Residues important for the function of a multihelical DNA binding domain in the new transcription factor family of Cam and Tet repressors

We report that some prokaryotic repressors including CamR andTetR belong to the same family. CamR and TetR bind to DNA usinga multihelical DNA binding domain (DBD) at the N-termini ofthe proteins, while the C-termini are important for regulatingthe DNA binding in a manner dependent on their co-factors (camphorfor CamR, tetracycline for TetR). In all, 11 important aminoacid positions have been identified in the CamR DBD by the systematicsubstitution of residues by Ala. Of the 11 positions, 10 areeither buried in the core, and thus important for creating thehydrophobic environment, or exposed on the surface, and thusimportant for binding to DNA. The eleventh residue, Gly, seemsto be important for a loop structure. The DNA binding mode ofthis type of DBD and a general mechanism of regulating theirDNA binding are discussed in reference to the crystal structureof TetR [Hinrichs et al., (1994) Science, 264, 418–420].     

FERM3D: A finite element R-matrix electron molecule scattering code

FERM3D is a three-dimensional finite element program, for the elastic scattering of a low energy electron from a general polyatomic molecule, which is converted to a potential scattering problem. The code is based on tricubic polynomials in spherical coordinates. The electron-molecule interaction is treated as a sum of three terms: electrostatic, exchange, and polarization. The electrostatic term can be extracted directly from ab initio codes (GAUSSIAN 98 in the work described here), while the exchange term is approximated using a local density functional. A local polarization potential based on density functional theory [C. Lee, W. Yang, R.G. Parr, Phys. Rev. B 37 (1988) 785] describes the long range attraction to the molecular target induced by the scattering electron. Photoionization calculations are also possible and illustrated in the present work. The generality and simplicity of the approach is important in extending electron-scattering calculations to more complex targets than it is possible with other methods.

Program summary

Title of program:FERM3DCatalogue identifier:ADYL_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYL_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer for which the program is designed and others on which it has been tested:Intel Xeon, AMD Opteron 64 bit, Compaq AlphaOperating systems or monitors under which the program has been tested:HP Tru64 Unix v5.1, Red Hat Linux Enterprise 3Programming language used:Fortran 90Memory required to execute with typical data:900 MB (neutral CO₂), 2.3 GB (ionic CO₂), 1.4 GB (benzene)No. of bits in a word:32No. of processors used:1Has the code been vectorized?:NoNo. of lines in distributed program, including test data, etc.:58 383No. of bytes in distributed program, including test data, etc.:561 653Distribution format:tar.gzip fileCPC Program library subprograms used:ADDA, ACDPNature of physical problem:Scattering of an electron from a complex polyatomic molecular target.Method of solution:Solution of a partial differential equation using a finite element basis, and direct sparse linear solvers.Restrictions on the complexity of the problem:Memory constraints.Typical running time:2 hours.Unusual features of the program:

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very extensive use of memory,

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requires installation of Lapack, Blas, a direct sparse solver library (SuperLU, freely available, or Pardiso, which requires a license, but is free of charge for academic use), and optionally the Cernlib and Arpack libraries, freely available,

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requires input from quantum chemistry programs (Gaussian, Molpro or PC Gamess).

     

Effects of tilt on high-resolution ADF-STEM imaging

A study of the effects of small-angle specimen tilt on high-resolution annular dark field images was carried out for scanning transmission electron microscopes with uncorrected and aberration-corrected probes using multislice simulations. The results indicate that even in the cases of specimen tilts of the order of 1 degree a factor of 2 reduction in the contrast of the high-resolution image should be expected. The effect holds for different orientations of the crystal. Calculations also indicate that as the tilted specimen gets thicker the contrast reduction increases. Images simulated with a low-angle annular dark field detector show that tilt effects are more pronounced in this case and suggest that these low-angle detectors can be used to correct specimen tilt during scanning transmission electron microscopes operation.     

Short-term irradiation behavior of minor actinide doped uranium plutonium mixed oxide fuels irradiated in an experimental fast reactor

A fuel irradiation program is being conducted using the experimental fast reactor ‘Joyo’. Two short-term irradiation tests in the program were completed in 2006 using a uranium and plutonium mixed oxide fuel which contains minor actinides (MA-MOX fuel). The objective of the tests is the investigation of early thermal behavior of MA-MOX fuel such as fuel restructuring and redistribution of minor actinides. Three fuel pins which contained MA-MOX: 2% neptunium and 2% americium doped uranium plutonium mixed oxide (Am,Pu,Np,U)O_2−x fuel were supplied for testing. The first test was conducted with high-linear heating rate of approximately 430 W cm⁻¹ for only 10 min. After the first test, one fuel pin was removed for examinations. Then the second test was conducted with the remaining two pins at nearly the same linear power for 24 h. In these tests, two oxygen-to-metal molar ratios were used for fuel pellets as a test parameter. Non-destructive and destructive post-irradiation examinations results are discussed with early on the behavior of the fuel during irradiation.     

