Modification of the sugar specificity of a plant lectin: structural studies on a point mutant of Erythrina corallodendron lectin

A mutant of Erythrina corallodendron lectin was generated with the aim of enhancing its affinity for N-acetylgalactosamine. A tyrosine residue close to the binding site of the lectin was mutated to a glycine in order to facilitate stronger interactions between the acetamido group of the sugar and the lectin which were prevented by the side chain of the tyrosine in the wild-type lectin. The crystal structures of this Y106G mutant lectin in complex with galactose and N-acetylgalactosamine have been determined. A structural rationale has been provided for the differences in the relative binding affinities of the wild-type and mutant lectins towards the two sugars based on the structures. A hydrogen bond between the O6 atom of the sugars and the variable loop of the carbohydrate-binding site of the lectin is lost in the mutant complexes owing to a conformational change in the loop. This loss is compensated by an additional hydrogen bond that is formed between the acetamido group of the sugar and the mutant lectin in the complex with N-acetylgalactosamine, resulting in a higher affinity of the mutant lectin for N-acetylgalactosamine compared with that for galactose, in contrast to the almost equal affinity of the wild-type lectin for the two sugars. The structure of a complex of the mutant with a citrate ion bound at the carbohydrate-binding site that was obtained while attempting to crystallize the complexes with sugars is also presented.

A survey of indian logic from the point of view of computer science

Indian logic has a long history. It somewhat covers the domains of two of the six schools (darsanas) of Indian philosophy, namely, Nyaya and Vaisesika. The generally accepted definition of Indian logic over the ages is the science which ascertains valid knowledge either by means of six senses or by means of the five members of the syllogism. In other words, perception and inference constitute the subject matter of logic. The science of logic evolved in India through three ages: the ancient, the medieval and the modern, spanning almost thirty centuries. Advances in Computer Science, in particular, in Artificial Intelligence have got researchers in these areas interested in the basic problems of language, logic and cognition in the past three decades. In the 1980s, Artificial Intelligence has evolved into knowledge-based and intelligent system design, and the knowledge base and inference engine have become standard subsystems of an intelligent system. One of the important issues in the design of such systems is knowledge acquisition from humans who are experts in a branch of learning (such as medicine or law) and transferring that knowledge to a computing system. The second important issue in such systems is the validation of the knowledge base of the system i.e. ensuring that the knowledge is complete and consistent. It is in this context that comparative study of Indian logic with recent theories of logic, language and knowledge engineering will help the computer scientist understand the deeper implications of the terms and concepts he is currently using and attempting to develop.

Explicit and Optimal Exact-Regenerating Codes for the Minimum-Bandwidth Point in Distributed Storage

In the distributed storage setting that we consider, data is stored across n nodes in the network such that the data can be recovered by connecting to any subset of k nodes. Additionally, one can repair a failed node by connecting to any d nodes while downloading beta units of data from each. Dimakis et al. show that the repair bandwidth d beta can be considerably reduced if each node stores slightly more than the minimum required and characterize the tradeoff between the amount of storage per node and the repair bandwidth. In the exact regeneration variation, unlike the functional regeneration, the replacement for a failed node is required to store data identical to that in the failed node. This greatly reduces the complexity of system maintenance. The main result of this paper is an explicit construction of codes for all values of the system parameters at one of the two most important and extreme points of the tradeoff - the Minimum Bandwidth Regenerating point, which performs optimal exact regeneration of any failed node. A second result is a non-existence proof showing that with one possible exception, no other point on the tradeoff can be achieved for exact regeneration.

Dynamic analysis of three point bend specimens under impact

A simple one dimensional inertial model is presented for transient response analysis of notched beams under impact, and extracting dynamic initiation toughness values. The model includes the effects of striker mass interactions, and contact deformations of the beam. Displacement time history of the striker mass is applied to the model as forcing function. The model is validated by comparison with the experimental investigation on ductile aluminium 6061 alloy and brittle polymer, PMMA.

Influence of anvil supports and overhangs in dynamic analysis of three point bend testing

Optimum design of dynamic fracture test rigs demands a thorough appreciation of beam vibration under impact. Analyses invariably presume rigid anvils, and neglect overhang effects. The beam response predicted analytically and numerically in this paper highlights the significant role of anvil rigidity and beam overhangs on the impact dynamics of three point bend (3PB) specimens.

