Comparative gene prediction in human and mouse

The completion of the sequencing of the mouse genome promises to help predict human genes with greater accuracy. While current ab initio gene prediction programs are remarkably sensitive (i.e., they predict at least a fragment of most genes), their specificity is often low, predicting a large number of false-positive genes in the human genome. Sequence conservation at the protein level with the mouse genome can help eliminate some of those false positives. Here we describe SGP2, a gene prediction program that combines ab initio gene prediction with TBLASTX searches between two genome sequences to provide both sensitive and specific gene predictions. The accuracy of SGP2 when used to predict genes by comparing the human and mouse genomes is assessed on a number of data sets, including single-gene data sets, the highly curated human chromosome 22 predictions, and entire genome predictions from ENSEMBL. Results indicate that SGP2 outperforms purely ab initio gene prediction methods. Results also indicate that SGP2 works about as well with 3x shotgun data as it does with fully assembled genomes. SGP2 provides a high enough specificity that its predictions can be experimentally verified at a reasonable cost. SGP2 was used to generate a complete set of gene predictions on both the human and mouse by comparing the genomes of these two species. Our results suggest that another few thousand human and mouse genes currently not in ENSEMBL are worth verifying experimentally.

Nonempirical cluster-model study of the chemisorption of atomic hydrogen on the (111) surface of diamondlike crystals

The interaction of atomic hydrogen with C4H9, Si4H9, and Ge4H9 model clusters has been studied using all-electron and pseudopotential ab initio Hartree-Fock computations with basis sets of increasing flexibility. The results show that the effect of polarization functions is important in order to reproduce the experimental findings, but their inclusion only for the atoms directly involved in the chemisorption bond is usually sufficient. For the systems H-C4H9 and H-Si4H9 all-electron and pseudopotential results are in excellent agreement when basis sets of comparable quality are used. Besides, semiempirical modified-neglect-of-differential-overlap computations provide quite reliable results both for diamond and silicon and have been used to investigate larger model clusters. The results confirm the local nature of chemisorption and further justify the use of minimal X4H9 model clusters.

Evidence for oxygen-island formation on Al(111): Cluster-model theory and x-ray photoelectron spectroscopy

The O 1s x-ray photoelectron spectroscopy spectrum for Al(111)/O at 300 K shows two components whose behavior as a function of time and variation of detection angle are consistent with either (a) a surface species represented by the higher binding-energy (BE) component and a subsurface species represented by the lower BE component, or (b) small close-packed oxygen islands with the interior atoms represented by the lower BE component and the perimeter atoms by the higher BE component. We have modeled both situations using ab initio Hartree-Fock wave functions for clusters of Al and O atoms. For an O atom in a threefold site, it was found that a below-surface position gave a higher O 1s BE than an above-surface position, incompatible with interpretation (a). This change in the O 1s BE could arise because the bond for O to Al may have a more covalent character when the O is below the surface than when it is above the surface. We present evidence consistent with this view. An O adatom island with all the O atoms in threefold sites gives calculated O 1s BE's which are significantly higher for the perimeter O atoms. Further, the results for an isolated O island without the Al substrate present also give higher BE¿s for the perimeter atoms. Both these results are consistent with interpretation (b). Published scanning-tunneling-microscopy data supports the suggestion that the chemisorbed state consists of small, close-packed islands, whereas the presence of two vibrational modes in high-resolution electron-energy-loss spectroscopy data has been interpreted as representing surface and subsurface oxygen atoms. In light of the present results, we suggest that a vibrational interpretation in terms of interior and perimeter adatoms should be considered.

Evidence for two different bonding mechanisms of Al on Si(111)

By means of the ab initio cluster-model approach, we present theoretical evidence for two different mechanisms of bonding of atomic Al to Si(111). On the atop site (T1) the interaction of atomic Al to Si(111) is characteristic of an ionic bond whereas interaction above the threefold eclipsed site (T4) leads to the formation of a typical covalent bond. Moreover, both sites have a similar interaction energy if electronic correlation effects are included. While the conclusions regarding the nature of the chemisorption bond in the two sites do not depend either on the cluster-model size, the kind of embedding hydrogen atoms used, or the quality of the wave function (Hartree-Fock or configuration interaction), the chemisorption energy depends strongly on the wave function used. In fact, inclusion of correlation energy is necessary to properly describe the interaction energies.

Absence of collective effects in Heisenberg systems with localized magnetic moments

Existence of collective effects in magnetic coupling in ionic solids is studied by mapping spin eigenstates of the Heisenberg and exact nonrelativistic Hamiltonians on cluster models representing KNiF3, K2NiF4, NiO, and La2CuO4. Ab initio techniques are used to estimate the Heisenberg constant J. For clusters with two magnetic centers, the values obtained are about the same for models having more magnetic centers. The absence of collective effects in J strongly suggests that magnetic interactions in this kind of ionic solids are genuinely local and entangle only the two magnetic centers involved.

Local character of magnetic coupling in ionic solids

Magnetic interactions in ionic solids are studied using parameter-free methods designed to provide accurate energy differences associated with quantum states defining the Heisenberg constant J. For a series of ionic solids including KNiF3, K2NiF4, KCuF3, K2CuF4, and high- Tc parent compound La2CuO4, the J experimental value is quantitatively reproduced. This result has fundamental implications because J values have been calculated from a finite cluster model whereas experiments refer to infinite solids. The present study permits us to firmly establish that in these wide-gap insulators, J is determined from strongly local electronic interactions involving two magnetic centers only thus providing an ab initio support to commonly used model Hamiltonians.

