PALI—a database of Phylogeny and ALIgnment of homologous protein structures

PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set comprises 604 families of homologous proteins involving 2739 protein domain structures with each family made up of at least two members. Each member in a family has been structurally aligned with every other member in the same family (pairwise alignment) and all the members in the family are also aligned using simultaneous super­position (multiple alignment). The structural alignments are performed largely automatically, with manual interventions especially in the cases of distantly related proteins, using the program STAMP (version 4.2). Every family is also associated with two dendrograms, calculated using PHYLIP (version 3.5), one based on a structural dissimilarity metric defined for every pairwise alignment and the other based on similarity of topologically equivalent residues. These dendrograms enable easy comparison of sequence and structure-based relationships among the members in a family. Structure-based alignments with the details of structural and sequence similarities, superposed coordinate sets and dendrograms can be accessed conveniently using a web interface. The database can be queried for protein pairs with sequence or structural similarities falling within a specified range. Thus PALI forms a useful resource to help in analysing the relationship between sequence and structure variation at a given level of sequence similarity. PALI also contains over 653 ‘orphans’ (single member families). Using the web interface involving PSI_BLAST and PHYLIP it is possible to associate the sequence of a new protein with one of the families in PALI and generate a phylogenetic tree combining the query sequence and proteins of known 3-D structure. The database with the web interfaced search and dendrogram generation tools can be accessed at http://pa uling.mbu.iisc.ernet.in/~pali.

Root-Growth Behavior of the Arabidopsis Mutant rgr11 : Roles of Gravitropism and Circumnutation in the Waving/Coiling Phenomenon

In this study we investigated the kinetics of the gravitropic response of the Arabidopsis mutant rgr1 (reduced root gravitropism). Although the rate of curvature in rgr1, which is allelic to axr4, was smaller than in the wild type (ecotype Wassilewskija), curvature was initiated in the same region of the root, the distal elongation zone. The time lag for the response was unaffected in the mutant; however, the gravitropic response of rgr1 contained a feature not found in the wild type: when roots growing along the surface of an agar plate were gravistimulated, there was often an upward curvature that initiated in the central elongation zone. Because this response was dependent on the tactile environment of the root, it most likely resulted from the superposition of the waving/coiling phenomenon onto the gravitropic response. We found that the frequency of the waving pattern and circumnutation, a cyclic endogenous pattern of root growth, was the same in rgr1 and in the wild type, so the waving/coiling phenomenon is likely governed by circumnutation patterns. The amplitudes of these oscillations may then be selectively amplified by tactile stimulation to provide a directional preference to the slanting.

Inhibition of sustained gamma oscillations (35-80 Hz) by fast transient responses in cat visual cortex.

Interactions between stimulus-induced oscillations (35-80 Hz) and stimulus-locked nonoscillatory responses were investigated in the visual cortex areas 17 and 18 of anaesthetized cats. A single square-wave luminance grating was used as a visual stimulus during simultaneous recordings from up to seven electrodes. The stimulus movement consisted of a superposition of a smooth movement with a sequence of dynamically changing accelerations. Responses of local groups of neurons at each electrode were studied on the basis of multiple unit activity and local slow field potentials (13-120 Hz). Oscillatory and stimulus-locked components were extracted from multiple unit activity and local slow field potentials and quantified by a combination of temporal and spectral correlation methods. We found fast stimulus-locked components primarily evoked by sudden stimulus accelerations, whereas oscillatory components (35-80 Hz) were induced during slow smooth movements. Oscillations were gradually reduced in amplitude and finally fully suppressed with increasing amplitudes of fast stimulus-locked components. It is argued that suppression of oscillations is necessary to prevent confusion during sequential processing of stationary and fast changing retinal images.

The invariant system of coordinates of antibody molecules: prediction of the "standard" C alpha framework of VL and VH domains.

