The LANS-alpha turbulence model in primitive-equation ocean modeling

The Lagrangian-Averaged Navier-Stokes alpha (LANS-α) and Leray turbulence parameterizations are demonstrated in a primitive-equation ocean model using an idealized channel domain. For LANS-α, turbulence statistics such as kinetic energy, eddy kinetic energy, and temperature profiles resemble doubled-resolution statistics with the standard model. In a North Atlantic domain with realistic topography, the Leray model increases eddy activity. The LANS-α and Leray models show great promise to improve heat transport and temperature distributions in global ocean-climate simulations, as these processes depend on better resolution of eddies near the grid-scale. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

A rapid method for cross-species quantitation of apolipoproteins A1, B48 and B100 in plasma by ultra-performance liquid chromatography/tandem mass spectrometry

Apolipoprotein B100 (apoB100) and apolipoprotein A1 (apoA1) are the primary protein components of low density lipoprotein (LDL) and high density lipoprotein (HDL) particles, respectively, and plasma levels of these proteins are associated with risks of cardiovascular disease. Existing apoB100 quantitation methods for animal models have been limited to affinity capture techniques such as enzyme-linked immunosorbent assay (ELISA) and Western blot which require specialized reagents for each species and in many cases are not readily available. Here we demonstrate a single translatable ultra-performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) assay that is fast and robust and can be used to measure apolipoprotein concentrations in plasma for six species. When possible, peptide sequences that are conserved across species were identified for this assay. The sample preparation is limited and can be carried out in 96-well microtiter plates and thus allows for multiplexed preparation of samples for analysis of large numbers of samples in a short time frame when combined with UPLC/MS/MS. Separation and quantitation of the tryptic peptides is carried out at 700 μL/min using a 1.7 μm core shell C18 column (2.1 × 50 mm). The chromatography is designed for the analysis of over 100 samples per day, and the UPLC run is less than 10 min. This assay is capable of supporting cardiovascular research by providing a single assay to measure critical biomarkers across multiple species without the need for antibodies, and does so in a high-throughput manner.     

Sulfoxide stretching mode as a structural reporter via dual-frequency two-dimensional infrared spectroscopy

The S=O stretching mode in sulfoxides, having a frequency in the 950-1150?cm(-1) range, is tested as a structural label via dual-frequency two-dimensional infrared (2DIR) spectroscopy. The properties of this structural reporter are studied in several compounds, including (4,4(')-dimethyl-2,2(')-bipyridyl)(o-methylsulfinylbenzoate) ruthenium II, [Ru(dmb)(2)(BzSO)](+), (RuBzSO), octylsulfinylpropionic acid (OSPA), and o- and p-methylsulfinyl-benzoic acid (oMSBA and pMSBA). The mode assignment in the fingerprint region for these compounds is made using a combination of density functional theory calculations and 2DIR and relaxation-assisted 2DIR (RA 2DIR) spectroscopies. The SO stretching mode frequency and IR intensity demonstrate substantial sensitivity to the molecular structure. Multiple cross peaks of the C=O and S=O stretching modes with modes in the fingerprint region (930-1450?cm(-1)) were recorded. The 2DIR and RA 2DIR spectra focusing at interactions of a high-frequency mode of a ligand with the modes in the fingerprint region provide a spectral fingerprint of a compound and help mode assignment in the often congested fingerprint region. The cross-peak amplitudes in oMSBA, pMSBA, and OSPA were compared with the theoretical predictions based on the computed values for the off-diagonal anharmonicities and a reasonable match is found. The SO stretching mode provides means for assigning other modes in the fingerprint region and constitutes a promising structural reporter for the 2DIR and RA 2DIR spectroscopy measurements.     

Quantum codes give counterexamples to the unique preimage conjecture of the N-representability problem

It is well known that the ground state energy of many-particle Hamiltonians involving only 2-body interactions can be obtained using constrained optimizations over density matrices which arise from reducing an N-particle state. While determining which 2-particle density matrices are "N-representable" is a computationally hard problem, all known extreme N-representable 2-particle reduced density matrices arise from a unique N-particle preimage, satisfying a conjecture established in 1972. We present explicit counterexamples to this conjecture through giving Hamiltonians with 2-body interactions which have degenerate ground states that cannot be distinguished by any 2-body operator. We relate the existence of such counterexamples to quantum error correction codes and topologically ordered spin systems.     

Synthesis of spiro-fused pyrazolidoylisoxazolines

Routes to structurally unique spiro-fused pyrazolidoylisoxazolines are reported. These methods start with monosubstituted hydrazines or hydrazides and utilize the nitrile oxide 1,3-dipolar cycloaddition reaction to generate the targeted spiro-fused bis-heterocycles. Molecular shape space diversity analyses were performed on these pyrazolidoylisoxazolines showing that manipulation of the appended R groups significantly changes the molecular shape.