Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures

Bacterial chaperonin, GroEL, together with its co-chaperonin, GroES, facilitates the folding of a variety of polypeptides. Experiments suggest that GroEL stimulates protein folding by multiple cycles of binding and release. Misfolded proteins first bind to an exposed hydrophobic surface on GroEL. GroES then encapsulates the substrate and triggers its release into the central cavity of the GroEL/ES complex for folding. In this work, we investigate the possibility to facilitate protein folding in molecular dynamics simulations by mimicking the effects of GroEL/ES namely, repeated binding and release, together with spatial confinement. During the binding stage, the (metastable) partially folded proteins are allowed to attach spontaneously to a hydrophobic surface within the simulation box. This destabilizes the structures, which are then transferred into a spatially confined cavity for folding. The approach has been tested by attempting to refine protein structural models generated using the ROSETTA procedure for ab initio structure prediction. Dramatic improvements in regard to the deviation of protein models from the corresponding experimental structures were observed. The results suggest that the primary effects of the GroEL/ES system can be mimicked in a simple coarse-grained manner and be used to facilitate protein folding in molecular dynamics simulations. Furthermore, the results Sur port the assumption that the spatial confinement in GroEL/ES assists the folding of encapsulated proteins.

Phase behavior of a phospholipid/fatty acid/water mixture studied in atomic detail

Molecular dynamics simulations have been used to study the phase behavior of a dipalmitoylphosphatidylcholine (DPPC)/palmitic acid (PA)/water 1:2:20 mixture in atomic detail. Starting from a random solution of DPPC and PA in water, the system adopts either a gel phase at temperatures below similar to 330 K or an inverted hexagonal phase above similar to 330 K in good agreement with experiment. It has also been possible to observe the direct transformation from a gel to an inverted hexagonal phase at elevated temperature (similar to 390 K). During this transformation, a metastable fluid lamellar intermediate is observed. Interlamellar connections or stalks form spontaneously on a nanosecond time scale and subsequently elongate, leading to the formation of an inverted hexagonal phase. This work opens the possibility of studying in detail how the formation of nonlamellar phases is affected by lipid composition and (fusion) peptides and, thus, is an important step toward understanding related biological processes, such as membrane fusion.

Structural evolution in a hydrothermal reaction between Nb2O5 and NaOH solution: From Nb2O5 grains to microporous Na2Nb2O6 center dot(2)/3H2O fibers and NaNbO3 cubes

Niobium pentoxide reacts actively with concentrate NaOH solution under hydrothermal conditions at as low as 120 degrees C. The reaction ruptures the corner-sharing of NbO7 decahedra and NbO6 octahedra in the reactant Nb2O5, yielding various niobates, and the structure and composition of the niobates depend on the reaction temperature and time. The morphological evolution of the solid products in the reaction at 180 degrees C is monitored via SEM: the fine Nb2O5 powder aggregates first to irregular bars, and then niobate fibers with an aspect ratio of hundreds form. The fibers are microporous molecular sieve with a monoclinic lattice, Na2Nb2O6 center dot(2)/3H2O. The fibers are a metastable intermediate of this reaction, and they completely convert to the final product NaNbO3 Cubes in the prolonged reaction of 1 h. This study demonstrates that by carefully optimizing the reaction condition, we can selectively fabricate niobate structures of high purity, including the delicate microporous fibers, through a direct reaction between concentrated NaOH solution and Nb2O5. This synthesis route is simple and suitable for the large-scale production of the fibers. The reaction first yields poorly crystallized niobates consisting of edge-sharing NbO6 octahedra, and then the microporous fibers crystallize and grow by assembling NbO6 octahedra or clusters of NbO6 octahedra and NaO6 units. Thus, the selection of the fibril or cubic product is achieved by control of reaction kinetics. Finally, niobates with different structures exhibit remarkable differences in light absorption and photoluminescence properties. Therefore, this study is of importance for developing new functional materials by the wet-chemistry process.