A new approach of comparing protein structures that does not involve the procedure of superposition is suggested. An invariant system of coordinates for immunoglobulin molecules that is based on the geometrical symmetry inherent to the variable domain light-chain (VL)-heavy-chain (VH) complex is described. The coordinates of the Calpha atoms in 22 immunoglobulin structures are calculated in the invariant system of coordinates. We found that 76 identical positions in this Calpha framework are symmetrical about the twofold axis. Comparison of the identical positions in these molecules allows us to select 96 positions in the light chains and 87 positions in the heavy chains whose Calpha atom coordinates are approximately the same. To check whether the average coordinates of Calpha atoms in these positions complies with the stereochemical requirements, we calculated Calpha-Calpha distances. Seventy-three positions of the light chains and 72 positions of the heavy chains satisfy the Calpha-Calpha distance criterion. The Calpha atoms in these positions are used for constructing the "standard" Calpha framework of VL and VH complexes. The average coordinates of Calpha atoms are presented.

Colored diffraction catastrophes.

On fine scales, caustics produced with white light show vividly colored diffraction fringes. For caustics described by the elementary catastrophes of singularity theory, the colors are characteristic of the type of singularity. We study the diffraction colors of the fold and cusp catastrophes. The colors can be simulated computationally as the superposition of monochromatic patterns for different wavelengths. Far from the caustic, where the luminosity contrast is negligible, the fringe colors persist; an asymptotic theory explains why. Experiments with caustics produced by refraction through irregular bathroom-window glass show good agreement with theory. Colored fringes near the cusp reveal fine lines that are not present in any of the monochromatic components; these lines are explained in terms of partial decoherence between rays with widely differing path differences.

Diverse transposable elements are mobilized in hybrid dysgenesis in Drosophila virilis.

We describe a system of hybrid dysgenesis in Drosophila virilis in which at least four unrelated transposable elements are all mobilized following a dysgenic cross. The data are largely consistent with the superposition of at least three different systems of hybrid dysgenesis, each repressing a different transposable element, which break down following the hybrid cross, possibly because they share a common pathway in the host. The data are also consistent with a mechanism in which mobilization of a single element triggers that of others, perhaps through chromosome breakage. The mobilization of multiple, unrelated elements in hybrid dysgenesis is reminiscent of McClintock's evidence [McClintock, B. (1955) Brookhaven Symp. Biol. 8, 58-74] for simultaneous mobilization of different transposable elements in maize.

Caractérisation pédologique et édaphique des sols argileux et analyse de leur occupation dans la région de Tessala (Algérie occidentale)

Les sols argileux restent dominants dans la région de Tessala (Sidi Bel Abbes) connue pour son relief érodé et accidenté où les pentes supérieures à 12% dominent. L’utilisation encore traditionnelle et irréfléchie de ces types de sols contribue à l’accélération des phénomènes d’érosion et de dessèchement agissant directement sur la végétation. Une connaissance des principales propriétés de ces sols permettra de maîtriser leurs caractéristiques physiques sources de contraintes dans leur exploitation et mise en valeur. Une maîtrise de ces éléments permettrait d’identifier des zones homo-écologiques. Il sera alors possible de travailler sur des unités physico-écologiques de mise en valeur et d’exploitation intégrée des différents types de sols. La végétation et les paramètres physiques analysés permettront de confirmer ou d’infirmer les unités de gestion préalablement déterminées. La superposition des ces zones climatique, biologique et édaphique dégagera des entités de mise en valeur claires. Une proposition d’occupation des sols selon leurs potentialités axées sur des techniques d’amélioration des caractéristiques qui constituent des entraves.

