrane protein structural research brought about by state-of-the-art near-atomic resolution cryo-electron microscopy techniques. E. coli has been the dominant host cell for recombinant protein production. Nonetheless, eukaryotic expression systems, including yeasts, insect cells and mammalian cells, are increasingly gaining prominence in the field. The yeast species Pichia pastoris, is a well-established recombinant expression system for a number of applications, including the production of a range of different membrane proteins. Byrne reviews high-resolution structures that have been determined using this methylotroph as an expression host. Although it is not yet clear why P. pastoris is suited to producing such a wide range of membrane proteins, its ease of use and the availability of diverse tools that can be readily implemented in standard bioscience laboratories mean that it is likely to become an increasingly popular option in structural biology pipelines. The contribution by Columbus concludes the membrane protein section of this volume. In her overview of post-expression strategies, Columbus surveys the four most common biochemical approaches for the structural investigation of membrane proteins. Limited proteolysis has successfully aided structure determination of membrane proteins in many cases. Deglycosylation of membrane proteins following production and purification analysis has also facilitated membrane protein structure analysis. Moreover, chemical modifications, such as lysine methylation and cysteine alkylation, have proven their worth to facilitate crystallization of membrane proteins, as well as NMR investigations of membrane protein conformational sampling. Together these approaches have greatly facilitated the structure determination of more than 40 membrane proteins to date. It may be an advantage to produce a target protein in mammalian cells, especially if authentic post-translational modifications such as glycosylation are required for proper activity. Chinese Hamster Ovary (CHO) cells and Human Embryonic Kidney (HEK) 293 cell lines have emerged as excellent hosts for heterologous production. The generation of stable cell-lines is often an aspiration for synthesizing proteins expressed in mammalian cells, in particular if high volumetric yields are to be achieved. In his report, Buessow surveys recent structures of proteins produced using stable mammalian cells and summarizes both well-established and novel approaches to facilitate stable cell-line generation for structural biology applications. The ambition of many biologists is to observe a protein's structure in the native environment of the cell itself. Until recently, this seemed to be more of a dream than a reality. Advances in nuclear magnetic resonance (NMR) spectroscopy techniques, however, have now made possible the observation of mechanistic events at the molecular level of protein structure. Smith and colleagues, in an exciting contribution, review emerging ‘in-cell NMR’ techniques that demonstrate the potential to monitor biological activities by NMR in real time in native physiological environments. A current drawback of NMR as a structure determination tool derives from size limitations of the molecule under investigation and the structures of large proteins and their complexes are therefore typically intractable by NMR. A solution to this challenge is the use of selective isotope labeling of the target protein, which results in a marked reduction of the complexity of NMR spectra and allows dynamic processes even in very large proteins and even ribosomes to be investigated. Kerfah and co-workers introduce methyl-specific isotopic labeling as a molecular tool-box, and review its applications to the solution NMR analysis of large proteins. Tyagi and Lemke next examine single-molecule FRET and crosslinking following the co-translational incorporation of non-canonical amino acids (ncAAs); the goal here is to move beyond static snap-shots of proteins and their complexes and to observe them as dynamic entities. The encoding of ncAAs through codon-suppression technology allows biomolecules to be investigated with diverse structural biology methods. In their article, Tyagi and Lemke discuss these approaches and speculate on the design of improved host organisms for ‘integrative structural biology research’. Our volume concludes with two contributions that resolve particular bottlenecks in the protein structure determination pipeline. The contribution by Crepin and co-workers introduces the concept of polyproteins in contemporary structural biology. Polyproteins are widespread in nature. They represent long polypeptide chains in which individual smaller proteins with different biological function are covalently linked together. Highly specific proteases then tailor the polyprotein into its constituent proteins. Many viruses use polyproteins as a means of organizing their proteome. The concept of polyproteins has now been exploited successfully to produce hitherto inaccessible recombinant protein complexes. For instance, by means of a self-processing synthetic polyprotein, the influenza polymerase, a high-value drug target that had remained elusive for decades, has been produced, and its high-resolution structure determined. In the contribution by Desmyter and co-workers, a further, often imposing, bottleneck in high-resolution protein structure determination is addressed: The requirement to form stable three-dimensional crystal lattices that diffract incident X-ray radiation to high resolution. Nanobodies have proven to be uniquely useful as crystallization chaperones, to coax challenging targets into suitable crystal lattices. Desmyter and co-workers review the generation of nanobodies by immunization, and highlight the application of this powerful technology to the crystallography of important protein specimens including G protein-coupled receptors (GPCRs). Recombinant protein production has come a long way since Peter Lobban's hypothesis in the late 1960s, with recombinant proteins now a dominant force in structural biology. The contributions in this volume showcase an impressive array of inventive approaches that are being developed and implemented, ever increasing the scope of recombinant technology to facilitate the determination of elusive protein structures. Powerful new methods from synthetic biology are further accelerating progress. Structure determination is now reaching into the living cell with the ultimate goal of observing functional molecular architectures in action in their native physiological environment. We anticipate that even the most challenging protein assemblies will be tackled by recombinant technology in the near future.

