Dynamics of Boolean networks: an exact solution

The dynamics of Boolean networks (BN) with quenched disorder and thermal noise is studied via the generating functional method. A general formulation, suitable for BN with any distribution of Boolean functions, is developed. It provides exact solutions and insight into the evolution of order parameters and properties of the stationary states, which are inaccessible via existing methodology. We identify cases where the commonly used annealed approximation is valid and others where it breaks down. Broader links between BN and general Boolean formulas are highlighted.

A comparative study of the structure of sodium borophosphates made by sol-gel and melt-quench methods

The atomic scale structure of sodium borophosphates made by the sol-gel method is compared to those made by the melt-quench method. It is found that although the sol-gel generated materials have a higher tendency towards crystallization, they nevertheless show a qualitatively similar crystallization trend with composition to their melt-quench analogues; the progressive introduction of boron oxide into the phosphate network initially inhibits then promotes crystallization. At the composition associated with the most stable amorphous sodium borophosphate (20 mol% boron oxide), it is found that the atomic scale structure of the sol-gel synthesized network glass is almost identical to that of the corresponding melt-quenched one.

Structural characterization of titanium-doped Bioglass using isotopic substitution neutron diffraction

Melt quenched silicate glasses containing calcium, phosphorus and alkali metals have the ability to promote bone regeneration and to fuse to living bone. Of these glasses 45S5 Bioglass® is the most widely used being sold in over 35 countries as a bone graft product for medical and dental applications; particulate 45S5 is also incorporated into toothpastes to help remineralize the surface of teeth. Recently it has been suggested that adding titanium dioxide can increase the bioactivity of these materials. This work investigates the structural consequences of incorporating 4 mol% TiO2 into Bioglass® using isotopic substitution (of the Ti) applied to neutron diffraction and X-ray Absorption Near Edge Structure (XANES). We present the first isotopic substitution data applied to melt quench derived Bioglass or its derivatives. Results show that titanium is on average surrounded by 5.2(1) nearest neighbor oxygen atoms. This implies an upper limit of 40% four-fold coordinated titanium and shows that the network connectivity is reduced from 2.11 to 1.97 for small quantities of titanium. Titanium XANES micro-fluorescence confirms the titanium environment is homogenous on the micron length scale within these glasses. Solid state magic angle spinning (MAS) NMR confirms the network connectivity model proposed. Furthermore, the results show the intermediate range order containing Na-O, Ca-O, O-P-O and O-Si-O correlations are unaffected by the addition of small quantities of TiO2 into these systems.

Microsegregation in nodular cast iron and its effect on mechanical properties

A review of the literature pertaining to the mechanical properties, solidification and segregation effects in nodular cast iron has been made. A series of investigations concerning the influence of microsegregation on mechanical properties of :pearlitic, ferritic and austenitic nodular cast iron have then been reported. The influence of section size on the tensile and impact properties of cornmercial purity and refined ferritic nodular cast iron has been studied. It has been shown. that an increase in section caused a decrease in impact transition temperature of the commercial purity material without greatly affecting the impact transition temperature of the purer material. This effect has been related to increased amounts of segregation effects such as cell boundary carbides in heavier sections of the commercial purity material. Microsegregation studies on the materials used in this thesis have been carried out using an electron probe microanalyser. This technique has shown that concentrations of chromium and manganese and depletions of nickel and silicon occurred at eutectic cell boundaries in nodular cast iron and were often associated with brittle carbides in these areas. These effects have been shown to be more prevalent in heavier sections. The nature of segregation during the solidification of nodular cast iron has been studied by quenching samples of nodular iron during the solidification process. Micro-analysis of such samples has shown that segregation of manganese and chromium occurs by a gradual build-up of these elements at the solid/liquid interface. The microstructures of the quenched specimens revealed carbide filaments connecting graphite nodules and areas of quenched liquid. These filaments have been used as evidence for a revised hypothesis for the solidification of nodular cast iron by a liquid diffusion mechanism. A similar series of experiments has been carried out on two high nickel austenitic irons containing 0.5 per cent manganese and 4 per cent manganese respectively. In both these materials a decrease in elongation was experienced with increasing section. This effect was more drastic in the 4 per cent manganese material which also contained much greater amounts of cell boundary carbide in heavy sections. Micro-analysis of samples of the 4 per cent manganese material quenched during solidification revealed that manganese concentrated in the liquid and that nickel concentrated in the solid during solidification. No segregation of silicon occurred in this material. Carbide filaments appeared in the microstructures of these specimens. A discussion of all the above effects in terms of current concepts is included.

