A Parallel Projection for the Multicommodity Network Model

We present an application of parallel computing techniques to the solution of a quadratic programme that arises in the resource-directive decomposition method for multicommodity problems. A sequential algorithm for the quadratic programme is discussed, and its extension to a parallel implementation is given. Computational testing of the sequential and parallel algorithms was done on the Sequent Symmetry S81 parallel computer located in the Parallel Processing Laboratory at Southern Methodist University. On several large test problems the parallel version achieved a speed-up of 10 with 12 processors.     

Field-induced phases of an orientable charged particle in a dilute background of point charges

We report numerical simulations of a two-dimensional dynamical model comprised of a rodlike particle surrounded by a cloud of smaller particles of the same charge, in the presence of an alternating electric field inside a box. We show that this system displays a remarkable dynamical effect; at low forcing frequencies the rod tends to align perpendicularly to the external field, whereas for higher field frequencies the standard orientation (parallel to the field) prevails. Interestingly, the transition between orientations is abrupt enough to resemble a phase transition. The fact that the "anomalous" orientation (perpendicular to the field) takes place is also interesting in the light of some recent laboratory experiments on colloidal solutions, where anomalous orientation at low frequencies was observed. Our toy model suggests that future physically realistic simulations of these systems should explore whether the anomalous orientation may be due to the collective dynamics of the colloidal particles, without necessarily involving more sophisticated electro-osmotic effects.     

Gravitational radiation from inspiralling compact binaries completed at the third post-Newtonian order

The gravitational radiation from point particle binaries is computed at the third post-Newtonian (3PN) approximation of general relativity. Three previously introduced ambiguity parameters, coming from the Hadamard self-field regularization of the 3PN source-type mass quadrupole moment, are consistently determined by means of dimensional regularization, and proved to have the values xi=-9871/9240, kappa=0, and zeta=-7/33. These results complete the derivation of the general relativistic prediction for compact binary inspiral up to 3.5PN order, and should be of use for searching and deciphering the signals in the current network of gravitational wave detectors.     

Single-capillary Teorell oscillator--studies with nonelectrolytes

It has been demonstrated that if in a Teorell oscillator, the membrane is replaced by a single capillary, the system behaves much better and becomes easily reproducible. It has also been demonstrated that oscillatory behavior in a Teorell-type setup is not limited to electrolytes; even nonelectrolytes can show oscillations. The only requirement seems to be that the nonelectrolyte should be capable of generating an electrical double layer in the capillary. This is the first report of a Teorell oscillator with a single capillary. Also, oscillations with nonelectrolytes in a Teorell-type setup have not been reported before.     

Ready access to 3-amino-2,3-dideoxysugars via regio- and stereo-selective tandem hydroamination-glycosylation of glycals

A highly stereoselective BF(3)·OEt(2)-promoted tandem hydroamination-glycosylation on a glycal scaffold has been developed to form 3-amino-2,3-dideoxysugars in a one-pot procedure. This efficient multicomponent reaction protocol offers simplicity and general applicability to a broad range of variations on each component.     

Synthesis and photophysical properties of neutral luminescent rhenium-based molecular rectangles

A series of neutral luminescent molecular rectangles [[Re(CO)(3)(mu-bpy)Br][Re(CO)(3)(mu-L)Br]](2) (1-4) having fac-Re(CO)(3)Br as corners and 4,4'-bipyridine (bpy) as the bridging ligand on one side and other bipyridyl ligands of varying length (L) on the other side have been synthesized and characterized. The crystal structure of 1 shows a rectangular cavity with the dimensions of 11.44 x 7.21 A. When the cavity size is tuned from 1 to 4, a dimension of 11.4 x 20.8 A could be achieved, as revealed by the molecular modeling. These rectangles exhibit luminescence in solution at room temperature. In particular, compound 4 containing 1,4-bis(4'-pyridylethynyl)benzene (bpeb) as bridging ligand shows the excited-state lifetime of 495 ns. Fine-tuning of the cavity size of the rectangles improves their excited-state properties. These properties facilitate the study of excited-state electron-transfer reactions with electron acceptors and donors and host-guest binding. Crystallographic information: 1.6CH(3)COCH(3) is monoclinic, P2(1)/c, with a = 12.0890(2), b = 24.2982(2), and c = 12.8721(2) A, beta = 107.923(1) degrees, and Z = 2.     

Applications of quantum-classical and quantum-stochastic molecular dynamics simulations for proton transfer processes

Quantum-classical and quantum-stochastic molecular dynamics models (QCMD/QSMD) are formulated and applied to describe proton transfer processes in three model systems - the proton bound ammonia-ammonia dimer in an external electrostatic field; malonaldehyde, which undergoes a quantum tautomeric rearrangement; and phospholipase A₂, an enzyme which induces a water dissociation process in its active site followed by proton hopping to a histidine imidazole ring. The proton dynamics are described by the time-dependent Schrödinger equation. The dynamics of the classical atoms are described using classical molecular dynamics. Coupling between the quantum proton (s) and the classical atoms is accomplished via conventional or extended Hellmann-Feynman forces, as well as the time-dependence of the potential energy function in the Schrödinger equation. The interaction of the system with its environment is described by stochastic forces. Possible extensions of the models as well as future applications in molecular structure and dynamics analysis will be briefly discussed.     

"Proteomineering" serum biomarkers. A study in scarlet

The performance of sera pre-treatment for biomarker searching via combinatorial peptide ligand libraries (CPLL) has recently been challenged (Proteomics 2010, 10, 1416-1425) and stated to allow discovery of only medium to high-abundance proteins. We have thus investigated four elution protocols, as published in recent reports: (i) in 4?M urea+1% CHAPS; (ii) in 4?M urea+1% CHAPS+5% acetic acid; (iii) in 8?M urea+2% CHAPS+5% acetic acid; (iv) in boiling 4% SDS+25?mM DTT. One milliliter of serum, in all cases, was captured with 50?μL of CPLL beads, which were then eluted with the four eluants described above. In the first three cases, after the first elution, the beads were re-eluted with cocktail (iv), known to offer maximal release of proteins adsorbed by the CPLL ligands. Eluant (i) released only ca. 20% of the species adsorbed, eluant (ii) ca. 60%, eluant (iii) ca. 80%. Thus, the poor performance of the CPLL methodology, as reported in (i) is not due to any fault of the capture technique, but simply to the adoption of a very poor elution protocol. Even those using eluants (ii) and (iii) should know that a substantial fraction of the captured species still remains bound to the beads and is thus not available to biomarker discovery. Once more, eluant (iv) is recognized as the only one able to offer optimal recovery from the CPLL baits.