New concept of designing Pu and MA containing fuel for fast reactors

New type of metal base fuel element is suggested for fast reactors. Basic approach to fuel element development - separated operations of fabricating uranium meat fuel element and introducing into it Pu or MA dioxides powder, that results in minimizing dust forming operations in fuel element fabrication. According to new fuel element design a framework fuel element having a porous uranium alloy meat is filled with standard PuO₂ powder of <50 μm fractions prepared by pyrochemical or other methods. In this way a high uranium content fuel meat metallurgically bonded to cladding forms a heat conducting framework, pores of which contain PuO₂ powder. Framework fuel element having porous meat is fabricated by capillary impregnation method with the use of Zr eutectic matrix alloys, which provides metallurgical bond between fuel and cladding and protects it from interaction. As compared to MOX fuel the new one features high thermal conductivity, higher uranium content, hence, high conversion ratio does not interact with fuel cladding and is more environmentally clean. Its principle advantage is a simple production process that is easily realized remotely, feasibility of involving high background Pu and MA isotopes into closed nuclear fuel cycle at the minimal influence on environment.     

Diffraction of fast atoms under axial surface channeling conditions

For scattering of fast atoms under axial channeling conditions from surfaces diffraction effects have been observed in the distributions for scattered projectiles. Basic features concerning this recently observed new phenomenon in ion/atom surface scattering will be demonstrated for collisions of light atoms with well ordered clean and adsorbate covered surfaces of insulators and metals. We will focus our discussion on the scattering of ³He atoms with keV energies from a LiF(0 0 1) surface along low indexed axial surface channels and deduce the corrugation of the He-LiF(0 0 1) interaction potential from intensity modulations of the diffraction spots. Furthermore, we observe for the first time interference effects also for He⁺ ions which undergo charge exchange during scattering from the surface. The potential of the method for the investigation of structures of surfaces is discussed.     

Monte Carlo calculation of electron Rutherford backscattering spectra and high-energy reflection electron energy loss spectra

The electron Rutherford backscattering spectra and high-energy reflection electron energy loss spectra have been calculated by a Monte Carlo method for bulk solids and overlayer/substrate systems. The simulation model is mainly based on the use of Mott cross section for elastic scattering and the use of Penn’s dielectric functional approach to the electron inelastic scattering inside the solid. Moreover, it has further considered the recoil energy loss of energetic electrons and the thermal vibration of atoms with an isotropic distribution of the velocity direction. The calculated energy loss spectra for Al/Pt and Al/Mo agree with the experimental spectra quite well. The signals owing to different kinds of atoms can be separated by taking the scatter for the maximum-scattering angle event along an electron trajectory as the Rutherford backscattering atom, enabling a theoretical estimation of the peak intensity ratio. Furthermore, the simulation has also indicated that the multiple scattering is the dominant process to the quasi-elastic and energy loss of the electrons and is responsible mainly to the difference on the peak intensity between the linear model and experiment.     

Quantum interference in grazing scattering of swift He atoms from LiF(0 0 1) surfaces: Surface eikonal approximation

This work deals with the interference effects recently observed in grazing collisions of few-keV atoms with insulator surfaces. The process is studied within a distorted-wave method, the surface eikonal approximation, based on the use of the eikonal wave function and involving axial channeled trajectories with different initial conditions. The theory is applied to helium atoms impinging on a LiF(0 0 1) surface along the 〈1 1 0〉 direction. The role played by the projectile polarization and the surface rumpling is investigated. We found that when both effects are included, the proposed eikonal approach provides angular projectile spectra in good agreement with the experimental findings.     

Experimental system for GaN thin films growth and in situ characterisation by electron spectroscopic methods

A double chamber vacuum system was constructed for the electron spectroscopy study of GaN layer growth. The samples are prepared by vacuum deposition from Knudsen-type Ga source in the afterglow atmosphere of active nitrogen produced by high-pressure RF-plasma source. The growth chamber is connected to the analysis chamber equipped with electron spectroscopy (XPS, AES) analysis, permitting to study the chemical composition of layers as a function of growing conditions. It is shown that the new RF-source is suitable for preparation of pure stoichiometric GaN layers.     

Selection of water-dispersible carbon black for fabrication of uranium oxicarbide microspheres

Fabrication of uranium oxicarbide microspheres, a component of TRISO fuel particles for high temperature nuclear power systems, is based on the internal gelation of uranium salts in the presence of carbon black. In order to obtain a high quality product, carbon black should remain dispersed during all phases of the gelation process. In this study, the surface and structural properties of several commercial carbon black materials, and the use of dispersing agents was examined with the goal of finding optimal conditions for stabilizing submicron-sized carbon black dispersions. Traditional methods for stabilizing dispersions, based on the use of dispersing agents, failed to stabilize carbon dispersions against large pH variations, typical for the internal gelation process. An alternate dispersing method was proposed, based on using surface-modified carbons functionalized with strongly ionized surface groups (sodium sulfonate). With a proper choice of surface modifiers, these advanced carbons disperse easily to particles in the range of 0.15-0.20 μm and the dispersions remain stable during the conditions of internal gelation.