Impact of natural organic matter (NOM) on freshwater amphipods

Natural organic matter (NOM) isolated from the eutrophic Sanctuary Pond (Point Pelee National Park, Canada) has an adverse impact on amphipod species (Gammarus tigrinus and Chaetogammarus ischnus from Lake Müggelsee, Germany, and Eulimnogammarus cyaneus, from Lake Baikal, Russia). Increases in amphipod mortality, changes in peroxidase activity and increases of heat shock protein (hsp70) expression were observed upon exposure to NOM. The highest resistance to the adverse impact of NOM was observed with the endemic Baikalian amphipod E. cyaneus. However, the mechanisms behind this finding remains obscure. If differences in the sensitivity of the hsp70 antibody may be excluded, different modes of action may be postulated: because the adverse impact of NOM may be caused by reactive oxygen species (ROS) and the NOM itself, the observed differences may be due to the action of ROS alone (with E. cyaneus) and a combination of both adverse modes of action (European species).     

DVR3D: a program suite for the calculation of rotation-vibration spectra of triatomic molecules

The DVR3D program suite calculates energy levels, wavefunctions, and where appropriate dipole transition moments, for rotating and vibrating triatomic molecules. Potential energy and, where necessary, dipole surfaces must be provided. Expectation values of geometrically defined functions can be calculated, a feature which is particularly useful for fitting potential energy surfaces. The programs use an exact (within the Born-Oppenheimer approximation) Hamiltonian and offer a choice of Jacobi or Radau internal coordinates and several body-fixed axes. Rotationally excited states are treated using an efficient two-step algorithm. The programs uses a Discrete Variable Representation (DVR) based on Gauss-Jacobi and Gauss-Laguerre quadrature for all 3 internal coordinates and thus yields a fully point-wise representation of the wavefunctions. The vibrational step uses successive diagonalisation and truncation which is implemented for a number of possible coordinate orderings. The rotational, expectation value and transition dipole programs exploit the savings offered by performing integrals on a DVR grid. The new version has been rewritten in FORTRAN 90 to exploit the dynamic array allocations and the algorithm for dipole and spectra calculations have been substantially improved. New modules allow the z-axis to be embedded perpendicular to the plane of the molecule and for the calculation of expectation values.

Program summary

Title of the program: DVR3D suiteCatalogue number: ADTIProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTIProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandProgramming language: Fortran 90No. of lines in distributed program, including test data, etc.: 61 574No. of bytes in distributed program, including test data, etc.: 972 404Distribution format: tar.gz

New version summary

Title of program: DVR3DRJZCatalogue number: ADTBProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTBProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandReference in CPC to previous version: 86 (1995) 175Catalogue identifier of previous version: ADAKAuthors of previous version: J. Tennyson, J.R. Henderson and N.G. FultonDoes the new version supersede the original program?: DVR3DRJZ supersedes DVR3DRJComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 Unix; SGI Origin 2000, Sunfire V750 and V880 systems running SunOS, IBM p690 Regatta running AIXProgramming language used in the new version: Fortran 90Memory required to execute: case dependentNo. of lines in distributed program, including test data, etc.: 4203No. of bytes in distributed program, including test data, etc.: 30 087Has code been vectorised or parallelised?: The code has been extensively vectorised. A parallel version of the code, PDVR3D has been developed [1], contact the first author for detailsAdditional keywords: perpendicular embeddingDistribution format: gzNature of physical problem: DVR3DRJZ calculates the bound vibrational or Coriolis decoupled rotational-vibrational states of a triatomic system in body-fixed Jacobi (scattering) or Radau coordinates [2]Method of solution: All coordinates are treated in a discrete variable representation (DVR). The angular coordinate uses a DVR based on (associated) Legendre polynomials and the radial coordinates utilise a DVR based on either Morse oscillator-like or spherical oscillator functions. Intermediate diagonalisation and truncation is performed on the hierarchical expression of the Hamiltonian operator to yield the final secular problem. DVR3DRJ provides the vibrational wavefunctions necessary for ROTLEV3, ROLEV3B or ROTLEV3Z to calculate rotationally excited states, DIPOLE3 to calculate rotational-vibrational transition strengths and XPECT3 to compute expectation valuesRestrictions on the complexity of the problem: (1) The size of the final Hamiltonian matrix that can practically be diagonalised. (2) The order of integration in the radial coordinates that can be dealt with within the machine exponent range. Some adjustment in the code may be necessary when large order Gauss-Laguerre quadrature is usedTypical running time: Case dependent but usually dominated by the final (3D) matrix diagonalisation. The test runs take minutes on a fast PCUnusual features of the program: A user supplied subroutine containing the potential energy as an analytic function is a program requirementReferences:

