Kinetics and intimate mechanism of protein crystal nucleation

Experimental and theoretical investigations on protein crystal nucleation are reviewed. Various experimental applications of the classical principle, which requires separation of the nucleation and growth stages of the crystallization process, are described. Temperature control is used most frequently, hypergravity and concentration changes being auxiliary techniques. Nucleation time-lags are measured by imposing temperature evoked supersaturation gradients. Application perspectives are revealed. Nucleation rates are measured according to the classical principle mentioned above, and energy barriers for crystal nucleation and numbers of molecules constituting the critical nuclei are calculated. Surprisingly, although requiring unusually high supersaturation, protein crystal nucleation occurs much more slowly than that with small molecule substances. On this basis novel notions are suggested for the elementary mechanism of protein crystal bond formation. Due to the selection of the crystalline bonding patches a successful collision between protein molecules, resulting in the formation of a crystalline connection, requires not only sufficiently close approach of the species, but also their proper spatial orientation. Imposing a rigid steric constraint, the latter requirement postpones the crystal nucleus formation. Besides, it was shown that cluster coalescence is not a factor, hampering the protein crystal nucleation. The comparison of the model predictions with experimental results proved that nucleation kinetics is governed by kinetic (not by energetic) factors.     

Large-scale simulations of sodium silicate glasses

Half million and million atom systems of sodium silicate glass have been simulated using classical molecular dynamics, and their structures have been examined. Although the structural features are reasonable for the intended glasses, and have a lower configurational energy than smaller systems, they contain features which are indicative of an effective internal, or configurational, temperature higher than the target temperature. This observation is ascribed to the use of a thermostat which controls only the kinetic energy, or momenta, of the particles, and because of the non-equilibrium nature of the simulations, there is no requirement that the potential, or configurational, energy and kinetic energy be coupled. The use of alternative thermostats is suggested.     

On the Iso‐Diameter Growth of β ‐BaB2O4 (BBO) Crystals by Flux Pulling Method

The iso‐diameter growth of β ‐BaB₂O₄ (BBO) crystals by the flux pulling method have been studied based on the phase equilibrium diagram in the BaB₂O₄‐Na₂O pseudo‐binary system and from the interface stability. The mathematical expressions for the cooling rate in the growth of the crystals with constant diameter under stable growth conditions are derived, the experimental phenomena such as diameter contraction and difficulty to grow a lengthy crystal by the flux pulling method are explained, the prerequisite for iso‐diameter BBO crystal growth from the flux is suggested; a new continuous charging flux pulling method is introduced to grow large‐sized high quality crystals with a relative high growth rate.     

On normal kinetics in the case of some refractory and transition metals' crystallization

In given work the crystal growth kinetics connected with some refractory and transition metals is considered. For melts of Fe, Co, Ni, Cr, Zr, Ti, Ag, Cu, and Pb in the vicinity of melting temperatures the solid phase growth is described by means of a fluctuation theory applied for the macro-systems. By virtue of the “unlimited” and limited spectrum solid state particle concentration fluctuations' theory some effective kinetic coefficients have been estimated in the work. The effective kinetic coefficients are specific in the case of normal crystal growth kinetics. In the case of the crystallization of Fe, Co, Ni, Cr, Zr, Ti, Ag, Cu, and Pb-melts a comparison between two effective kinetic coefficients (based on the fluctuation theory and so-called equilibrium growth points density) has been realized. In most cases a satisfactory agreement between the effective kinetic coefficients has been observed.     

A critical analysis of the glass-forming ability of alloys

Several empirical rules have been proposed during the past few years to synthesize bulk metallic glasses. But, the real reasons for the improved glass-forming ability of these alloys are still not clear and the ability to design alloy compositions to enable synthesis of larger diameter rods has not improved. The present work conducts a critical analysis of the existing data in terms of the different glass-forming criteria and concludes that the available parameters cannot satisfactorily predict the GFA and explain all the observed data. Reasons for this failure have been suggested.     

The effect of local centers on conduction and luminescence of boron nitride

Energetic and kinetic characteristics of charge carrier trapping and recombination centres in graphite-like boron nitride produced by gas-phase deposition are discussed. Local levels in X-ray excited PBN are studied using the method of thermally activated spectroscopy of luminescence and conduction, and their position in the band gap is determined from the temperature dependences of the diffusive current and depolarization current. Acceptor and donor level models for different PBN are developed. Their influence on conduction and on luminescence is determined. The scheme of hole-electron transitions by luminescence is suggested. The carbon influence on the nature of the defects creating local levels is discussed.     

Studies of vapour transport reactions for III–V compounds

Although the III-V compounds and their alloys are increasingly important in the ever widening range of electronic and electro- optic devices, fundamental thermodynamic and chemical kinetic data for the chemical transport reactions used for their preparation is sparse, with few exceptions. The modified entrainment method developed by Faktor, Garrett and co-workers can be used to study chemical transport reactions and to obtain thermodynamic and chemical kinetic data. The direct analogy between the results of these experiments and corresponding crystal growth experiments is emphasised. Results from the systems GaAs-HCl, GaAs-HBr, AlAs-HBr, InSb-HCl, GaP-HBr, and InAs-HCl are discussed and used to illustrate the effects of competing transport reactions and the interplay between gas transport and surface reaction kinetics. Some of the pitfalls in simplistic calculations relating crystal growth rates to thermodynamic data are pointed out.     

