General local and rectilinear vibrational coordinates consistent with Eckart's conditions

We present a general method to construct a set of local rectilinear vibrational coordinates for a nonlinear molecule whose reference structure does not necessarily correspond to a stationary point of the potential-energy surface. We show both analytically and with a numerical example that the vibrational coordinates satisfy Eckart's conditions. In addition, we find that the Watson Hamiltonian provides a fairly robust description even of highly excited vibrational states of triatomic molecules, except for a few states of large amplitude motion sampling the singular region of the Hamiltonian. These states can be identified through slow convergence.

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.

Analytically continued generalized continuum distorted waves

The continuum distorted-wave eikonal-initial-state (CDW-EIS) theory of Crothers and McCann (Crothers DSF and McCann JF, 1983 J. Phys. B: At. Mol. Opt. Phys. 16 3229 ) used to describe ionization in ion-atom collisions is generalized (G) to GCDW-EIS, to incorporate the azimuthal ange dependence into the final-state wavefunction. This is accomplished by the analytic continuation of hydrogenic-like wavefunctions from below to above threshold, using parabolic coordinates and quantum numbers including magnetic quantum numbers, thus providing a more complete set of states. At impact energies lower than 25 ke V u^{-1}, the total CDW-EIS ionization cross section falls off, with decreasing energy, too quickly in comparison with experimental data by Crothers and McCann. The idea behind and motivation for the GCDW-EIS model is to improve the theory with respect to experiment, by including contributions from non-zero magnetic quantum numbers. We also therefore incidentally provide a new derivation of the theory of continuum distorted waves for zero magnetic quantum numbers while simultaneously generalizing it.

Magnetically quantized continuum distorted-wave theory in atomic and molecular collisions

The continuum distorted-wave eikonal initial-state (CDW-EIS) theory of Crothers and McCann (J Phys B 1983, 16, 3229) used to describe ionization in ion-atom collisions is generalized (G) to GCDW-EIS to incorporate the azimuthal angle dependence of each CDW in the final-state wave function. This is accomplished by the analytic continuation of hydrogenic-like wave functions from below to above threshold, using parabolic coordinates and quantum numbers including magnetic quantum numbers, thus providing a more complete set of states. At impact energies lower than 25 keVu(-1), the total ionization cross-section falls off, with decreasing energy, too quickly in comparison with experimental data. The idea behind and motivation for the GCDW-EIS model is to improve the theory with respect to experiment by including contributions from nonzero magnetic quantum numbers. We also therefore incidentally provide a new derivation of the theory of continuum distorted waves for zero magnetic quantum numbers while simultaneously generalizing it. (C) 2004 Wiley Periodicals, Inc.

High-pressure deformation mechanism in scolecite: A combined computational-experimental study

Pressure-induced structural modifications in scolecite were studied by means of in situ synchrotron X-ray powder diffraction and density functional computations. The experimental cell parameters were refined up to 8.5 GPa. Discontinuities in the slope of the unit-cell parameters vs. pressure dependence were observed; as a consequence, an increase in the slope of the linear pressure-volume dependence is observed at about 6 GPa, suggesting an enhanced compressibility at higher pressures. Weakening and broadening of the diffraction peaks reveals increasing structural disorder with pressure, preventing refinement of the lattice parameters above 8.5 GPa. Diffraction patterns collected during decompression show that the disorder is irreversible. Atomic coordinates within unit cells of different dimensions were determined by means of Car-Parrinello simulations. The discontinuous rise in compressibility at about 6 GPa is reproduced by the computation, allowing us to attribute it to re-organization of the hydrogen bonding network, with the formation of water dimers. Moreover we found that, with increasing pressure, the tetrahedral chains parallel to c rotate along their elongation axis and display an increasing twisting along a direction perpendicular to c. At the same time, we observed the compression of the channels. We discuss the modification of the Ca polyhedra under pressure, and the increase in coordination number (from 4 to 5) of one of the two Al atoms, resulting from the approach of a water molecule. We speculate that this last transformation triggers the irreversible disordering of the system.