Non-Fermi liquid behavior in a mean-field study of the t-J model: Role of zero-point spin fluctuations

We present analytic results to show that the Schwinger-boson hole-fermion mean-field state exhibits non-Fermi liquid behavior due to spin-charge separation. The physical electron Green's function consists of three additive components. (a) A Fermi-liquid component associated with the bose condensate. (b) A non-Fermi liquid component which has a logarithmic peak and a long tail that gives rise to a linear density of states that is symmetric about the Fermi level and a momentum distribution function with a logarithmic discontinuity at the Fermi surface. (c) A second non-Fermi liquid component associated with the thermal bosons which leads to a constant density of states. It is shown that zero-point fluctuations associated with the spin-degrees of freedom are responsible for the logarithmic instabilities and the restoration of particle-hole symmetry close to the Fermi surface.

Combining Bayes Classification and Point Group Symmetry under Boolean Framework for Enhanced Protein Quaternary Structure Inference

Our ability to infer the protein quaternary structure automatically from atom and lattice information is inadequate, especially for weak complexes, and heteromeric quaternary structures. Several approaches exist, but they have limited performance. Here, we present a new scheme to infer protein quaternary structure from lattice and protein information, with all-around coverage for strong, weak and very weak affinity homomeric and heteromeric complexes. The scheme combines naive Bayes classifier and point group symmetry under Boolean framework to detect quaternary structures in crystal lattice. It consistently produces >= 90% coverage across diverse benchmarking data sets, including a notably superior 95% coverage for recognition heteromeric complexes, compared with 53% on the same data set by current state-of-the-art method. The detailed study of a limited number of prediction-failed cases offers interesting insights into the intriguing nature of protein contacts in lattice. The findings have implications for accurate inference of quaternary states of proteins, especially weak affinity complexes.

Resonant absorption of alfvén waves near a neutral point

It is shown that, although the mathematical analysis of the Alfven-wave equation does not show any variation at non-zero or zero singular points, the role of surface waves in the physical mechanism of resonant absorption of Alfven waves is very different at these points. This difference becomes even greater when resistivity is taken into account. At the neutral point the zero-frequency surface waves that are symmetric surface modes of the structured neutral layer couple to the tearing mode instability of the layer. The importance of this study for the energy balance in tearing modes and the association of surface waves with driven magnetic reconnection is also pointed out.

Construction of solid model from measured point data

This paper describes an algorithm for constructing the solid model (boundary representation) from pout data measured from the faces of the object. The poznt data is assumed to be clustered for each face. This algorithm does not require any compuiier model of the part to exist and does not require any topological infarmation about the part to be input by the user. The property that a convex solid can be constructed uniquely from geometric input alone is utilized in the current work. Any object can be represented a5 a combznatzon of convex solids. The proposed algorithm attempts to construct convex polyhedra from the given input. The polyhedra so obtained are then checked against the input data for containment and those polyhedra, that satisfy this check, are combined (using boolean union operation) to realise the solid model. Results of implementation are presented.

Basis set dependence of the molecular electrostatic potential topography. A case study of substituted benzenes

The basis set dependence of the topographical structure of the molecular electrostatic potential (MESP), as well as the effect of substituents on the MESP distribution, has been investigated with substituted benzenes as test cases. The molecules are studied at HF-SCF 3�21G and 6�31G** levels, with a further MESP topographical investigation at the 3�21G, double-zeta, 6�31G*, 6�31G**, double-zeta polarized and triple-zeta polarized levels. The MESP critical points for a 3�21G optimized/6�31G** basis are similar to the corresponding 6�31G** optimized/6�31G** ones. More generally, the qualitative features of the MESP topography computed at the polarized level are independent of the level at which optimization is carried out. For a proper representation of oxygen lone pairs, however, optimization using a polarized basis set is required. The nature of the substituent drastically changes the MESP distribution over the phenyl ring. The values and positions of MESP minima indicate the most active site for electrophilic attack. This point is strengthened by a study of disubstituted benzenes.