Process design for the shape control of crystals grown by Kyropoulos or SAPMAC method

A mathematical model has been proposed to design the process for growing a shaped crystals by Kyropoulos method or SAPMAC method. Crystal shape evolution behaviours under various processes were analysed. The results show that the crystal would go through a transitory shoulder‐expanding stage after which the crystal diameter rapidly decreases under a constant pulling rate and a constant heater temperature. Reducing pulling rate and heater temperature could depress the decrease of crystal diameter after the shoulder‐expanding stage so that enhance the length of crystal. However, the crystal diameter is more sensitive to pulling rate than to heater temperature, and an equal‐diameter crystal can not be grown in non‐undercooled melt by soley reducing the heater temperature. That means that adjusting the pulling rate is the most effective and convenient approach for controlling crystal diameter evolution and simultaneously decreasing both the pulling rate and the heater temperature is the optimal process for growing an equal‐diameter crystal. Moreover, a numerical approach for quantifactional designing crystal shape and corresponding growth processes was proposed according to the model, an example of crystal shape design was given out. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Anomalous viscoelastic properties of polymers: Experiments and explanations

On this occasion recognizing Kia L. Ngai’s contributions to the understanding of the relaxations of many-body interacting molecular systems I present a brief critical review of current research, which is related to our collaborative efforts on polymer viscoelastic properties, which have extended over a quarter of a century. These research efforts include the observations and explanations of violations to some seemingly established principles held in the realm of the kinetic behavior of glass-forming systems both polymeric and small molecules. Successful time-temperature reduction, which has come to be known as thermorheological simplicity (TS), requires that a single monomeric friction coefficient controls the entire spectrum of the primary or α viscoelastic response. Secondary β, γ, and δ mechanisms are recognized to follow different temperature dependences, which reflect different friction coefficients. Summarized herein are the violations of TS that I and my collaborators have encountered, which in the collaborative efforts with Ngai have been extensively rationalized with Ngai’s Coupling Model. Our results have been confirmed many times by others during the past decade. A recent study published by other workers has suggested an additional universal property. In view of this recent research activity on this important subject, previously unpublished data are presented to test the proposed ‘universal’ behavior.     

Fundamental aspects of VLS growth

The kinetics and the mechanism of the vapor-liquid-solid (VLS) growth are discussed. Emphasis is placed on the dependence of the growth rate on the whisker diameter. It is found that the rate decreases abruptly for submicron diameters and vanishes at some critical diameter d_c ? 0,1 μm according to the Gibbs-Thomson effect. A new method for simultaneous determination of kinetic coefficients and of supersaturations has been developed. The method can be used to measure the coefficients of some materials as well as the temperature dependence of the coefficient for silicon and the activation energy of the process. From the dependence of supersaturation on the diameter we conclude that whiskers grow by a poly-nuclear mechanism. The periodic instability of the diameter is discussed and the rate-determining step is analysed. We conclude that phenomena on the liquid-solid interface are the decisive ones. In determining the role of liquid phase in vapor growth we measured the “liquid phase effectivity coefficient” as a function of crystallization condition; the coefficient typically was about 10²?10³. It is stressed that the liquid phase reduces the activation energy both on vapor-liquid interfaces (for chemical reactions) and on liquid-solid interfaces (for nucleation). The liquid phase ensures growth rates as high as 1 cm/sec, provided there are no barriers between the interfaces. The growth mechanism of the side faces was studied, and it was observed that the faces grow mainly by a chain mechanism rather than by two-dimensional nucleation. In work on surface diffusion in the VLS whiskers growth by CVD, we found that the whiskers grow mainly by direct deposition rather than by diffusion on the side faces. It is concluded that the VLS mechanism is important also for the vapor growth of platelets, films, and bulk crystals.     

Combined kinetic analysis for crystallization kinetics of non-crystalline solids

A new method of kinetic analysis that allows the combined analysis of data obtained under different experimental conditions, i.e. heating pathway, is presented for the crystallization of non-crystalline solids. The method consists of a two-stage procedure. Firstly, an optimization procedure is applied for the determination of the Johnson, Mehl and Avrami (JMA). This optimization procedure is based on the linearization of the rate equation throw a logarithmic transformation; where the correlation coefficient function is the objective function, and the JMA order is the adjustable parameter. The JMA order obtained from this optimization procedure allows one to determine in a second stage the other kinetic parameters, i.e. activation energy and pre-exponential Arrhenius factor. The method proposed here allows one to analyze in a combined way data obtained under any heating profile, because no assumptions are made on the heating profile for the derivation of the rate equation. The method is tested with computed and experimental curves obtained under different heating conditions. The crystallization kinetics of (GeS₂)_0.3(Sb₂S₃)_0.7 glass are studied from the combined analysis of several curves.     