[1]

H.Y. Mussa, J. Tennyson, Comput. Phys. Commun. 128 (2000) 434.

[2]

J. Tennyson, B.T. Sutcliffe, Internat. J. Quantum Chem. 42 (1992) 941.

New version summary

Title of program: ROTLEV3Catalogue number: ADTCProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTCProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandReference in CPC to previous version: 86 (1995) 175Catalogue identifier of previous version: ADALAuthors of previous version: J. Tennyson, J.R. Henderson and N.G. FultonDoes the new version supersede the original program?: YesComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 Unix; SGI Origin 2000, Sunfire V750 and V880 systems running SunOSProgramming language used: Fortran 90High speed storage required: case dependentNo. of lines in distributed program, including test data, etc.: 1514No. of bytes in distributed program, including test data, etc.: 12 652Has code been vectorised or parallelised?: The code has been extensively vectorised. A parallel version of the code, PROTLEV3 has been developed [1], contact the first author for detailsDistribution format: gzNature of physical problem: ROTLEV3 performs the second step in a two-step variational calculation for the bound rotational-vibrational levels of a triatomic system represented in either Jacobi or unsymmetrised Radau coordinatesMethod of solution: A basis is constructed from the solutions of the Coriolis decoupled problem provided by DVR3DRJZ. The angular coordinate is transformed back to a basis set representation. The sparse Hamiltonian matrix can be diagonalised iteratively or in coreRestrictions on the complexity of the problem: The size of matrix that can practically be diagonalisedTypical running time: Case dependent. The sample data takes less than a minute on a fast PCUnusual features of the program: Most data is read directly from DVR3DRJZ. ROTLEV3 can provide data to drive DIPOLE3 and/or XPECT3References: [1] H.Y. Mussa, J. Tennyson, Comput. Phys. Commun. 128 (2000) 434.

New version summary

Title of program: ROTLEV3BCatalogue number: ADTDProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTDProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandReference in CPC to previous version: 86 (1995) 175Catalogue identifier of previous version: ADAMAuthors of previous version: J. Tennyson, J.R. Henderson and N.G. FultonDoes the new version supersede the original program?: YesComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 Unix, Sunfire V750 and V880 systems running SunOSProgramming language used: Fortran 90High speed storage required: case dependentNo. of lines in distributed program, including test data, etc.: 2215No. of bytes in distributed program, including test data, etc.: 16 595Has code been vectorised or parallelised?: The code has been extensively vectorised. A parallel version of the code, PROTLEV3B has been developed [1], contact the first author for detailsDistribution format: gzNature of physical problem: ROTLEV3B performs the second step in a two-step variational calculation for the bound rotational-vibrational levels of a triatomic system represented by symmetrised Radau coordinates using a bisector embedding [2]Method of solution: A basis is constructed from the solutions of the Coriolis decoupled problem provided by DVR3DRJZ. The problem is constructed entirely within the DVR. The Hamiltonian matrix can be diagonalised iteratively or in coreRestrictions on the complexity of the problem: The size of matrix that can practically be diagonalisedTypical running time: Case dependent. The sample data takes a few minutes on a fast PCUnusual features of the program: Most data is read directly from DVR3DRJZ. ROTLEV3B can provide data to drive DIPOLE3 and/or XPECT3References:

[1]

H.Y. Mussa, J. Tennyson, Comput. Phys. Commun. 128 (2000) 434.