Comparison between conventional and stochastic pinning control

Theoretical developments on pinning control of complex dynamical networks have mainly focused on the deterministic versions of the model dynamics. However, the dynamical behavior of most real networks is often affected by stochastic noise components. In this paper the pinning control of a stochastic version of the coupled map lattice network with spatiotemporal characteristics is studied. The control of these complex dynamical networks have functional uncertainty which should be considered when calculating stabilizing control signals. Two feedback control methods are considered: the conventional feedback control and modified stochastic feedback control. It is shown that the typically-used conventional control method suffers from the ignorance of model uncertainty leading to a reduction and potentially a collapse in the control efficiency. Numerical verification of the main result is provided for a chaotic coupled map lattice network. © 2011 IEEE.

Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation

Background: DNA-binding proteins play a pivotal role in various intra- and extra-cellular activities ranging from DNA replication to gene expression control. Identification of DNA-binding proteins is one of the major challenges in the field of genome annotation. There have been several computational methods proposed in the literature to deal with the DNA-binding protein identification. However, most of them can't provide an invaluable knowledge base for our understanding of DNA-protein interactions. Results: We firstly presented a new protein sequence encoding method called PSSM Distance Transformation, and then constructed a DNA-binding protein identification method (SVM-PSSM-DT) by combining PSSM Distance Transformation with support vector machine (SVM). First, the PSSM profiles are generated by using the PSI-BLAST program to search the non-redundant (NR) database. Next, the PSSM profiles are transformed into uniform numeric representations appropriately by distance transformation scheme. Lastly, the resulting uniform numeric representations are inputted into a SVM classifier for prediction. Thus whether a sequence can bind to DNA or not can be determined. In benchmark test on 525 DNA-binding and 550 non DNA-binding proteins using jackknife validation, the present model achieved an ACC of 79.96%, MCC of 0.622 and AUC of 86.50%. This performance is considerably better than most of the existing state-of-the-art predictive methods. When tested on a recently constructed independent dataset PDB186, SVM-PSSM-DT also achieved the best performance with ACC of 80.00%, MCC of 0.647 and AUC of 87.40%, and outperformed some existing state-of-the-art methods. Conclusions: The experiment results demonstrate that PSSM Distance Transformation is an available protein sequence encoding method and SVM-PSSM-DT is a useful tool for identifying the DNA-binding proteins. A user-friendly web-server of SVM-PSSM-DT was constructed, which is freely accessible to the public at the web-site on http://bioinformatics.hitsz.edu.cn/PSSM-DT/.

Fiber bragg gratings:advances in fabrication process and tools

Successful commercialization of a technology such as Fiber Bragg Gratings requires the ability to manufacture devices repeatably, quickly and at low cost. Although the first report of photorefractive gratings was in 1978 it was not until 1993, when phase mask fabrication was demonstrated, that this became feasible. More recently, draw tower fabrication on a production level and grating writing through the polymer jacket have been realized; both important developments since they preserve the intrinsic strength of the fiber. Potentially the most significant recent development has been femtosecond laser inscription of gratings. Although not yet a commercial technology, it provides the means of writing multiple gratings in the optical core providing directional sensing capability in a single fiber. Femtosecond processing can also be used to machine the fiber to produce micronscale slots and holes enhancing the interaction between the light in the core and the surrounding medium. © 2011 Bentham Science Publishers Ltd. All rights reserved.