The role of water vapour on the oxidation of two Ln-Si-Al-O-N glasses (Ln=Y, La)

The oxidation behaviour of LnSiAlON (Ln=Y, La) glasses was studied at different temperatures (990-1150 °C) and under different water vapour pressures (360-2690 Pa). These results were also compared with those obtained under O₂, N₂/H₂O or O₂/H₂O mixtures. When glasses are treated under a N₂/H₂O mixture, optical and SEM observations show porous scales. Transformations of the reaction rate data and a kinetic model show that there is only one limiting process occurring during oxidation. This rate limiting step is the progress of the chemical reaction at the internal interface. Determination of the pressure law dependence and thermodynamics calculations of water vapour molecules dissociation at the investigated temperatures allow us to suggest that the mechanism of oxidation corresponds to decomposition of water molecules on the oxynitride glass surface.     

Kinetic studies of the growth of III–V compounds using modulated molecular beam techniques

A knowledge of the interaction kinetics of vapour species of elements of Groups III and V with the surfaces of III–V compounds is of fundamental importance to the understanding of growth from the vapour phase of thin films of these compounds. The use of molecular beams provides a powerful means of obtaining surface kinetic data, and the method has been extensively developed over the past decade, with particular emphasis on beam modulation and ac mass spectrometric detection. In addition, UHV and surface analysis techniques now available enable a detailed assessment of the substrate surface to be made. In this paper the application of such an approach to the study of the interaction kinetics of group III and V elements with surfaces of single crystals of III–V compounds will be reviewed. Starting from a known substrate surface conditions measurements have been made of thermal accommodation coefficients, surface lifetimes, sticking coefficients, desorption energies and reaction orders, mainly in the GaAs-Ga-As₄ and GaAs-Ga-As₂ systems. The important results obtained from this work will be described, and possible kinetic models proposed. By a time of flight measurement of the velocity distribution of species desorbed from the surface it is possible to obtain information on energy exchange processes occurring between incident molecules and surface atoms. The polymetric nature of Group Velements appears to influence the translational energy with which they leave the substrate surface, and possible mechanisms of this effect will be considered.     

Modern possibilities for calculating some properties of molecules and crystals from the experimental electron density

Methods for calculating some properties of molecules and crystals from the electron density reconstructed from a precise X-ray diffraction experiment using the multipole model are considered. These properties include, on the one hand, the characteristics of the electron density and the inner-crystal electrostatic field and, on the other hand, the local electronic energies (kinetic, potential, total), the exchange energy density, the electron-pair localization function, the localized-orbital locator, the effective crystal potential, and others. It is shown that the integration of these characteristics over pseudoatomic volumes bounded by the surfaces of the zero flux of the electron density gradient makes it possible to characterize directly from an experiment the properties of molecules and crystals in terms of the atomic contributions. The computer program WinXPRO2004, realizing these possibilities, is briefly described.     

Enhancement of the Automatic Diameter Control System for the Czochralski Growth of Nd:GdVO4 Crystals

The automatic diameter control system was enhanced for the growth of Nd-doped GdVO₄ single crystals by the Czochralski method. It was estimated that excessive amount of feedback in the control system is the effective way to improve the shape of rare-earth vanadate single crystals. The spectral analysis for crystal weight and generator power signals was carried out in real time during growth process for determination of oscillations in the control system.     

A test of distribution function method in the case of liquid transition metals alloys

Atomic transport properties namely the shear viscosity and diffusion coefficients for Ni_xCo_1-x, Co_xFe_1-x and Ni_xFe_1-x liquid transition metal alloys are investigated systematically by employing statistical mechanical theory known as the distribution function method. As required we describe the interionic interaction by a local pseudopotential model that can take into account d-band effect adequately and, the pair correlation function is derived from the Percus-Yevick theory for hard spheres where the effective hard sphere diameter is determined by the LWCA thermodynamic perturbation theory. Results for shear viscosity agree well with the available experimental data for the whole range of concentration.     

Remarks on the Proton NMR of Di-Heptyloxyazoxybenzene in the Smectic-C Phase

It is suggested that the ideal smectic-C reorientation model be modified to include both some rotational slipping of the smectic-C domains and hindered reorientation of a small percentage of molecules to account for the behaviour of proton NMR in smectic-C di-heptyloxyazoxybenzene. The calculated poly-domain line shapes are rather insensitive to the characteristic biaxial order parameter predicted by molecular models of the smectic-C phase.     

Possible Ultrasonic Evidence for the Existence of Vortex-Antivortex Pairs

The attenuation of surface acoustic waves in the 700 MHz frequency range passing through 1000 Å NbN films has been measured on several NbN films. The films have a columnar structure where the columns are about 200 Å in diameter separated by 20 Å voids. In the superconducting state the attenuation does not follow the usual BCS curve. It appears to be composed of the sum of a BCS curve plus another curve which has a maximum below the superconducting transition temperature. The attenuation data may also be analyzed to yield an effective energy gap which is quenched at about one fifth of the BCS zero temperature energy gap. Tentatively, the Kosterlitz-Thouless vortex-antivortex model is used to determine the temperature dependence of an effective order parameter that yields reduced attenuation data which agree qualitatively with the experimental results.