[2]

J. Tennyson, B.T. Sutcliffe, Internat. J. Quantum Chem. 42 (1992) 941.

Program summary

Title of program: ROTLEV3ZCatalogue number: ADTEProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTEProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 Unix, Sunfire V750 and V880 systems running SunOSProgramming language used: Fortran 90High speed storage required: case dependentNo. of lines in distributed program, including test data, etc.: 2919No. of bytes in distributed program, including test data, etc.: 17 241Keywords: rotationally excited state, Coriolis coupling, secondary variational method, sparse matrix, vectorised, perpendicular embedding, Radau coordinatesHas code been vectorised or parallelised?: The code has been extensively vectorisedDistribution format: gzNature of physical problem: ROTLEV3Z performs the second step in a two-step variational calculation for the bound rotational-vibrational levels of a triatomic system represented by symmetrised Radau coordinates using a perpendicular embedding [1]Method of solution: A basis is constructed from the solutions of the Coriolis decoupled problem provided by DVR3DRJZ. The problem is constructed entirely within the DVR. The Hamiltonian matrix is diagonalised in coreRestrictions on the complexity of the problem: The size of matrix that can practically be diagonalisedTypical running time: Case dependent. The sample data takes a few minutes on a fast PCUnusual features of the program: Most data is read directly from DVR3DRJZReferences: [1] M.A. Kostin, O.L. Polyansky, J.Tennyson, J. Chem. Phys. 116 (2002) 7564.

New version summary

Title of program: DIPOLE3Catalogue number: ADTFProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTFProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandReference in CPC to previous version: 86 (1995) 175Catalogue identifier of previous version: ADANAuthors of previous version: J. Tennyson, J.R. Henderson and N.G. FultonDoes the new version supersede the original program?: YesComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 Unix; SGI Origin 2000; sunfire V750 and V880 systemsProgramming language used: Fortran 90High speed storage required: case dependentNo. of lines in distributed program, including test data, etc.: 1921No. of bytes in distributed program, including test data, etc.: 15 685Has code been vectorised or parallelised?: The code has been extensively vectorised. Commands to parallelise the code using OpenMP are included in the sourceDistribution format: gzNature of physical problem: DIPOLE3 calculates dipole transition intensities between previously calculated wavefunction for both rotational and rotational-vibrational transitionsMethod of solution: Integrals over dipole surfaces are constructed using a DVR in all three coordinates, this requires a transformation of the angular wavefunctions. Wavefunctions generated by DVR3DRJZ and ROTLEV3 or ROTLEV3B are then used to give transition intensities for individual pairs of statesRestrictions on the complexity of the problem: The complexity of the problem that can be solved by DVR3DRJZ, ROTLEV3 or ROTLEV3BTypical running time: Case dependent. The test data takes a few seconds on a fast PCUnusual features of the program: Most data is read directly from DVR3DRJZ and ROTLEV3 or ROTLEV3B. DIPOLE provides data to drive SPECTRA

New version summary

Title of program: SPECTRACatalogue number: ADTGProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTGProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 UnixReference in CPC to previous version: 75 (1993) 339Catalogue identifier of previous version: ACNBAuthors of previous version: J. Tennyson, S. Miller and C.R. Le SueurDoes the new version supersede the original program?: YesProgramming language used: Fortran 90High speed storage required: case dependentNo. of lines in distributed program, including test data, etc.: 1037No. of bytes in distributed program, including test data, etc.: 9159Has code been vectorised or parallelised?: As execution times are very short this is usually not importantDistribution format: gzNature of physical problem: SPECTRA generates synthetic, frequency ordered spectra as a function of temperature. Absolute intensities can be calculated if the necessary data to calculate the partition function is suppliedMethod of solution: Transitions are sorted by frequency and weighted using Boltzmann statisticsRestrictions on the complexity of the problem: The complexity of problem that can be solved by other programs in the suiteTypical running time: Case dependent, but very small for sample dataUnusual features of the program: Most data is read directly from DIPOLE3. Some data from DVR3DRJZ and ROTLEV3 or ROTLEV3B may also be required