Examining crystallographic orientation dependence of hardness of silica stishovite

We conducted nanoindentation to explore the hardness and elastic properties of silica stishovite, synthesized at high pressure and quenched to ambient conditions. A total of 10 crystallographic orientations were examined on selected grains with a maximum load of 4 or 20 mN. We observed discontinuity in the load-displacement curve (pop-in) for the [2 5 over(1, -)] and [6 2 over(1, -)] grains subjected to a maximum load of 20 mN. The single-crystal hardness at high plastic deformation is quasi-isotropic with an average of 32 ± 1 GPa, similar to the polycrystalline hardness reported earlier; the theoretical hardness determined from the experiments is about 54 ± 3 GPa. These two hardnesses suggest that stishovite is one of the hardest oxides. The measured indentation moduli are close to the predictions at low load (minor plasticity) but are considerably lower at high load (high plasticity). Both indentation hardness and modulus decrease with increasing plasticity. Our results underscore the necessity of considering the degree of plastic deformation when interpreting hardness and elastic moduli from indentation experiments. © 2007 Elsevier B.V. All rights reserved.

Fluctuations and correlations in sandpiles and interfaces with boundary pinning

Interfaces are studied in an inhomogeneous critical state where boundary pinning is compensated with a ramped force. Sandpiles driven off the self-organized critical point provide an example of this ensemble in the Edwards-Wilkinson (EW) model of kinetic roughening. A crossover from quenched to thermal noise violates spatial and temporal translational invariances. The bulk temporal correlation functions have the effective exponents β1D∼0.88±0.03 and β2D∼0.52±0.05, while at the boundaries βb,1D/2D∼0.47±0.05. The bulk β1D is shown to be reproduced in a randomly kicked thermal EW model.

Fluctuations and correlations in sandpiles and interfaces with boundary pinning

Interfaces are studied in an inhomogeneous critical state where boundary pinning is compensated with a ramped force. Sandpiles driven off the self-organized critical point provide an example of this ensemble in the Edwards-Wilkinson (EW) model of kinetic roughening. A crossover from quenched to thermal noise violates spatial and temporal translational invariances. The bulk temporal correlation functions have the effective exponents β1D∼0.88±0.03 and β2D∼0.52±0.05, while at the boundaries βb,1D/2D∼0.47±0.05. The bulk β1D is shown to be reproduced in a randomly kicked thermal EW model.

Effect of thermal residual stresses on fatigue crack opening and propagation behavior in an Al/SiCp metal matrix composite

The effects of a thermal residual stress field on fatigue crack growth in a silicon carbide particle-reinforced aluminum alloy have been measured. Stress fields were introduced into plates of material by means of a quench from a solution heat-treatment temperature. Measurements using neutron diffraction have shown that this introduces an approximately parabolic stress field into the plates, varying from compressive at the surfaces to tensile in the center. Long fatigue cracks were grown in specimens cut from as-quenched plates and in specimens which were given a stress-relieving overaging heat treatment prior to testing. Crack closure levels for these cracks were determined as a function of the position of the crack tip in the residual stress field, and these are shown to differ between as-quenched and stress-relieved samples. By monitoring the compliance of the specimens during fatigue cycling, the degree to which the residual stresses close the crack has been evaluated. © 1995 The Minerals, Metals & Material Society.

Effect of cooling rate on intercritically reheated microstructure and toughness in high strength low alloy steel