Stress Inversion Using LiDAR Tunnel Deformation Measurements

Far-field stresses are those present in a volume of rock prior to excavations being created. Estimates of the orientation and magnitude of far-field stresses, often used in mine design, are generally obtained by single-point measurements of stress, or large-scale, regional trends. Point measurements can be a poor representation of far-field stresses as a result of excavation-induced stresses and geological structures. For these reasons, far-field stress estimates can be associated with high levels of uncertainty. The purpose of this thesis is to investigate the practical feasibility, applications, and limitations of calibrating far-field stress estimates through tunnel deformation measurements captured using LiDAR imaging. A method that estimates the orientation and magnitude of excavation-induced principal stress changes through back-analysis of deformation measurements from LiDAR imaged tunnels was developed and tested using synthetic data. If excavation-induced stress change orientations and magnitudes can be accurately estimated, they can be used in the calibration of far-field stress input to numerical models. LiDAR point clouds have been proven to have a number of underground applications, thus it is desired to explore their use in numerical model calibration. The back-analysis method is founded on the superposition of stresses and requires a two-dimensional numerical model of the deforming tunnel. Principal stress changes of known orientation and magnitude are applied to the model to create calibration curves. Estimation can then be performed by minimizing squared differences between the measured tunnel and sets of calibration curve deformations. In addition to the back-analysis estimation method, a procedure consisting of previously existing techniques to measure tunnel deformation using LiDAR imaging was documented. Under ideal conditions, the back-analysis method estimated principal stress change orientations within ±5° and magnitudes within ±2 MPa. Results were comparable for four different tunnel profile shapes. Preliminary testing using plastic deformation, a rough tunnel profile, and profile occlusions suggests that the method can work under more realistic conditions. The results from this thesis set the groundwork for the continued development of a new, inexpensive, and efficient far-field stress estimate calibration method.

Quantum computation with optical coherent states

We show that quantum computation circuits using coherent states as the logical qubits can be constructed from simple linear networks, conditional photon measurements, and "small" coherent superposition resource states.

Deterministic generation of tailored-optical-coherent-state superpositions

Pulsed coherent excitation of a two-level atom strongly coupled to a resonant cavity mode will create a superposition of two coherent states of opposite amplitudes in the field. By choosing proper parameters of interaction time and pulse shape the field after the pulse will be almost disentangled from the atom and can be efficiently outcoupled through cavity decay. The fidelity of the generation approaches unity if the atom-field coupling strength is much larger than the atomic and cavity decay rates. This implies a strong difference between even and odd output photon number counts. Alternatively, the coherence of the two generated field components can be proven by phase-dependent annihilation of the generated nonclassical superposition state by a second pulse.

Conditional production of superpositions of coherent states with inefficient photon detection

It is shown that a linear superposition of two macroscopically distinguishable optical coherent states can be generated using a single photon source and simple all-optical operations. Weak squeezing on a single photon, beam mixing with an auxiliary coherent state, and photon detecting with imperfect threshold detectors are enough to generate a coherent state superposition in a free propagating optical field with a large coherent amplitude (alpha>2) and high fidelity (F>0.99). In contrast to all previous schemes to generate such a state, our scheme does not need photon number resolving measurements nor Kerr-type nonlinear interactions. Furthermore, it is robust to detection inefficiency and exhibits some resilience to photon production inefficiency.

ELA-ICP-MS U-Pb zircon geochronology of regional volcanism hosting the Bajo de la Alumbrera Cu-Au deposit: implications for porphyry-related mineralization

