Nucleation and crystallization process of silicon using Stillinger-Weber potential

We study the homogeneous nucleation process in Stillinger-Weber silicon in the NVT ensemble. A clear first-order transition from the liquid to crystal phase is observed thermodynamically with kinetic and structural evidence of the transformation. At 0.75 T_m, the critical cluster size is about 175 atoms. The lifetime distribution of clusters as a function of the maximum size their reach follows an inverse gaussian distribution as was predicted recently from the classical theory of nucleation (CNT). However, while there is a qualitative agreement with the CNT, the free energy curve obtained from the simulations differs significantly from the theoretical predictions, suggesting that the low-density liquid phase found recently could play a role in the nucleation process.Comment: 21 page

Liquid-liquid phase transition in Stillinger-Weber silicon

It was recently demonstrated that the Stillinger-Weber silicon undergoes a liquid-liquid first-order phase transition deep into the supercooled region (Sastry and Angell, Nature Materials 2, 739 (2003)). Here we study the effects of perturbations on this phase transition. We show that the order of the liquid-liquid transition changes with negative pressure. We also find that the liquid-liquid transition disappears when the three-body term of the potential is strengthened by as little as 5 %. This implies that the details of the potential could affect strongly the nature and even the existence of the liquid-liquid phase.Comment: 13 page

Coupled wake boundary layer model of wind-farms

We present and test the coupled wake boundary layer (CWBL) model that describes the distribution of the power output in a wind-farm. The model couples the traditional, industry-standard wake model approach with a "top-down" model for the overall wind-farm boundary layer structure. This wake model captures the effect of turbine positioning, while the "top-down" portion of the model adds the interactions between the wind-turbine wakes and the atmospheric boundary layer. Each portion of the model requires specification of a parameter that is not known a-priori. For the wake model, the wake expansion coefficient is required, while the "top-down" model requires an effective spanwise turbine spacing within which the model's momentum balance is relevant. The wake expansion coefficient is obtained by matching the predicted mean velocity at the turbine from both approaches, while the effective spanwise turbine spacing depends on turbine positioning and thus can be determined from the wake model. Coupling of the constitutive components of the CWBL model is achieved by iterating these parameters until convergence is reached. We illustrate the performance of the model by applying it to both developing wind-farms including entrance effects and to fully developed (deep-array) conditions. Comparisons of the CWBL model predictions with results from a suite of large eddy simulations (LES) shows that the model closely represents the results obtained in these high-fidelity numerical simulations. A comparison with measured power degradation at the Horns Rev and Nysted wind-farms shows that the model can also be successfully applied to real wind-farms.Comment: 25 pages, 21 figures, submitted to Journal of Renewable and Sustainable Energy on July 18, 201

The scattering from generalized Cantor fractals

We consider a fractal with a variable fractal dimension, which is a generalization of the well known triadic Cantor set. In contrast with the usual Cantor set, the fractal dimension is controlled using a scaling factor, and can vary from zero to one in one dimension and from zero to three in three dimensions. The intensity profile of small-angle scattering from the generalized Cantor fractal in three dimensions is calculated. The system is generated by a set of iterative rules, each iteration corresponding to a certain fractal generation. Small-angle scattering is considered from monodispersive sets, which are randomly oriented and placed. The scattering intensities represent minima and maxima superimposed on a power law decay, with the exponent equal to the fractal dimension of the scatterer, but the minima and maxima are damped with increasing polydispersity of the fractal sets. It is shown that for a finite generation of the fractal, the exponent changes at sufficiently large wave vectors from the fractal dimension to four, the value given by the usual Porod law. It is shown that the number of particles of which the fractal is composed can be estimated from the value of the boundary between the fractal and Porod regions. The radius of gyration of the fractal is calculated analytically.Comment: 8 pages, 4 figures, accepted for publication in J. Appl. Crys

Nonmonotonic dependence of the absolute entropy on temperature in supercooled Stillinger-Weber silicon

Using a recently developed thermodynamic integration method, we compute the precise values of the excess Gibbs free energy (G^e) of the high density liquid (HDL) phase with respect to the crystalline phase at different temperatures (T) in the supercooled region of the Stillinger-Weber (SW) silicon [F. H. Stillinger and T. A. Weber, Phys. Rev. B. 32, 5262 (1985)]. Based on the slope of G^e with respect to T, we find that the absolute entropy of the HDL phase increases as its enthalpy changes from the equilibrium value at T \ge 1065 K to the value corresponding to a non-equilibrium state at 1060 K. We find that the volume distribution in the equilibrium HDL phases become progressively broader as the temperature is reduced to 1060 K, exhibiting van-der-Waals (VDW) loop in the pressure-volume curves. Our results provides insight into the thermodynamic cause of the transition from the HDL phase to the low density phases in SW silicon, observed in earlier studies near 1060 K at zero pressure.Comment: This version is accepted for publication in Journal of Statistical Physics (11 figures, 1 table