Prediction of the equilibrium structures and photomagnetic properties of the Prussian blue analogue RbMn[Fe(CN)6] by density functional theory

A periodic density functional theory method using the B3LYP hybrid exchange-correlation potential is applied to the Prussian blue analogue RbMn[Fe(CN)6] to evaluate the suitability of the method for studying, and predicting, the photomagnetic behavior of Prussian blue analogues and related materials. The method allows correct description of the equilibrium structures of the different electronic configurations with regard to the cell parameters and bond distances. In agreement with the experimental data, the calculations have shown that the low-temperature phase (LT; Fe(2+)(t(6)2g, S = 0)-CN-Mn(3+)(t(3)2g e(1)g, S = 2)) is the stable phase at low temperature instead of the high-temperature phase (HT; Fe(3+)(t(5)2g, S = 1/2)-CN-Mn(2+)(t(3)2g e(2)g, S = 5/2)). Additionally, the method gives an estimation for the enthalpy difference (HT LT) with a value of 143 J mol(-1) K(-1). The comparison of our calculations with experimental data from the literature and from our calorimetric and X-ray photoelectron spectroscopy measurements on the Rb0.97Mn[Fe(CN)6]0.98 x 1.03 H2O compound is analyzed, and in general, a satisfactory agreement is obtained. The method also predicts the metastable nature of the electronic configuration of the high-temperature phase, a necessary condition to photoinduce that phase at low temperatures. It gives a photoactivation energy of 2.36 eV, which is in agreement with photoinduced demagnetization produced by a green laser.

Studies of clay minerals and their decomposition products

Mõssbauer spectroscopy and X-ray diffraction of five coals revealed the presence of pyrite, illite, kaolinite and Quartz, together with other minor phases. Analysis of the coal ashes indicated the formation of hematite and an Fe (3+) paramagnetic phase, the latter resulting from .the dehydroxylation of the clay minerals during ashing at 700 to 750 C. By using a combination of several physicochemical methods, different successive stages of dehydroxylation, structural consolidation, and recrystallisation of illite, montmorillonite and hectorite upon thermal treatment to 1300 C were investigated. Dehydroxylation of the clay minerals occurred between 450 and 750 C, the X-ray crysdallinity of illite and montmorillonite remaining until 800 C. Hectorite gradually recrystallises to enstatite at temperatures above 700°C. At 900 C the crystalline structure of all three clay minerals had totally collapsed. Solid state reactions occurred above 900 C producing such phases as spinel, hematite, enstatite, cristobalite and mullite. Illite and montmorillonite started to melt between 1200 and 1300°C, producing a silicate glass that contained Fe(3+) and Fe(2+) ions. Ortho-pnstatite, clino-enstatite and proto-enstatite were identified in the thermal products of hectorite, their relative proportions varying with temperature. Protoenstatite was stabilised with respect to metastable clinoenstatite upon cooling from 12000 C by the presence of exchanged transition metal cations. Solid state Nuclear Magnetic Resonance spectroscopy of thermally treated transition metal exchanged hectorite indicated the levels at which paramagnetic cations could be loaded on to the clay before spectral resolution is significantly diminished.

The creep behaviour of pressure diecast zinc-aluminium based alloys

The creep behaviour of three pressure diecast commercial zinc-aluminium based alloys: Mazak 3, corresponding to BS 1004A, and the new alloys ZA.8 and ZA.27 with a series of alloys with compositions ranging from 0% to 30% aluminium was investigated. The total creep elongation of commercial alloys was shown to be well correlated using an empirical equation. Based on this a parametrical relationship was derived which allowed the total creep extension to be related to the applied stress, the temperature and the time of test, so that a quantitative assessment of creep of the alloys could be made under different conditions. Deviation from the normal creep kinetics occurred in alloys ZA.8 and ZA.27 at very low stresses, 150°C, due to structural coarsening combined with partial transformation of ε -phase into T' phase. The extent of primary creep was found to increase with aluminium content, but secondary creep rates decreased in the order Mazak 3, ZA.8 and ZA.27. Thus, based on the above equation, ZA.8 was found to have a substantially better total creep resistance than ZA.27, which in turn was marginally better than Mazak 3 for strains higher than 0.5%, but inferior for smaller strains, due to its higher primary creep extension. The superior creep resistance of ZA.8 was found to be due to the presence of strictly-orientated, thin plate-like precipitates of ε(CuZn4) phase in the zinc matrix of the eutectic and the lamellarly decomposed β phase, in which the precipitation morphology and orientation of ε in the zinc matrix was determined. Over broad ranges of temperature and stresses, the stress exponents and activation energies for creep were found to be consistent with some proposed creep rate mechanisms; i.e. viscous glide for Mazak 3, dislocation climb over second phase particles for ZA.8 and dislocation climb for ZA.27, controlled by diffusion in the zinc-rich phase. The morphology of aluminium and copper-rich precipitates formed from the solid solution of zinc was clearly revealed. The former were found to further increase the creep rate of inherently low creep resistant zinc, but the latter contributed significantly to the creep resistance. Excess copper in the composition, however, was not beneficial in improving the creep resistance. Decomposition of β in copper-containing alloys was found to be through a metastable Zn-Al phase which is strongly stabilised by copper, and the final products of the decomposition had a profound effect on the creep strength of the alloys. The poor creep resistance of alloy ZA.27 was due to the presence of particulate products derived from decomposed β-phase and a large volume of fine, equiaxed products of continuously decomposed α-dendrites.