ELA-ICP-MS U-Pb zircon geochronology has been used to show that the porphyritic intrusions related to the formation of the Bajo de la Alumbrera porphyry Cu-Au deposit, NW Argentina, are cogenetic with stratigraphically well-constrained volcanic and volcaniclastic rocks of the Late Miocene Farallon Negro Volcanic Complex. Zircon geochronology for intrusions in this deposit and the host volcanic sequence show that multiple mineralized porphyries were emplaced in a volcanic complex that developed over 1.5 million years. Volcanism occurred in a multivent volcanic complex in a siliciclastic intermontane basin. The complex evolved from early mafic-intermediate effusive phases to a later silicic explosive phase associated with mafic intrusions. Zircons from the basal mafic-intermediate lavas have ages that range from 8.46 +/- 0.14 to 7.94 +/- 0.27 Ma. Regionally extensive silicic explosive volcanism occurred at similar to8.0 Ma (8.05 +/- 0.13 and 7.96 +/- 0.11 Ma), which is co-temporal with intrusion of the earliest mineralized porphyries at Bajo de la Alumbrera (8.02 +/- 0.14 and 7.98 +/- 0.14 Ma). Regional uplift and erosion followed during which the magmatic-hydrothermal system was probably unroofed. Shortly thereafter, dacitic lava domes were extruded (7.95 +/- 0.17 Ma) and rhyolitic diatremes (7.79 +/- 0.13 Ma) deposited thick tuff blankets, across the region. Emplacement of large intermediate composition stocks occurred at 7.37 +/- 0.22 Ma, shortly before renewed magmatism occurred at Bajo de la Alumbrera (7.10 +/- 0.07 Ma). The latest porphyry intrusive event is temporally associated with new ore-bearing magmatic-hydrothermal fluids. Other dacitic intrusions are associated with subeconomic deposits that formed synchronously with the mineralized porphyries at Bajo de la Alumbrera. However, their emplacement continued (from 7.10 +/- 0.06 to 6.93 +/- 0.07 Ma) after the final intrusion at Bajo de al Alumbrera. Regional volcanism had ceased by 6.8 Ma (6.92 +/- 0.07 Ma). The brief history of the volcanic complex hosting the Bajo de la Alumbrera Cu-Au deposit differs from that of other Andean provinces hosting porphyry deposits. For example, at the El Salvador porphyry copper district in Chile, magmatism related to Cu mineralization was episodic in regional igneous activity that occurred over tens of millions of years. Bajo de la Alumbrera resulted from the superposition of multiple porphyry-related hydrothermal systems, temporally separated by a million years. It appears that the metal budget in porphyry ore deposits is not simply a function of their longevity and/or the superposition of multiple porphyry systems. Nor is it a function of the duration of the associated cycle of magmatism. Instead, the timing of processes operating in the parental magma body is the controlling factor in the formation of a fertile porphyry-related ore system.

High-fidelity Z-measurement error encoding of optical qubits

We demonstrate a quantum error correction scheme that protects against accidental measurement, using a parity encoding where the logical state of a single qubit is encoded into two physical qubits using a nondeterministic photonic controlled-NOT gate. For the single qubit input states vertical bar 0 >, vertical bar 1 >, vertical bar 0 > +/- vertical bar 1 >, and vertical bar 0 > +/- i vertical bar 1 > our encoder produces the appropriate two-qubit encoded state with an average fidelity of 0.88 +/- 0.03 and the single qubit decoded states have an average fidelity of 0.93 +/- 0.05 with the original state. We are able to decode the two-qubit state (up to a bit flip) by performing a measurement on one of the qubits in the logical basis; we find that the 64 one-qubit decoded states arising from 16 real and imaginary single-qubit superposition inputs have an average fidelity of 0.96 +/- 0.03.

Adaptive phase measurements in linear optical quantum computation

Photon counting induces an effective non-linear optical phase shift in certain states derived by linear optics from single photons. Although this non-linearity is non-deterministic, it is sufficient in principle to allow scalable linear optics quantum computation (LOQC). The most obvious way to encode a qubit optically is as a superposition of the vacuum and a single photon in one mode-so-called 'single-rail' logic. Until now this approach was thought to be prohibitively expensive (in resources) compared to 'dual-rail' logic where a qubit is stored by a photon across two modes. Here we attack this problem with real-time feedback control, which can realize a quantum-limited phase measurement on a single mode, as has been recently demonstrated experimentally. We show that with this added measurement resource, the resource requirements for single-rail LOQC are not substantially different from those of dual-rail LOQC. In particular, with adaptive phase measurements an arbitrary qubit state a alpha/0 > + beta/1 > can be prepared deterministically.

Nonclassicality of a photon-subtracted Gaussian field

We investigate the nonclassicality of a photon-subtracted Gaussian field, which was produced in a recent experiment, using negativity of the Wigner function and the nonexistence of well-behaved positive P function. We obtain the condition to see negativity of the Wigner function for the case including the mixed Gaussian incoming field, the threshold photodetection and the inefficient homodyne measurement. We show how similar the photon-subtracted state is to a superposition of coherent states.