Program summary

Title of program: XPECT3Catalogue number: ADTHProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADTHProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer: PC running LinuxInstallation: desktopOther machines on which program tested: Compaq running True64 UnixProgramming language used: Fortran 90High speed storage required: case dependentNo. of lines in distributed program, including test data, etc.: 1214No. of bytes in distributed program, including test data, etc.: 9361Distribution format: gzKeywords: Expectation values, Hellmann-Feynman theorem, potential fittingHas code been vectorised or parallelised?: The code has been extensively vectorisedNature of physical problem: XPECT3 calculates expectation of geometrically defined operators using previously calculated wavefunctionsMethod of solution: Integrals over the user defined surfaces are constructed using a DVR in all three coordinates. Wavefunctions generated by DVR3DRJZ and ROTLEV3 or ROTLEV3B are then used to give expectation values for each stateRestrictions on the complexity of the problem: The complexity of problem that can be solved by DVR3DRJZ, ROTLEV3 or ROTLEV3BTypical running time: Case dependent. The test data takes a few seconds on a fast PCUnusual features of the program: Most data is read directly from DVR3DRJZ and ROTLEV3 or ROTLEV3B.     

Synthesis of Intercalation Compounds in the Graphite–HNO3–H3PO4System

The highly oriented pyrolytic graphite–HNO₃–H₃PO₄system was studied by x-ray diffraction and potentiometry at different acid concentrations. The results demonstrate that chemical and electrochemical intercalation in the graphite–98% HNO₃–85% H₃PO₄system yields graphite nitrate, a binary graphite intercalation compound (GIC). H₃PO₄is shown to have an ambiguous effect on the concentration ranges of different stages of graphite nitrate, shifting them to lower HNO₃concentrations as compared to the graphite–HNO₃–H₂O system. In the graphite–98% HNO₃–100% H₃PO₄system, a stage II ternary GIC is obtained, with an intercalate layer thickness d _i 4.7 Å. Stages II–VI of this GIC were prepared via exchange reaction between graphite nitrate and 100% H₃PO₄. A mechanism for the formation of the ternary GIC is proposed. The synthesis of the cointercalated GIC is likely to involve two steps: in the first step, graphite nitrate is formed; subsequent reaction in the intercalate layer leads to partial replacement of solvated HNO₃by H₃PO₄molecules.     

A Fully Integrated 0.13- μm CMOS Digital Low-IF DBS Satellite Tuner Using a Ring Oscillator-Based Frequency Synthesizer

A low-IF fully integrated tuner for DBS satellite TV applications has been realized in 0.13-mum CMOS. A wideband ring oscillator-based frequency synthesizer having a large frequency step was used to downconvert a cluster of channels to a sliding low-IF frequency, while the second downconversion to baseband was performed in the digital domain. Eliminating the inductors and using a small-area oscillator has reduced both the parasitic magnetic and substrate coupling, allowing single-chip integration of the sensitive tuner and the noisy digital demodulator. A significant reduction in die area was achieved by using a single oscillator to cover the entire satellite TV spectrum, while a noise attenuator was cascaded with the PLL passive loop filter to reduce the equivalent VCO tuning gain. This improves PLL noise and spur performance and allows the on-chip integration of the loop filter. The digital low-IF tuner allows the use of a discrete step AGC loop that results in lower noise figure and higher linearity. Automatic signal path gain and bandwidth digital calibration was realized using replica ring oscillators. Tuner specifications include: 90 dB gain range, 10 dB noise figure at max gain, +25dBm IIP3 at min gain, 1.3deg rms integrated phase noise, <-50dBc spurs, 0.5-W power consumption from dual 1.8/3.3-V supplies, and 1.8times1.2 mm² die area     