Morphology and photoluminescence study of titania nanoparticles

Titania nanoparticles are prepared by sol–gel chemistry with a poly(ethylene oxide) methyl ether methacrylate-block-poly(dimethylsiloxane)-block-poly(ethylene oxide) methyl ether methacrylate triblock copolymer acting as the templating agent. The sol–gel components—hydrochloric acid, titanium tetraisopropoxide, and triblock copolymer—are varied to investigate their effect on the resulting titania morphology. An increased titania precursor or polymer content yields smaller primary titania structures. Microbeam grazing incidence small-angle X-ray scattering measurements, which are analyzed with a unified fit model, reveal information about the titania structure sizes. These small structures could not be observed via the used microscopy techniques. The interplay among the sol–gel components via our triblock copolymer results in different sized titania nanoparticles with higher packing densities. Smaller sized titania particles, (∼13–20 nm in diameter) in the range of exciton diffusion length, are formed by 2% by weight polymer and show good crystallinity with less surface defects and high oxygen vacancies

A biocompatible hybrid material with simultaneous calcium and strontium release capability for bone tissue repair

The increasing interest in the effect of strontium in bone tissue repair has promoted the development of bioactive materials with strontium release capability. According to literature, hybrid materials based on the system PDMS–SiO2 have been considered a plausible alternative as they present a mechanical behavior similar to the one of the human bone. The main purpose of this study was to obtain a biocompatible hybrid material with simultaneous calcium and strontium release capability. A hybrid material, in the system PDMS–SiO2–CaO–SrO, was prepared with the incorporation of 0.05 mol of titanium per mol of SiO2. Calcium and strontium were added using the respective acetates as sources, following a sol–gel technique previously developed by the present authors. The obtained samples were characterized by FT-IR, solid-state NMR, and SAXS, and surface roughness was analyzed by 3D optical profilometry. In vitro studies were performed by immersion of the samples in Kokubo's SBF for different periods of time, in order to determine the bioactive potential of these hybrids. Surfaces of the immersed samples were observed by SEM, EDS and PIXE, showing the formation of calcium phosphate precipitates. Supernatants were analyzed by ICP, revealing the capability of the material to simultaneously fix phosphorus ions and to release calcium and strontium, in a concentration range within the values reported as suitable for the induction of the bone tissue repair. The material demonstrated to be cytocompatible when tested with MG63 osteoblastic cells, exhibiting an inductive effect on cell proliferation and alkaline phosphatase activity

Ion-induced folding of a kink turn that departs from the conventional sequence

Kink turns (k-turns) are important structural motifs that create a sharp axial bend in RNA. Most conform to a consensus in which a three-nucleotide bulge is followed by consecutive G•A and A•G base pairs, and when these G•A pairs are modified in vitro this generally leads to a failure to adopt the k-turn conformation. Kt-23 in the 30S ribosomal subunit of Thermus thermophilus is a rare exception in which the bulge-distal A•G pair is replaced by a non-Watson–Crick A•U pair. In the context of the ribosome, Kt-23 adopts a completely conventional k-turn geometry. We show here that this sequence is induced to fold into a k-turn structure in an isolated RNA duplex by Mg2+ or Na+ ions. Therefore, the Kt-23 is intrinsically stable despite lacking the key A•G pair; its formation requires neither tertiary interactions nor protein binding. Moreover, the Kt-23 k-turn is stabilized by the same critical hydrogen-bonding interactions within the core of the structure that are found in more conventional sequences such as the near-consensus Kt-7. T. thermophilus Kt-23 has two further non-Watson–Crick base pairs within the non-canonical helix, three and four nucleotides from the bulge, and we find that the nature of these pairs influences the ability of the RNA to adopt k-turn conformation, although the base pair adjacent to the A•U pair is more important than the other

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

We have achieved the ability to synthesize thousands of unique, long oligonucleotides (150mers) in fmol amounts using parallel synthesis of DNA on microarrays. The sequence accuracy of the oligonucleotides in such large-scale syntheses has been limited by the yields and side reactions of the DNA synthesis process used. While there has been significant demand for libraries of long oligos (150mer and more), the yields in conventional DNA synthesis and the associated side reactions have previously limited the availability of oligonucleotide pools to lengths <100 nt. Using novel array based depurination assays, we show that the depurination side reaction is the limiting factor for the synthesis of libraries of long oligonucleotides on Agilent Technologies’ SurePrint® DNA microarray platform. We also demonstrate how depurination can be controlled and reduced by a novel detritylation process to enable the synthesis of high quality, long (150mer) oligonucleotide libraries and we report the characterization of synthesis efficiency for such libraries. Oligonucleotide libraries prepared with this method have changed the economics and availability of several existing applications (e.g. targeted resequencing, preparation of shRNA libraries, site-directed mutagenesis), and have the potential to enable even more novel applications (e.g. high-complexity synthetic biology)