Ionic-covalent transition in titanium oxides

The nature of the chemical bond in three titanium oxides of different crystal structure and different formal oxidation state has been studied by means of the ab initio cluster-model approach. The covalent and ionic contributions to the bond have been measured from different theoretical techniques. All the analysis is consistent with an increasing of covalence in the TiO, Ti2O3, and TiO2 series as expected from chemical intuition. Moreover, the use of the ab initio cluster-model approach combined with different theoretical techniques has permitted us to quantify the degree of ionic character, showing that while TiO can approximately be described as an ionic compound, TiO2 is better viewed as a rather covalent oxide.

Precession electron diffraction in the transmission electron Microscope: electron crystallography and orientational mapping

Precession electron diffraction (PED) is a hollow cone non-stationary illumination technique for electron diffraction pattern collection under quasikinematicalconditions (as in X-ray Diffraction), which enables “ab-initio” solving of crystalline structures of nanocrystals. The PED technique is recently used in TEMinstruments of voltages 100 to 300 kV to turn them into true electron iffractometers, thus enabling electron crystallography. The PED technique, when combined with fast electron diffraction acquisition and pattern matching software techniques, may also be used for the high magnification ultra-fast mapping of variable crystal orientations and phases, similarly to what is achieved with the Electron Backscatter Diffraction (EBSD) technique in Scanning ElectronMicroscopes (SEM) at lower magnifications and longer acquisition times.

Reliability of the density functional approximation to describe the charge transfer and electrostatic complexes involved in the modeling of organic conducting polymers

Both the intermolecular interaction energies and the geometries for M ̄ thiophene, M ̄ pyrrole, M n+ ̄ thiophene, and M n+ ̄ pyrrole ͑with M = Li, Na, K, Ca, and Mg; and M n+ = Li+ , Na+ , K+ , Ca2+, and Mg2+͒ have been estimated using four commonly used density functional theory ͑DFT͒ methods: B3LYP, B3PW91, PBE, and MPW1PW91. Results have been compared to those provided by HF, MP2, and MP4 conventional ab initio methods. The PBE and MPW1PW91 are the only DFT methods able to provide a reasonable description of the M ̄ complexes. Regarding M n+ ̄ ␲ complexes, the four DFT methods have been proven to be adequate in the prediction of these electrostatically stabilized systems, even though they tend to overestimate the interaction energies.

Bandwidth allocation based on real time calculations using the convolution approach

This paper focuses on one of the methods for bandwidth allocation in an ATM network: the convolution approach. The convolution approach permits an accurate study of the system load in statistical terms by accumulated calculations, since probabilistic results of the bandwidth allocation can be obtained. Nevertheless, the convolution approach has a high cost in terms of calculation and storage requirements. This aspect makes real-time calculations difficult, so many authors do not consider this approach. With the aim of reducing the cost we propose to use the multinomial distribution function: the enhanced convolution approach (ECA). This permits direct computation of the associated probabilities of the instantaneous bandwidth requirements and makes a simple deconvolution process possible. The ECA is used in connection acceptance control, and some results are presented

Automatic generation of active coordinates for quantum dynamics calculations: application to the dynamics of benzene photochemistry

A new practical method to generate a subspace of active coordinates for quantum dynamics calculations is presented. These reduced coordinates are obtained as the normal modes of an analytical quadratic representation of the energy difference between excited and ground states within the complete active space self-consistent field method. At the Franck-Condon point, the largest negative eigenvalues of this Hessian correspond to the photoactive modes: those that reduce the energy difference and lead to the conical intersection; eigenvalues close to 0 correspond to bath modes, while modes with large positive eigenvalues are photoinactive vibrations, which increase the energy difference. The efficacy of quantum dynamics run in the subspace of the photoactive modes is illustrated with the photochemistry of benzene, where theoretical simulations are designed to assist optimal control experiments

Systematic trends in self-consistent calculations of linear quantum wires

Systematic trends in the properties of a linear split-gate heterojunction are studied by solving iteratively the Poisson and Schrödinger equations for different gate potentials and temperatures. A two-dimensional approximation is presented that is much simpler in the numerical implementation and that accurately reproduces all significant trends. In deriving this approximation, we provide a rigorous and quantitative basis for the formulation of models that assumes a two-dimensional character for the electron gas at the junction.

Density-functional calculations of magnetoplasmons in quantum rings

We have studied the structure and dipole charge-density response of nanorings as a function of the magnetic field using local-spin-density-functional theory. Two small rings consisting of 12 and 22 electrons confined by a positively charged background are used to represent the cases of narrow and wide rings. The results are qualitatively compared with experimental data existing on microrings and on antidots. A smaller ring containing five electrons is also analyzed to allow for a closer comparison with a recent experiment on a two-electron quantum ring.

Helium in polygonal nanopores at zero temperature: Density functional theory calculations

We investigate adsorption of helium in nanoscopic polygonal pores at zero temperature using a finite-range density functional theory. The adsorption potential is computed by means of a technique denoted as the elementary source method. We analyze a rhombic pore with Cs walls, where we show the existence of multiple interfacial configurations at some linear densities, which correspond to metastable states. Shape transitions and hysterectic loops appear in patterns which are richer and more complex than in a cylindrical tube with the same transverse area.