Defect‐Mediated Polarization Switching in Ferroelectrics and Related Materials: From Mesoscopic Mechanisms to Atomistic Control

The plethora of lattice and electronic behaviors in ferroelectric and multiferroic materials and heterostructures opens vistas into novel physical phenomena including magnetoelectric coupling and ferroelectric tunneling. The development of new classes of electronic, energy‐storage, and information‐technology devices depends critically on understanding and controlling field‐induced polarization switching. Polarization reversal is controlled by defects that determine activation energy, critical switching bias, and the selection between thermodynamically equivalent polarization states in multiaxial ferroelectrics. Understanding and controlling defect functionality in ferroelectric materials is as critical to the future of oxide electronics and solid‐state electrochemistry as defects in semiconductors are for semiconductor electronics. Here, recent advances in understanding the defect‐mediated switching mechanisms, enabled by recent advances in electron and scanning probe microscopy, are discussed. The synergy between local probes and structural methods offers a pathway to decipher deterministic polarization switching mechanisms on the level of a single atomically defined defect.     

Pulsed eddy current testing with variable duty cycle on rivet joints

In pulsed eddy current testing, repetitive excitation signals with different duty cycles have different spectral representations. This work studies the influence of duty cycle on the ability to detect holes and EDM notches beneath rivet heads in subsurface layers of stratified samples. Feature patterns for the integrity of rivet joints are proposed and verified. The proposed method has the added advantage in that no reference sample is needed while employing multiple pulse measurements, with different pulse widths. Experimental testing and modelling approaches are discussed in connection with defect depth quantification, which can be extended to the quantification of complex defects.     

Organ-specific antigens of the human intestines detectable in tumors

Rabbit antisera to an organospecific intestinal antigen are obtained. This antigen has beta 2-electromobility, is thermolabile, is not extracted by perchloric acid and phenol and immunologically differs from CEA. The antigen is found in bottom zone of colonic crypt and in carcinomas of colon and rectum.     

Optimisation of isolation and purification of the jack bean enzyme urease by extraction and subsequent crystallization

A detailed investigation into the isolation by extraction and the purification by crystallization of the enzyme urease from jack bean meal is presented with a view to developing a large-scale process. The effect of different extraction solvents and additives upon the resulting crystals is characterised in terms of crystal size, protein yield and protein purity. The enzymatic activity of urease is exploited in order to quantify the amount and purity of the protein obtained. The extraction procedure was optimised and all stages of the process were monitored in order to provide as detailed a picture as possible of the impact of different process stages upon the intermediate products. Almost all protein is extracted in a single extraction step. Further extraction steps using the same meal but fresh solvent yield only small additional protein yields. Less than 10% of total protein is extracted in a second step, less than 3% in a third extraction. Different solvents lead to clear differences in product quality, with no single solvent optimising all quality criteria. In addition, the point at which the acetone precipitant is introduced into the process has a clear influence on the product. Judicious choice of extraction conditions can significantly increase the size of the urease crystals at the cost of product purity, quantified by specific activity. High product purity (a maximum 138-fold increase in purity was observed with a maximum yield of 8.4%), in contrast, leads to smaller crystals. Comparison to the purest commercially available urease revealed a similar urease content.     

Temperature and Time Effects on the Acid Corrosion of Steel in the Presence of Acetylenic Inhibitors

Potentiostatic and gravimetric methods were used to reveal that the inhibition effect of acetylenic inhibitors (namely propargyl alcohol and propargyl chloride) on the electrode processes of iron and steel corrosion in hydrochloric and sulfuric acids grows with time and temperature, owing to the formation of a polymeric film on the metal surface. In sulfuric acid, propargyl alcohol is easily hydrogenated to give removable reduction products, which lowers its protection effect on steel corrosion.