Planarity relations for the sextic centrifugal distortion constants of triangular triatomic molecules

Four linearly independent linear combinations of the ten sextic centrifugal distortion coefficients of triangular triatomic molecules are presented. These combinations are formed in such a way that the resulting expressions depend only on the equilibrium geometry and the harmonic force field parameters of the molecule, quantities which are ordinarily known to considerably better precision than the sextic constants. The relations obtained thus constitute a set of planarity constraints on the ten sextic coefficients which arise in connection with the Nielsen-Amat expansion of the Darling-Dennison Hamiltonian. The planarity expressions can be utilized to effect a reduction of the sextic portion of the Hamiltonian.     

Optical trirefringence in photonic crystal waveguides

We demonstrate that 2D photonic crystals can possess optical trirefringence in which there are six field orientations for which linear incident light is not perturbed on reflection or transmission. Such a property is rigorously forbidden in homogeneous nonmagnetic dielectrics which can possess only optical birefringence. We experimentally demonstrate this phenomena in silicon-based mesostructures formed from photonic crystal waveguides embedded in a Fabry-Perot cavity. Multirefringence is controlled by the presence of submicron dielectric patterning and is well explained by an exact scattering matrix theory.     

k-space inherited parallel acquisition (KIPA): application on dynamic magnetic resonance imaging thermometry

In this study, a novel method for dynamic parallel image acquisition and reconstruction is presented. In this method, called k-space inherited parallel acquisition (KIPA), localized reconstruction coefficients are used to achieve higher reduction factors, and lower noise and artifact levels compared to that of generalized autocalibrating partially parallel acquisition (GRAPPA) reconstruction. In KIPA, the full k-space for the first frame and the partial k-space for later frames are required to reconstruct a whole series of images. Reconstruction coefficients calculated for different segments of k-space from the first frame data set are used to estimate missing k-space lines in corresponding k-space segments of other frames. The local determination of KIPA reconstruction coefficients is essential to adjusting them according to the local signal-to-noise ratio characteristics of k-space data. The proposed algorithm is applicable to dynamic imaging with arbitrary k-space sampling trajectories. Simulations of magnetic resonance thermometry using the KIPA method with a reduction factor of 6 and using dynamic imaging studies of human subjects with reduction factors of 4 and 6 have been performed to prove the feasibility of our method and to show apparent improvement in image quality in comparison with GRAPPA for dynamic imaging.     

Differential temperature Carnot heat analysis shows that computing machines are thermodynamically irreversible

We perform a differential temperature Carnot analysis of the changes in energy and entropy (degrees of freedom) associated with an ideal classical computing machine. Assuming that Carnot’s maximum efficiency law is as equally applicable to a computing machine as to a mechanical machine, we find that useful computation is necessarily dissipative and thermodynamically irreversible. In addition, we find that copying or cloning of information is as dissipative as the original process employed to create the information (through a computation) in the first place. We prove minimum heat dissipation kT ln 2 per output calculation bit, where T is the thermodynamic temperature of unavoidable by-product bits (i.e. not the output calculation bits) rather than a generally assumed ‘surrounding environment’ temperature. Overall, this places computers into the same category as conventional machines, obeying the second law of thermodynamics and always operating below 100% efficiency, such that a perpetual calculating machine cannot exist.     

Surface displacements accompanying the propagation of acoustic waves within an underground pipe

Theoretical expressions for surface displacements accompanying the propagation of acoustic waves in a buried gas-filled pipe are derived. It is shown that the radiated field consists of both shear and compressional components of comparable amplitude which interfere with one another because of the large difference in the respective propagation velocites. This is manifested at the surface by a series of maxima and minima in the vertical and horizontal displacements. Comparing the theoretical calculation to experimental data on vertical surface displacements generated by plane progressive waves at frequencies ranging from 200 to 2000 Hz within an underground pipe shows that only axisymmetric radial and longitudinal vibration of the pipe wall is important. This stands in marked constant to experiments carried out by others in an air medium in which the contribution of bending mode excitation was shown to be significant, particularly at lower frequencies. The theory can be fitted to the experimental data only if the compressional and shear velocities α and β, respectively, are narrowly specified, leading to α = 259 m/s and β = 164 m/s, the latter being in reasonable agreement with the results of other investigators for clay soil.     

Spin polarization of CrO2 at and across an artificial barrier

We report a systematic study of the spin polarization of epitaxial CrO2 films at and across an interface using planar junctions with a superconducting counterelectrode. By chemical modification of the CrO2 surface before the deposition of the superconductor, junctions with a wide range of barrier strength were obtained. Analysis of the conductance data on these junctions, especially under Zeeman splitting of the superconducting density of states, yields consistent, close to full spin polarization for CrO2 regardless of the barrier strength.     