New uniform solid catalyst for the low-temperature oxidation of carbon monoxide: A triple-layered rare earth perovskite containing Co and Cu ions

Oxygen reactivity and catalytic activity of the cobalt-containing layered defect perovskites, YBa2Cu2CoO7+delta and LaBa2Cu2CoO7+delta, in comparison with LaBa2Cu3O7-delta have been investigated employing temperature-programmed desorption (TPD) and temperature-programmed surface reactions (TPSR) in the stoichiometric and catalytic mode using carbon monoxide as a probe molecule. TPD studies showed evidence for the presence of two distinct labile oxygen species, one at (0 0 1/2) sites and the other at (0 1/2 0) sites in LaBa2Cu2CoO7+delta against a single labile species at (0 1/2 0) in the case of two other oxides. The activation energies for the catalytic oxidation of carbon monoxide by oxygen over LaBa2Cu3O7-delta, YBa2Cu2CoO7+delta, and LaBa2Cu2CoO7+delta have been estimated to be 24.2, 15.9, and 13.6 kcal/mol, respectively. The reactivity and catalytic activity of the oxide systems have been interpreted in terms of the structural changes brought about by substituents, guided by a directing effect of the larger rare earth cation. TPSR profiles, structural analysis, and infrared spectroscopic investigations suggest that the oxygen present at (0 0 1/2) sites in the case of LaBa2Cu2CoO7+delta is accessible to catalytic oxidation of CO through a Mars-Van Krevelen pathway. Catalytic conversion of CO to CO2 over LaBa2Cu2CoO7+delta occurs at 200 degrees C. The enhanced reactivity is explained in terms of changes brought about in the coordination polyhedra around transition metals, enhanced basal plane oxygen diffusivity, and redox potentials of the different transition metal cations.

Perturbative growth of cosmological clustering .2. The two-point correlation

We use the BBGKY hierarchy equations to calculate, perturbatively, the lowest order nonlinear correction to the two-point correlation and the pair velocity for Gaussian initial conditions in a critical density matter-dominated cosmological model. We compare our results with the results obtained using the hydrodynamic equations that neglect pressure and find that the two match, indicating that there are no effects of multistreaming at this order of perturbation. We analytically study the effect of small scales on the large scales by calculating the nonlinear correction for a Dirac delta function initial two-point correlation. We find that the induced two-point correlation has a x(-6) behavior at large separations. We have considered a class of initial conditions where the initial power spectrum at small k has the form k(n) with 0 < n less than or equal to 3 and have numerically calculated the nonlinear correction to the two-point correlation, its average over a sphere and the pair velocity over a large dynamical range. We find that at small separations the effect of the nonlinear term is to enhance the clustering, whereas at intermediate scales it can act to either increase or decrease the clustering. At large scales we find a simple formula that gives a very good fit for the nonlinear correction in terms of the initial function. This formula explicitly exhibits the influence of small scales on large scales and because of this coupling the perturbative treatment breaks down at large scales much before one would expect it to if the nonlinearity were local in real space. We physically interpret this formula in terms of a simple diffusion process. We have also investigated the case n = 0, and we find that it differs from the other cases in certain respects. We investigate a recently proposed scaling property of gravitational clustering, and we find that the lowest order nonlinear terms cause deviations from the scaling relations that are strictly valid in the linear regime. The approximate validity of these relations in the nonlinear regime in l(T)-body simulations cannot be understood at this order of evolution.

The concentration dependent cooperative friction coefficient of dilute polymer solutions at the theta point

We combine multiple scattering and renormalization group methods to calculate the leading order dimensionless virial coefficient k(s) for the friction coefficient of dilute polymer solutions under conditions where the osmotic second virial coefficient vanishes (i.e., at the theta point T-theta). Our calculations are formulated in terms of coupled kinetic equations for the polymer and solvent, in which the polymers are modeled as continuous chains whose configurations evolve under the action of random forces in, the velocity field of the solvent. To lowest order in epsilon=4-d, we find that k(s) = 1.06. This result compares satisfactorily with existing experimental estimates of k(s), which are in the range 0.7-0.8. It is also in good agreement with other theoretical results on chains and suspensions at T-theta. Our calculated k(s) is also found to be identical to the leading order virial coefficient of the tracer friction coefficient at the theta point. We discuss possible reasons for the difficulties encountered when attempting to evaluate k(s) by extrapolating prior renormalization group calculations from semidilute concentrations to the infinitely dilute limit. (C) 1996 American Institute of Physics.

Free convection in power-law fluids near a three-dimensional stagnation point

Numerical results are presented for the free-convection boundary-layer equations of the Ostwald de-Waele non-Newtonian power-law type fluids near a three-dimensional (3-D) stagnation point of attachment on an isothermal surface. The existence of dual solutions that are three-dimensional in nature have been verified by means of a numerical procedure. An asymptotic solution for very large Prandtl numbers has also been derived. Solutions are presented for a range of values of the geometric curvature parameter c, the power-law index n, and the Prandtl number Pr.