DFIG machine design for maximizing power output based on surrogate optimization algorithm

This paper presents a surrogate-model-based optimization of a doubly-fed induction generator (DFIG) machine winding design for maximizing power yield. Based on site-specific wind profile data and the machine's previous operational performance, the DFIG's stator and rotor windings are optimized to match the maximum efficiency with operating conditions for rewinding purposes. The particle swarm optimization-based surrogate optimization techniques are used in conjunction with the finite element method to optimize the machine design utilizing the limited available information for the site-specific wind profile and generator operating conditions. A response surface method in the surrogate model is developed to formulate the design objectives and constraints. Besides, the machine tests and efficiency calculations follow IEEE standard 112-B. Numerical and experimental results validate the effectiveness of the proposed technologies.

Developing a new SVPWM control strategy for open-winding brushless doubly fed reluctance generators

In this paper, a new open-winding control strategy is proposed for a brushless doubly fed reluctance generator (BDFRG) used for stand-alone wind turbine or ship generators. The BDFRG is characterized with two windings on the stator: a power winding and a control winding. The control winding is fed with dual two-level three-phase converters, and a vector control scheme based on space vector pulsewidth modulation is designed. Compared with traditional three-level inverter systems, the dc-link voltage and the voltage rating of power devices in the proposed system are reduced by 50% while still greatly improving the reliability, redundancy, and fault tolerance of the proposed system by increasing the switching modes. Its performance is evaluated by simulation in MATLAB/Simulink and an experimental study on a 42-kW prototype machine.

Rotor retaining sleeve design for a 1.12-MW high-speed PM machine

Permanent-magnet (PM) synchronous machines (PMSMs) can provide excellent performance in terms of torque density, energy efficiency, and controllability. However, PMs on the rotor are prone to centrifugal force, which may break their physical integrity, particularly at high-speed operation. Typically, PMs are bound with carbon fiber or retained by alloy sleeves on the rotor surface. This paper is concerned with the design of a rotor retaining sleeve for a 1.12-MW 18-kr/min PM machine; its electromagnetic performance is investigated by the 2-D finite-element method (FEM). Theoretical and numerical analyses of the rotor stress are carried out. For the carbon fiber protective measure, the stresses of three PM configurations and three pole filler materials are compared in terms of operating temperature, rotor speed, retaining sleeve thickness, and interference fit. Then, a new hybrid protective measure is proposed and analyzed by the 2-D FEM for operational speeds up to 22 kr/min (1.2 times the rated speed). The rotor losses and machine temperatures with the carbon fiber retaining sleeve and the hybrid retaining sleeve are compared, and the sleeve design is refined. Two rotors using both designs are prototyped and experimentally tested to validate the effectiveness of the developed techniques for PM machines. The developed retaining sleeve makes it possible to operate megawatt PM machines at high speeds of 22 kr/min. This opens doors for many high-power high-speed applications such as turbo-generator, aerospace, and submarine motor drives.

Design and flux-weakening control of an interior permanent magnet synchronous motor for electric vehicles

Permanent magnet synchronous motors (PMSMs) provide a competitive technology for EV traction drives owing to their high power density and high efficiency. In this paper, three types of interior PMSMs with different PM arrangements are modeled by the finite element method (FEM). For a given amount of permanent magnet materials, the V shape interior PMSM is found better than the U-shape and the conventional rotor topologies for EV traction drives. Then the V shape interior PMSM is further analyzed with the effects of stator slot opening and the permanent magnet pole chamfering on cogging torque and output torque performance. A vector-controlled flux-weakening method is developed and simulated in matlab to expand the motor speed range for EV drive system. The results show good dynamic and steady-state performance with a capability of expanding speed up to 4 times of the rated. A prototype of the V shape interior PMSM is also manufactured and tested to validate the numerical models built by the finite element method.

Control of pattern formation by time-delay feedback with global and local contributions

We consider the suppression of spatiotemporal chaos in the complex GinzburgLandau equation by a combined global and local time-delay feedback. Feedback terms are implemented as a control scheme, i.e., they are proportional to the difference between the time-delayed state of the system and its current state. We perform a linear stability analysis of uniform oscillations with respect to space-dependent perturbations and compare with numerical simulations. Similarly, for the fixed-point solution that corresponds to amplitude death in the spatially extended system, a linear stability analysis with respect to space-dependent perturbations is performed and complemented by numerical simulations. © 2010 Elsevier B.V. All rights reserved.