Identification of amyloidogenic peptide sequences using a coarse-grained physicochemical model

Cross-beta amyloid is implicated in over 20 human diseases. Experiments suggest that specific sequence elements within amyloidogenic proteins play a major role in seeding amyloid formation. Identifying these seeding sequences is important for rationalizing the molecular mechanisms of amyloid formation and for elaborating therapeutic strategies that target amyloid. Theoretical techniques play an important role in facilitating the identification and structural characterization of putative seeding sequences; most amyloid species are not amenable to high resolution experimental structure techniques. In this study we have combined a coarse-grained physicochemical protein model with a highly efficient Monte Carlo sampling technique to identify amyloidogenic sequences in four proteins for which respective experimental peptide fragmentation data exist. Peptide sequences were defined as amyloidogenic if the ensemble structure predicted for three interacting peptides described a stable and regular three-stranded beta-sheet. For such peptides, free energies were calculated to provide a measure of amyloid propensity. The overall agreement between the experimental and predicted data is good, and we correctly identify several self-recognition motifs proposed to define the cross-beta amyloid fibril architectures of two of the proteins. Our results compare very favorably with those obtained using atomistic molecular dynamics methods, though our simulations are 30-40 times faster.     

A collaborative hit-to-lead investigation leveraging medicinal chemistry expertise with high throughput library design, synthesis and purification capabilities

High throughput screening (HTS) campaigns, where laboratory automation is used to expose biological targets to large numbers of materials from corporate compound collections, have become commonplace within the lead generation phase of pharmaceutical discovery. Advances in genomics and related fields have afforded a wealth of targets such that screening facilities at larger organizations routinely execute over 100 hit-finding campaigns per year. Often, 10(5) or 10(6) molecules will be tested within a campaign/cycle to locate a large number of actives requiring follow-up investigation. Due to resource constraints at every organization, traditional chemistry methods for validating hits and developing structure activity relationships (SAR) become untenable when challenged with hundreds of hits in multiple chemical families per target. To compound the issue, comparison and prioritization of hits versus multiple screens, or physical chemical property criteria, is made more complex by the informatics issues associated with handling large data sets. This article describes a collaborative research project designed to simultaneously leverage the medicinal chemistry and drug development expertise of the Novartis Institutes for Biomedical Research Inc. (NIBRI) and ArQule Inc.'s high throughput library design, synthesis and purification capabilities. The work processes developed by the team to efficiently design, prepare, purify, assess and prioritize multiple chemical classes that were identified during high throughput screening, cheminformatics and molecular modeling activities will be detailed.     

A highly crystalline microporous hybrid organic-inorganic aluminosilicate resembling the AFI-type zeolite

ECS-14, a crystalline microporous hybrid organic-inorganic aluminosilicate, has been synthesized by using 1,4-bis-(triethoxysilyl)-benzene (BTEB) as a source of silica. Its structure contains a system of linear channels with 12-membered ring openings, running along the [001] direction, resembling the pore architecture of the AFI framework type.     

PAH formation under single collision conditions: reaction of phenyl radical and 1,3-butadiene to form 1,4-dihydronaphthalene

The crossed beam reactions of the phenyl radical (C(6)H(5), X(2)A(1)) with 1,3-butadiene (C(4)H(6), X(1)A(g)) and D6-1,3-butadiene (C(4)D(6), X(1)A(g)) as well as of the D5-phenyl radical (C(6)D(5), X(2)A(1)) with 2,3-D2-1,3-butadiene and 1,1,4,4-D4-1,3-butadiene were carried out under single collision conditions at collision energies of about 55 kJ mol(-1). Experimentally, the bicyclic 1,4-dihydronaphthalene molecule was identified as a major product of this reaction (58 ± 15%) with the 1-phenyl-1,3-butadiene contributing 34 ± 10%. The reaction is initiated by a barrierless addition of the phenyl radical to the terminal carbon atom of the 1,3-butadiene (C1/C4) to form a bound intermediate; the latter underwent hydrogen elimination from the terminal CH(2) group of the 1,3-butadiene molecule leading to 1-phenyl-trans-1,3-butadiene through a submerged barrier. The dominant product, 1,4-dihydronaphthalene, is formed via an isomerization of the adduct by ring closure and emission of the hydrogen atom from the phenyl moiety at the bridging carbon atom through a tight exit transition state located about 31 kJ mol(-1) above the separated products. The hydrogen atom was found to leave the decomposing complex almost parallel to the total angular momentum vector and perpendicularly to the rotation plane of the decomposing intermediate. The defacto barrierless formation of the 1,4-dihydronaphthalene molecule involving a single collision between a phenyl radical and 1,3-butadiene represents an important step in the formation of polycyclic aromatic hydrocarbons (PAHs) and their partially hydrogenated counterparts in combustion and interstellar chemistry.