Equilibrium structure of erbium-oxygen complexes in crystalline silicon

The equilibrium structure of ErOn (nless than or equal to6) complexes in crystalline silicon has been investigated by density-functional computations. Two different geometries have been considered, corresponding to the substitutional and tetrahedral interstitial site for erbium. All atomic coordinates have been optimized by Car-Parrinello molecular dynamics. The resulting structures have low symmetry, with E-O distances of similar to2.35 Angstrom. The substitutional site is the most stable one for nless than or equal to2, while the tetrahedral interstitial is favored for n>2.

A dielectric continuum molecular dynamics method

We introduce a novel method to simulate hydrated macromolecules with a dielectric continuum representation of the surrounding solvent. In our approach, the interaction between the solvent and the molecular degrees of freedom is described by means of a polarization density free energy functional which is minimum at electrostatic equilibrium. After a pseudospectral expansion of the polarization and a discretization of the functional, we construct the equations of motion for the system based on a Car-Parrinello technique. In the limit of the adiabatic evolution of the polarization field variables, our method provides the solution of the dielectric continuum problem "on the fly," while the molecular coordinates are propagated. In this first study, we show how our dielectric continuum molecular dynamics method can be successfully applied to hydrated biomolecules, with low cost compared to free energy simulations with explicit solvent. To our knowledge, this is the first time that stable and conservative molecular dynamic simulations of solutes can be performed for a dielectric continuum model of the solvent. (C) 2001 American Institute of Physics.

Ruthenium complexes of the 1,4-bis(diphenylphosphino)-1,3-butadiene-bridged diphosphine 1,2,3,4-Me-4-NUPHOS: Solvent-dependent interconversion of four- and six-electron donor coordination and transfer hydrogenation activity

In chloroform, [RuCl2(nbd)(py)(2)] (1) (nbd = norbornadiene; py = pyridine) reacts with 1,4-bis(diphenylphosphino)-1,2,3,4-tetramethyl-1,3-butadiene (1,2,3,4-Me-4-NUPHOS) to give the dimer [Ru2Cl3(eta(4)-1,2,3,4-Me-4-NUPHOS)(2)]Cl (2a), whereas, in THF [RuCl2(1,2,3,4-Me-4-NUPHOS)(PY)(2)] (3) is isolated as the sole product of reaction. Compound 2 exists as a 4:1 mixture of two noninterconverting isomers, the major with C, symmetry and the minor with either C, or C-2 symmetry. A single-crystal X-ray analysis of [Ru2Cl3 (eta(4)-1,2,3,4-Me-4-NUPHOS)(2)] [SbF6] (2b), the hexafluoroantimonate salt of 2a, revealed that the diphosphine coordinates in an unusual manner, as a eta(4)-six-electron donor, bonded through both P atoms and one of the double bonds of the butadiene tether. Compounds 2a and 3 react with 1,2-ethylenediamine (en) in THF to afford [RuCl2(1,2,3,4-Me-4-NUPHOS)(en)] (4), which rapidly dissociates a chloride ligand in chloroform to give [RuCl(eta(4)-1,2,3,4-Me-4-NUPHOS)(en)] [Cl] (5a). Complexes 4 and 5a cleanly and quantitatively interconvert in a solvent-dependent equilibrium, and in THF 5a readily adds chloride to displace the eta(2)-interaction and re-form 4. A single-crystal X-ray structure determination of [RuCl(eta(4)-1,2,3,4-Me-4-NUPHOS)(en)][ClO4] (5b) confirmed that the diphosphine coordinates in an eta(4)-manner as a facial six-electron donor with the eta(2)-coordinated double bond occupying the site trans to chloride. The eta(4)-bonding mode can be readily identified by the unusually high-field chemical shift associated with the phosphorus atom adjacent to the eta(2)-coordinated double bond. Complexes 2a, 2b, 4, and 5a form catalysts that are active for transfer hydrogenation of a range of ketones. In all cases, catalysts formed from precursors 2a and 2b are markedly more active than those formed from 4 and 5a.