The fatigue properties of pressure diecast zinc-aluminium based alloys

The fatigue behaviour of the cold chamber pressure-die-cast alloys: Mazak3, ZA8, ZA27, M3K, ZA8K, ZA27K, K1, K2 and K3 was investigated at temperature of 20°C. The alloys M3K, ZA8K and ZA27K were also examined at temperatures of 50 and 100°C. The ratio between fatigue strength and tensile strength was established at 20°C at 107 cycles. The fatigue life prediction of the alloys M3K, ZA8K and ZA27K was formulated at 20, 50 and 100°C. The prediction formulae were found to be reasonably accurate. All of the experimental alloys were heterogeneous and contained large but varying amounts of pores. These pores were a major contribution and dominated the alloys fatigue failure. Their effect, however, on tensile failure was negligible. The ZA27K possessed the highest tensile strength but the lowest fatigue strength. The relationship between the fracture topography and the microstructure was also determined by the use of a mixed signal of a secondary electron and a back-scattered electron on the SEM. The tensile strength of the experimental alloys was directly proportional to the aluminium content within the alloys. The effect of copper content was also investigated within the alloys K1, K2, ZA8K and K3 which contained 0%, 0.5%, 1.0% and 2.0% respectively. It was determined that the fatigue and tensile strengths improved with higher copper contents. Upon ageing the alloys Mazak3, ZA8 and ZA27 at an ambient temperature for 5 years, copper was also found to influence and maintain the metastable Zn-Al (αm) phase. The copper free Mazak3 upon ageing lost this metastable phase. The 1.0% copper ZA8 alloy had lost almost 50% of its metastable phase. Finally the 2.0% copper ZA27 had merely lost 10% of its metastable phase. The cph zinc contained a limited number of slip systems, therefore twinning deformation was unavoidable in both fatigue and tensile testing.

Remobilisation of uranium and thorium by ore-forming fluids: a mineralogical study. Available in 2 volumes.

Mineralogical investigations have determined the sites of u and Th associated with two radioelement-enriched granites from different geological settings. In the Ririwai ring complex, Nigeria, the u- and Th-bearing accessories have been greatly affected by post-magmatic alteration of the biotite granite. Primary thorite, zircon and monazite were altered to Zr(±Y)-rich thorite, partially metamict zircon (enriched in Th, U, Y, P, Fe, Mn, Ca) and an unidentified LREE-phase respectively, by pervasive fluids which later precipitated Zr-rich coffinite. More intense, localised alteration and albitisation completely remobilised primary accessories and gave rise to a distinctive generation of haematite- and uranothorite-enriched zircon with clear, Hi-enriched rims and xenotime overgrowths. In the Ririwai lode, microclinisation and later greisenisation locally remobilised or altered zircon and deposited Y-ricl1 coffinite and Y(±Zr)-rich thorite which was overgrown by traces of xenotime and LREE-phase(s) of complex and variable composition. Compositions indicating extensive solid-solution among thorite, coffinite, xenotime and altered zircon are probably metastable and formed at low temperatures. The widespread occurrence of REE-rich fluorite suggests that F-complexing aided the mobility of REE, Y, U, Th and Zr during late-magmatic to post-magmatic alteration, while uranyl-carbonate complexing may have occurred during albitisation. The Caledonian, Helmsdale granite in northern Scotland has undergone pervasive and localised hydrothermal alteration associated with U enrichment. Zircon xenocrysts, primary sphene and apatite contain a small.proportion of this U which is largely adsorbed on to secondary iron-oxide, TiOand phyllosilicates.Additional sites for U in the overlying, Lower Devonian Ousdale arkose include coffinite, secondary uranyl phosphates, hydrocarbon and traces of xenotime and unidentified LREE-phases. U may have been leached from the granite and deposited in the arkose, along channelways associated with the Helmsdale fault, by convecting, hydrothermal fluids

