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

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

A comprehensive map of the mTOR signaling network

The mammalian target of rapamycin (mTOR) is a central regulator of cell growth and proliferation. mTOR signaling is frequently dysregulated in oncogenic cells, and thus an attractive target for anticancer therapy. Using CellDesigner, a modeling support software for graphical notation, we present herein a comprehensive map of the mTOR signaling network, which includes 964 species connected by 777 reactions. The map complies with both the systems biology markup language (SBML) and graphical notation (SBGN) for computational analysis and graphical representation, respectively. As captured in the mTOR map, we review and discuss our current understanding of the mTOR signaling network and highlight the impact of mTOR feedback and crosstalk regulations on drug-based cancer therapy. This map is available on the Payao platform, a Web 2.0 based community-wide interactive process for creating more accurate and information-rich databases. Thus, this comprehensive map of the mTOR network will serve as a tool to facilitate systems-level study of up-to-date mTOR network components and signaling events toward the discovery of novel regulatory processes and therapeutic strategies for cancer

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 critical base pair in k-turns that confers folding characteristics and correlates with biological function

Kink turns (k-turns) are widespread elements in RNA that mediate tertiary contacts by kinking the helical axis. We have found that the ability of k-turns to undergo ion-induced folding is conferred by a single base pair that follows the conserved A·G pairs, that is, the 3b·3n position. A Watson–Crick pair leads to an inability to fold in metal ions alone, while 3n=G or 3b=C (but not both) permits folding. Crystallographic study reveals two hydrated metal ions coordinated to O6 of G3n and G2n of Kt-7. Removal of either atom impairs Mg(2+)-induced folding in solution. While SAM-I riboswitches have 3b·3n sequences that would predispose them to ion-induced folding, U4 snRNA are strongly biased to an inability to such folding. Thus riboswitch sequences allow folding to occur independently of protein binding, while U4 should remain unfolded until bound by protein. The empirical rules deduced for k-turn folding have strong predictive value

Divalent and Multivalent Activation in Phosphate Triesters: A Versatile Method for the Synthesis of Advanced Polyol Synthons

This is the peer reviewed version of the following article: Thomas, C. D., McParland, J. P. and Hanson, P. R. (2009), Divalent and Multivalent Activation in Phosphate Triesters: A Versatile Method for the Synthesis of Advanced Polyol Synthons. Eur. J. Org. Chem., 2009: 5487–5500. doi:10.1002/ejoc.200900560, which has been published in final form at http://doi.org/10.1002/ejoc.200900560. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.The construction of mono- and bicyclic phosphate trimesters possessing divalent and multivalent activation and their subsequent use in the production of advanced polyol synthons is presented. The method highlights efforts to employ phosphate tethers as removable, functionally active tethers capable of multipositional activation and their subsequent role as leaving groups in selective cleavage reactions. The development of phosphate tethers represents an integrated platform for a new and versatile tether for natural product synthesis and sheds light on new approaches to the facile construction of small molecules

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs

All-atom force fields are important for predicting thermodynamic, structural, and dynamic properties of RNA. In this paper, results are reported for thermodynamic integration calculations of free energy differences of duplex formation when CG pairs in the RNA duplexes r(CCGG)2, r(GGCC)2, r(GCGC)2, and r(CGCG)2 are replaced by isocytidine–isoguanosine (iCiG) pairs. Agreement with experiment was improved when ε/ζ, α/γ, β, and χ torsional parameters in the AMBER99 force field were revised on the basis of quantum mechanical calculations. The revised force field, AMBER99TOR, brings free energy difference predictions to within 1.3, 1.4, 2.3, and 2.6 kcal/mol at 300 K, respectively, compared to experimental results for the thermodynamic cycles of CCGG → iCiCiGiG, GGCC → iGiGiCiC, GCGC → iGiCiGiC, and CGCG → iCiGiCiG. In contrast, unmodified AMBER99 predictions for GGCC → iGiGiCiC and GCGC → iGiCiGiC differ from experiment by 11.7 and 12.6 kcal/mol, respectively. In order to test the dynamic stability of the above duplexes with AMBER99TOR, four individual 50 ns molecular dynamics (MD) simulations in explicit solvent were run. All except r(CCGG)2 retained A-form conformation for ≥82% of the time. This is consistent with NMR spectra of r(iGiGiCiC)2, which reveal an A-form conformation. In MD simulations, r(CCGG)2 retained A-form conformation 52% of the time, suggesting that its terminal base pairs may fray. The results indicate that revised backbone parameters improve predictions of RNA properties and that comparisons to measured sequence dependent thermodynamics provide useful benchmarks for testing force fields and computational methods