High strength low alloy steels have been shown to be adversely affected by the existence of regions of poor impact toughness within the heat affected zone (HAZ) produced during multipass welding. One of these regions is the intercritically reheated coarse grained HAZ or intercritical zone. Since this region is generally narrow and discontinuous, of the order of 0.5 mm in width, weld simulators are often employed to produce a larger volume of uniform microstructure suitable for toughness assessment. The steel usedfor this study was a commercial quenched and tempered steel of 450 MN m -2 yield strength. Specimen blanks were subjected to a simulated welding cycle to produce a coarse grained structure of upper bainite during the first thermal cycle, followed by a second thermal cycle where the peak temperature T p2 was controlled. Charpy tests carried out for T p2 values in the range 650-850°C showed low toughness for T p2 values between 760 and 790°C, in the intercritical regime. Microstructural investigation of the development of grain boundary martensite-retained austenite (MA) phase has been coupled with image analysis to measure the volume fraction of MAformed. Most of the MA constituent appears at the prior austenite grain boundaries during intercritical heating, resulting in a 'necklace' appearance. For values of T p2 greater than 790°C the necklace appearance is lost and the second phase areas are observed throughout the structure. Concurrent with this is the development of the fine grained, predominantly ferritic structure that is associated with the improvement in toughness. At this stage the microstructure is transforming from the intercritical regime structure to the supercritically reheated coarse grained HAZ structure. The toughness improvement occurs even though the MA phase is still present, suggesting that the embrittlement is associated with the presence of a connected grain boundary network of the MA phase. The nature of the second phase particles can be controlled by the cooling rate during the second cycle and variesfrom MA phase at high cooling rates to a pearlitic structure at low cooling rates. The lowest toughness of the intercritical zone is observed only when MA phase is present. The reason suggested for this is that only the MA particles debond readily, a number of debonded particles in close proximity providing sufficient stress concentration to initiate local cleavage. © 1993 The Institute of Materials.

Crack closure and residual stress effects in fatigue of a particle-reinforced metal matrix composite

A study of the influence of macroscopic quenching stresses on long fatigue crack growth in an aluminium alloy-SiC composite has been made. Direct comparison between quenched plate, where high residual stresses are present, and quenched and stretched plate, where they have been eliminated, has highlighted their rôle in crack closure. Despite similar strength levels and identical crack growth mechanisms, the stretched composite displays faster crack growth rates over the complete range of ΔK, measured at R = 0.1, with threshold being displaced to a lower nominal ΔK value. Closure levels are dependent upon crack length, but are greater in the unstretched composite, due to the effect of surface compressive stresses acting to close the crack tip. These result in lower values of ΔKeff in the unstretched material, explaining the slower crack growth rates. Effective ΔKth values are measured at 1.7 MPa√m, confirmed by constant Kmax testing. In the absence of residual stress, closure levels of approximately 2.5 MPa√m are measured and this is attributed to a roughness mechanism.

Serrated yielding and the localized shear failure mode in aluminium alloys

A study has been made of serrated yielding in two commercial Al-Zn-Mg alloys in the as-quenched condition. The different serration types produced in the two alloys and the shear failure mechanism observed in both notched-bend and tensile testing are related to the mechanisms of dynamic strain ageing occurring during the test. An estimate of 19.7 kJ/mole for the activation energy for exchange of a solute atom and a vacancy in Al-6.2 wt% Zn, 2.5 wt% Mg has been made. © 1981.

Fatigue behaviour of C-Mn-B steels:effects of heat treatment prestrain and residual stress

The fatigue-crack propagation and threshold behaviour of a C-Mn steel containing boron has been investigated at a range of strength levels suitable for mining chain applications. The heat-treatment variables examined include two austenitizing temperatures (900 degree C and 1250 degree C) and a range of tempering treatments from the as-quenched condition to tempering at 400 degree C. In mining applications the haulage chains undergo a 'calibration' process which has the effect of imposing a tensile prestrain on the chain links before they go into service. Prestrain is shown to reduce threshold values in these steels and this behaviour is related to its effects on the residual stress distribution in the test specimens.

Aspects of 350 ºC (500 ºF) embrittlement in a CrMoV steel

A study has been made of the fracture modes associated with toughness minima, observed in notched impact tests at 173K, for a weldable CrMoV steel, quenched from different austenitising temperatures, and tempered in the range 300-900K. The fracture mode at 623K varied from 100% transgranular cleavage for an austenitising temperature of 1523K. The results are discussed in terms of mechanisms for 350 ºC embrittlement, such mechanisms require modification to allow for the difficulty of dissolving alloy carbides at low austenitising temperatures.

Toughness variations during the tempering of a plain carbon, martensitic steel

The aim of this paper is to present results of toughness measurements and fractographic observations made on a quenched and tempered 0. 6%, carbon steel and to use these as a basis for a discussion of the factors affecting "623K (350 °C) embrittlement" (one-step temper embrittlement).

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.