Adaptive chemistry lookup tables for combustion simulations using optimal B-spline interpolants

Flamelet models, which enable the storing of precomputed detailed chemistry into lookup tables, are widely used in combustion simulations. They allow the computation of accurate results at low computational cost, but standard implementations can lead to numerical problems due to a non-smooth representation, and their applicability is limited by memory requirements. Here, the methods used by a newly developed and optimised lookup table generator based on B-spline interpolation are presented. The creation of smooth representations of flamelet solutions requiring less than one fifth of the number of points in each direction compared to the non-smooth representations of standard lookup tables based on linear interpolation is shown to be possible. The new B-spline interpolation based tables are also applied within a large-eddy simulation of the Swirling Methane/Hydrogen Flame 1 and the results are compared to simulations using lookup tables based on linear interpolation or optimised artificial neural networks. Better performance of the B-spline interpolation based tables with respect to physical accuracy and numerical performance is demonstrated.     

Matrix isolation infrared observation of N3 using a nitrogen microwave discharge plasma source

The asymmetric stretching band of the N₃ radical in a nitrogen matrix at 1657.5?cm^?1 has been observed by directing the output of a nitrogen microwave discharge plasma source onto a CsI window at 12?K. The identification and assignment of this band to the N₃ radical has been accomplished by performing isotopic experiments, matrix annealing experiments, and photolysis experiments. The observed N₃ band positions are compared to literature frequencies observed in matrix isolation experiments using other generation sources and to literature theoretical frequencies calculated using high level ab initio and density functional theory methods. Temperature-dependent deposition experiments (10–20?K) and additional isotopic discharge plus co-deposition experiments are also performed in an effort to determine if the N₃ radical is being formed in the gas phase or by matrix surface reactions, and in order to gain insight into the reaction mechanism. After considering all of the mechanistic evidence (temperature-dependent and isotopic discharge/co-deposition spectra, theoretical reaction energetics, gas phase reaction kinetics, isotopic N₃ distributions), it is concluded that the N₃ radicals are being formed from the reaction of N(²D) atoms with vibrationally excited N₂ molecules in the nitrogen matrix via a linear (end-on) pathway.     

Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior

Fixed‐charge empirical force fields have been developed and widely used over the past three decades for all‐atom molecular simulations. Most simulation programs providing these methods enable only one set of force field parameters to be used for the entire system. Whereas this is generally suitable for single‐phase systems, the molecular environment at the interface between two phases may be sufficiently different from the individual phases to require a different set of parameters to be used to accurately represent the system. Recently published simulations of peptide adsorption to material surfaces using the CHARMM force field have clearly demonstrated this issue by revealing that calculated values of adsorption free energy substantially differ from experimental results. Whereas nonbonded parameters could be adjusted to correct this problem, this cannot be done without also altering the conformational behavior of the peptide in solution, for which CHARMM has been carefully tuned. We have developed a dual‐force‐field approach (Dual‐FF) to address this problem and implemented it in the CHARMM simulation package. This Dual‐FF method provides the capability to use two separate sets of nonbonded force field parameters within the same simulation: one set to represent intraphase interactions and a separate set to represent interphase interactions. Using this approach, we show that interfacial parameters can be adjusted to correct errors in peptide adsorption free energy without altering peptide conformational behavior in solution. This program thus provides the capability to enable both intraphase and interphase molecular behavior to be accurately and efficiently modeled in the same simulation. © 2012 Wiley Periodicals, Inc.     

Microfluidic reactions using [11C]carbon monoxide solutions for the synthesis of a positron emission tomography radiotracer

Microfluidic technology has been used to perform [(11)C]carbonylation reactions using solutions containing [(11)C]CO in the form of the complex, copper(i)tris(3,5-dimethylpyrazolyl)borate-[(11)C]carbonyl (Cu(Tp*)[(11)C]CO). The synthesis of the model compound [(11)C]N-benzylbenzamide and the known tracer molecule [(11)C]trans-N-[5-(2-flurophenyl)-2-pyrimidinyl]-3-oxospiro[5-azaisobenzofurane-1(3H),1'-cyclohexane]-4'-carboxamide ([(11)C]MK-0233), a ligand for the neuropeptide Y Y5 receptor, have been performed using this technique. Following semi-preparative HPLC purification and reformulation, 1262 ± 113 MBq of [(11)C]MK-0233 was produced at the end of the synthesis with a specific activity of 100 ± 30 GBq μmol(-1) and a >99% radiochemical purity. This corresponds to a decay corrected radiochemical yield of 7.2 ± 0.7%. Using a 3 mL vial as the reaction vessel, and following semi-preparative HPLC purification and reformulation, 1255 ± 392 MBq of [(11)C]MK-0233 was produced at the end of the synthesis with a specific activity of 100 ± 15 GBq μmol(-1) and a >99% radiochemical purity. This corresponds to a decay corrected radiochemical yield of 7.1 ± 2.2%.     

Quantitative top-down proteomics of SILAC labeled human embryonic stem cells

Human embryonic stem cells (hESCs) are self-renewing pluripotent cells with relevance to treatment of numerous medical conditions. However, a global understanding of the role of the hESC proteome in maintaining pluripotency or triggering differentiation is still largely lacking. The emergence of top-down proteomics has facilitated the identification and characterization of intact protein forms that are not readily apparent in bottom-up studies. Combined with metabolic labeling techniques such as stable isotope labeling by amino acids in cell culture (SILAC), quantitative comparison of intact protein expression under differing experimental conditions is possible. Herein, quantitative top-down proteomics of hESCs is demonstrated using the SILAC method and nano-flow reverse phase chromatography directly coupled to a linear-ion-trap Fourier transform ion cyclotron resonance mass spectrometer (nLC-LTQ-FT-ICR-MS). In this study, which to the best of our knowledge represents the first top-down analysis of hESCs, we have confidently identified 11 proteins by accurate intact mass, MS/MS, and amino acid counting facilitated by SILAC labeling. Although quantification is challenging due to the incorporation of multiple labeled amino acids (i.e., lysine and arginine) and arginine to proline conversion, we are able to quantitatively account for these phenomena using a mathematical model.     

Cytotoxicity of Bacterial-Derived Toxins to Immortal Lung Epithelial and Macrophage Cells

Health risks associated with inhalation and deposition of biological materials have been a topic of great concern due to highly publicized cases of inhalation anthrax, of new regulations on the release of particulate matter, and to increased concerns on the hazards of indoor air pollution. Here, we present an evaluation of the sensitivity of two immortal cell lines (A549, human lung carcinoma epithelia) and NR8383 (rat alveolar macrophages) to a variety of bacterial-derived inhalation hazards and simulants including etoposide, gliotoxin, streptolysin O, and warfarin. The cell response is evaluated through quantification of changes in mitochondrial succinate dehydrogenase activity, release of lactate dehydrogenase, initiation of apoptosis, and through changes in morphology as determined by visible light microscopy and scanning electron microscopy. These cells display dose–response relations to each toxin, except for triton which has a step change response. The first observable responses of the epithelial cells to these compounds are changes in metabolism for one toxin (warfarin) and alterations in membrane permeability for another (gliotoxin). The other four toxins display a similar time course in response as gauged by changes in metabolism and loss of membrane integrity. Macrophages are more sensitive to most toxins; however, they display a lower level of stability. This information can be used in the design of cell-based sensors responding to these and similar hazards.