Statistical mechanics of distribution networks

This thesis presents an analysis of the stability of complex distribution networks. We present a stability analysis against cascading failures. We propose a spin [binary] model, based on concepts of statistical mechanics. We test macroscopic properties of distribution networks with respect to various topological structures and distributions of microparameters. The equilibrium properties of the systems are obtained in a statistical mechanics framework by application of the replica method. We demonstrate the validity of our approach by comparing it with Monte Carlo simulations. We analyse the network properties in terms of phase diagrams and found both qualitative and quantitative dependence of the network properties on the network structure and macroparameters. The structure of the phase diagrams points at the existence of phase transition and the presence of stable and metastable states in the system. We also present an analysis of robustness against overloading in the distribution networks. We propose a model that describes a distribution process in a network. The model incorporates the currents between any connected hubs in the network, local constraints in the form of Kirchoff's law and a global optimizational criterion. The flow of currents in the system is driven by the consumption. We study two principal types of model: infinite and finite link capacity. The key properties are the distributions of currents in the system. We again use a statistical mechanics framework to describe the currents in the system in terms of macroscopic parameters. In order to obtain observable properties we apply the replica method. We are able to assess the criticality of the level of demand with respect to the available resources and the architecture of the network. Furthermore, the parts of the system, where critical currents may emerge, can be identified. This, in turn, provides us with the characteristic description of the spread of the overloading in the systems.

The effect of heat treatment on mechanical properties of pulsed Nd:YAG welded thin Ti6Al4V

Pulsed Nd:YAG has been adopted successfully in welding process of thin (0.7 mm) Ti6Al4V. Laser welding of such thin sheet requires a small focal spot, good laser beam quality and fast travel speed, since too much heat generation can cause distortion for thin sheet weld. The microstructures of Ti6Al4V were complex and strongly affected the mechanical properties. These structures include: a´ martensite, metastable ß, Widmanstätten, bimodal, lamellar and equiaxed microstructure. Bimodal and Widmanstätten structures exhibit a good-balance between strength and ductility. The microstructure of pulsed Nd:YAG welded Ti6Al4V was primarily a´ martensite, which showed the lowest ductility but not significantly high strength. A heat treatment at 950 followed by furnace cooling can transform the microstructure in the weld from a´ martensite structure into Widmanstätten structure.

Water-peptide dynamics during conformational transitions

Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions and the dynamical correlations of water with the peptide's configurational motions indicate that the water molecules represent an integral part of the molecular system during the conformational changes, in contrast to the metastable periods when water and peptide dynamics are essentially decoupled.

Bulk and surface switching in Mn-Fe-based Prussian blue analogues

Many Prussian Blue Analogues are known to show a thermally induced phase transition close to room temperature and a reversible, photo-induced phase transition at low temperatures. This work reports on magnetic measurements, X-ray photoemission and Raman spectroscopy on a particular class of these molecular heterobimetallic systems, specifically on Rb0.81Mn[Fe(CN)6]0.95_1.24H2O, Rb0.97Mn[Fe(CN)6]0.98_1.03H2O and Rb0.70Cu0.22Mn0.78[Fe(CN)6]0.86_2.05H2O, to investigate these transition phenomena both in the bulk of the material and at the sample surface. Results indicate a high degree of charge transfer in the bulk, while a substantially reduced conversion is found at the sample surface, even in case of a near perfect (Rb:Mn:Fe=1:1:1) stoichiometry. Thus, the intrinsic incompleteness of the charge transfer transition in these materials is found to be primarily due to surface reconstruction. Substitution of a large fraction of charge transfer active Mn ions by charge transfer inactive Cu ions leads to a proportional conversion reduction with respect to the maximum conversion that is still stoichiometrically possible and shows the charge transfer capability of metal centers to be quite robust upon inclusion of a neighboring impurity. Additionally, a 532 nm photo-induced metastable state, reminiscent of the high temperature Fe(III)Mn(II) ground state, is found at temperatures 50-100 K. The efficiency of photo-excitation to the metastable state is found to be maximized around 90 K. The photo-induced state is observed to relax to the low temperature Fe(II)Mn(III) ground state at a temperature of approximately 123 K.