Neuropeptide Y (NPY) and NPY Y1 receptor in periodontal health and disease

Abstract
OBJECTIVES:
Neuropeptide Y (NPY) coordinates inflammation and bone metabolism which are central to the pathogenesis of periodontitis. The present study was designed to determine whether NPY was quantifiable in human gingival crevicular fluid (GCF) and to test the null hypothesis that GCF levels of NPY were the same in periodontal health and disease. A subsidiary aim was to determine the potential functionality of released NPY by detecting the presence of NPY Y1 receptors in gingival tissue.
DESIGN:
The periodontitis group consisted of 20 subjects (10 females and 10 males) mean age 41.4 (S.D. 9.6 years). The control group comprised 20 subjects (10 females and 10 males) mean age 37.4 (S.D. 11.7 years). NPY levels in GCF were measured in periodontal health and disease by radioimmunoassay. NPY Y1 receptor expression in gingival tissue was determined by Western blotting of membrane protein extracts from healthy and inflamed gum.
RESULTS:
Healthy sites from control subjects had significantly higher levels of NPY than diseased sites from periodontitis subjects. NPY Y1 receptor protein was detected in both healthy and inflamed gingival tissue by Western blotting.
CONCLUSIONS:
The significantly elevated levels of NPY in GCF from healthy compared with periodontitis sites suggests a tonic role for NPY, the functionality of which is indicated by the presence of NPY Y1 receptors in local gingival tissue.

3,5-dimethyl-4-amino-1,2,4-triazole (Dat) as a tridentate ligand in the polymeric cations of [Ag-3(Dat)(2)](NO3)(3)

Colourless single crystals of [Ag-3(Dat)(2)](NO3)(3) were obtained from a reaction of silver(l) nitrate and 3,5-dimethyl-4-amino-1,2,4-triazole (Dat). In the crystal structure (orthorhombic, Fdd2, Z = 8, a = 1100.1(2), b = 3500.3(2), c = 1015.4(3) pm, R, = 0.0434) there are two crystallographically non-equivalent silver sites in a one (Ag1) to two ratio (Ag2). Both resemble linear N-Ag-N coordination although angles are 163 degrees and 144 degrees, respectively Each Dat ligand coordinates with the two ring nitrogen atoms at 216 to 219 pm and with one amino-nitrogen atom at 229 pro. According to the composition [Ag-3(Dat)(2)](3+) = [(Dat)Ag-3/2](3+), a polymeric structure is built with all Ag+ ions bridging.

Mechanism of Activation of a G Protein-coupled Receptor, the Human Cholecystokinin-2 Receptor

G protein-coupled receptors (GPCRs) represent a major focus in functional genomics programs and drug development research, but their important potential as drug targets contrasts with the still limited data available concerning their activation mechanism. Here, we investigated the activation mechanism of the cholecystokinin-2 receptor (CCK2R). The three-dimensional structure of inactive CCK2R was homology-modeled on the basis of crystal coordinates of inactive rhodopsin. Starting from the inactive CCK2R modeled structure, active CCK2R (namely cholecystokinin-occupied CCK2R) was modeled by means of steered molecular dynamics in a lipid bilayer and by using available data from other GPCRs, including rhodopsin. By comparing the modeled structures of the inactive and active CCK2R, we identified changes in the relative position of helices and networks of interacting residues, which were expected to stabilize either the active or inactive states of CCK2R. Using targeted molecular dynamics simulations capable of converting CCK2R from the inactive to the active state, we delineated structural changes at the atomic level. The activation mechanism involved significant movements of helices VI and V, a slight movement of helices IV and VII, and changes in the position of critical residues within or near the binding site. The mutation of key amino acids yielded inactive or constitutively active CCK2R mutants, supporting this proposed mechanism. Such progress in the refinement of the CCK2R binding site structure and in knowledge of CCK2R activation mechanisms will enable target-based optimization of nonpeptide ligands.