Precipitation studies on alloys from the system copper chromium zirconium

The precipitation reactions occurring in a series of copper-based alloys selected from the system copper-chromium-zirconium have been studied by resistometric and metallographic techniques. A survey of the factors influencing the development of copper-based alloys for high strength, high conductivity applications is followed by a more general review of contemporary materials, and illustrates that the most promising alloys are those containing chromium and zirconium. The few systematic attempts to study alloys from this system have been collated, discussed, and used as a basis for the selection of four alloy compositions viz:- Cu - 0.4% Cr Cu - 0.24. Zr Cu - 0. 3% Cr - 0.1% Zr Cu - 0.2% Cr - 0.2% Zr A description of the experimental techniques used to study the precipitation behaviour of these materials is preceeded by a discussion of the currently accepted theories relating to precipitate nucleation and growth. The experimental results are presented and discussed for each of the alloys independently, and are then treated jointly to obtain an overall assessment of the way in which the precipitation kinetics, metallography and mechanical properties vary with alloy composition and heat treatment. The metastable solid solution of copper-chromium is found to decompose by the rejection of chromium particles which maintain a coherent interface and a Kurdjumov-Sachs type crystallographic orientation relationship with the copper matrix. The addition of 0.1% zirconium to the alloy retards the rate of transformation by a factor of ten and modifies the dispersion characteristics of the precipitate without markedly altering the morphology. Further additions of zirconium lead to the growth of stacking faults during ageing, which provide favourable nucleation sites for the chromium precipitate. The partial dislocations bounding such stacking faults are also found to provide mobile heterogeneous nucleation sources for the precipitation reactions occurring in copper-zirconium.

A new 3-D polymeric spin transition compound: [tris(1,4-bis-(tetrazol-1-yl) butane-N1,N1′)iron(II)] bis(perchlorate)

A series of novel polymeric compounds of formula [M(btzb)3][ClO4]2 (Mll = Fe, Ni or Cu) with btzb = 1,4-bis-(tetrazol-1-yl)butane have been prepared and their physical properties investigated. The btzb ligand has been prepared and its crystal structure determined, together with a tentative crystal structure of the 3-D compound [Fe(btzb)3][ClO4]2. The model of the latter shows two symmetry-related, interpenetrating Fe-btzb networks in which the iron(II) ions approach each other as close as 8.3 and 9.1 Å. This supramolecular catenane undergoes a sharp thermal spin transition around 160 K with hysteresis (20 K) along with a pronounced thermochromic effect. The spin crossover behaviour has been followed by magnetic, DSC, optical spectroscopy and 57Fe Mössbauer spectroscopy measurements. Irradiation with green light at low temperature leads to population of the metastable high-spin state for the thermally active iron(ll) ions. The nature of the spin crossover behaviour has been discussed in detail.

A 2D [FeII-bistetrazole] coordination polymer exhibiting spin-crossover properties

The reaction of 1,3-bis(tetrazol-1-yl)-2-propanol (btzpol) with Fe(BF4)2 · 6H2O in acetonitrile yields the remarkable 2D coordination polymer [FeII(btzpol)1.8(btzpol-OBF3)1.2](BF4)0.8 · (H2O)0.8(CH3CN) (1). This compound has been structurally characterized using an X-ray single-crystal synchrotron radiation source. The iron(II) centers are bridged by means of double btzpol bridges along the c direction, and by single btzpol bridges along the b direction. The reaction of part of the ligand with the counterion has forced the compound to crystallize in this extended two dimensional structure. The compound shows spin-transition properties, both induced by temperature and light, with T½ = 112 K and T(LIESST) = 46 K, respectively. The relaxation of the metastable high-spin state created by irradiation is exponential, following an Arrhenius type behavior at high temperature, and dominated by a temperature independent tunneling process at lower temperatures.