A framework for collaborative working environments

To utilize the advantages of existing and emerging Internet techniques and to meet the demands for a new generation of collaborative working environments, a framework with an upperware–middleware architecture is proposed, which consists of four layers: resource layer, middleware layer, upperware layer and application layer. The upperware contains intelligent agents and plug/play facilities; the former coordinates and controls multiple middleware techniques such as Grid computing, Web-services and mobile agents, while the latter are used for the applications, such as semantic CAD, to plug and loose couple into the system. The method of migrating legacy software using automatic wrapper generation technique is also presented. A prototype mobile environment for collaborative product design is presented to illustrate the utilization of the CWE framework in collaborative design and manufacture.

Coordination, Efficiency and Two-Sided Cheap Talk

We consider the Battle of the Sexes game with incomplete information and allow two-sided cheap talk before the game is played. We characterise the set of fully revealing symmetric cheap talk equilibria. The best fully revealing symmetric cheap talk equilibrium, when exists, has a desirable characteristic. When the players' types are different, it fully coordinates on the ex-post efficient pure Nash equilibrium. We also analyse the mediated communication equilibria of the game. We find the range of the prior for which this desirable equilibrium exists under unmediated and mediated communication processes.

Combined R-matrix eigenstate basis set and finite-difference propagation method for the time-dependent Schrodinger equation: The one-electron case

In this work we present the theoretical framework for the solution of the time-dependent Schrödinger equation (TDSE) of atomic and molecular systems under strong electromagnetic fields with the configuration space of the electron’s coordinates separated over two regions; that is, regions I and II. In region I the solution of the TDSE is obtained by an R-matrix basis set representation of the time-dependent wave function. In region II a grid representation of the wave function is considered and propagation in space and time is obtained through the finite-difference method. With this, a combination of basis set and grid methods is put forward for tackling multiregion time-dependent problems. In both regions, a high-order explicit scheme is employed for the time propagation. While, in a purely hydrogenic system no approximation is involved due to this separation, in multielectron systems the validity and the usefulness of the present method relies on the basic assumption of R-matrix theory, namely, that beyond a certain distance (encompassing region I) a single ejected electron is distinguishable from the other electrons of the multielectron system and evolves there (region II) effectively as a one-electron system. The method is developed in detail for single active electron systems and applied to the exemplar case of the hydrogen atom in an intense laser field.

A TMA De-Arraying Method for High Throughput Biomarker Discovery in Tissue Research

Background: Tissue MicroArrays (TMAs) represent a potential high-throughput platform for the analysis and discovery of tissue biomarkers. As TMA slides are produced manually and subject to processing and sectioning artefacts, the layout of TMA cores on the final slide and subsequent digital scan (TMA digital slide) is often disturbed making it difficult to associate cores with their original position in the planned TMA map. Additionally, the individual cores can be greatly altered and contain numerous irregularities such as missing cores, grid rotation and stretching. These factors demand the development of a robust method for de-arraying TMAs which identifies each TMA core, and assigns them to their appropriate coordinates on the constructed TMA slide.

Methodology: This study presents a robust TMA de-arraying method consisting of three functional phases: TMA core segmentation, gridding and mapping. The segmentation of TMA cores uses a set of morphological operations to identify each TMA core. Gridding then utilises a Delaunay Triangulation based method to find the row and column indices of each TMA core. Finally, mapping correlates each TMA core from a high resolution TMA whole slide image with its name within a TMAMap.

Conclusion: This study describes a genuine robust TMA de-arraying algorithm for the rapid identification of TMA cores from digital slides. The result of this de-arraying algorithm allows the easy partition of each TMA core for further processing. Based on a test group of 19 TMA slides (3129 cores), 99.84% of cores were segmented successfully, 99.81% of cores were gridded correctly and 99.96% of cores were mapped with their correct names via TMAMaps. The gridding of TMA cores were also extensively tested using a set of 113 pseudo slide (13,536 cores) with a variety of irregular grid layouts including missing cores, rotation and stretching. 100% of the cores were gridded correctly.