Modes of binding of guanosine monophosphates to ribonuclease T1 - A computer modelling study

Computer-modelling studies on the modes of binding of the three guanosine monophosphate inhibitors 2'-GMP, 3'-GMP, and 5'-GMP to ribonuclease (RNase) T1 have been carried out by energy minimization in Cartesian-coordinate space. The inhibitory power was found to decrease in the order 2'-GMP > 3'-GMP > 5'-GMP in agreement with the experimental observations. The ribose moiety was found to form hydrogen bonds with the protein in all the enzyme-inhibitor complexes, indicating that it contributes to the binding energy and does not merely act as a spacer between the base and the phosphate moieties as suggested earlier. 2'-GMP and 5'-GMP bind to RNase T1 in either of the two ribose puckered forms (with C3'-endo more favoured over the C2'-endo) and 3'-GMP binds to RNase T1 predominantly in C3'-endo form. The catalytically important residue His-92 was found to form hydrogen bond with the phosphate moiety in all the enzyme-inhibitor complexes, indicating that this residue may serve as a general acid group during catalysis. Such an interaction was not found in either X-ray or two-dimensional NMR studies.

Affine Matching with Bounded Sensor Error: A Study of Geometric Hashing and Alignment

Affine transformations are often used in recognition systems, to approximate the effects of perspective projection. The underlying mathematics is for exact feature data, with no positional uncertainty. In practice, heuristics are added to handle uncertainty. We provide a precise analysis of affine point matching, obtaining an expression for the range of affine-invariant values consistent with bounded uncertainty. This analysis reveals that the range of affine-invariant values depends on the actual $x$-$y$-positions of the features, i.e. with uncertainty, affine representations are not invariant with respect to the Cartesian coordinate system. We analyze the effect of this on geometric hashing and alignment recognition methods.

Interpretação de anomalias magnéticas usando integrais finitas dos momentos das componentes

O objetivo do trabalho consiste em desenvolver uma metodologia para determinar os parâmetros de um corpo causador de uma anomalia magnética. Essa metodologia baseia-se na utilização de expressões analíticas, deduzidas para as integrais finitas dos momentos da anomalia de intensidade total e das componentes H_x, H_y e H_z ao longo dos três eixos de um sistema de coordenadas cartesianas. Por meio do ajuste entre essas expressões analíticas e as integrais numéricas finitas dos momentos das componentes magnéticas obtidas a partir de um levantamento geofísico, pode-se computar, através de um processo iterativo, os parâmetros de magnetização, posição, profundidade e dimensões de um corpo anômalo. No caso em que são conhecidas as medidas de somente uma componente magnética, ainda é possível aplicar o método pois as demais componentes podem ser obtidas por um esquema de filtragem matemática. A metodologia foi testada com sucesso para modelos dipolo pontual e linha de dipolos os quais são muito utilizados em Geofísica para interpretar anomalias magnéticas produzidas por corpos geológicos que possuem uma ou duas dimensões horizontais muito menores do que a profundidade.

Robot navigation in sensor space

This thesis investigates the problem of robot navigation using only landmark bearings. The proposed system allows a robot to move to a ground target location specified by the sensor values observed at this ground target posi- tion. The control actions are computed based on the difference between the current landmark bearings and the target landmark bearings. No Cartesian coordinates with respect to the ground are computed by the control system. The robot navigates using solely information from the bearing sensor space. Most existing robot navigation systems require a ground frame (2D Cartesian coordinate system) in order to navigate from a ground point A to a ground point B. The commonly used sensors such as laser range scanner, sonar, infrared, and vision do not directly provide the 2D ground coordi- nates of the robot. The existing systems use the sensor measurements to localise the robot with respect to a map, a set of 2D coordinates of the objects of interest. It is more natural to navigate between the points in the sensor space corresponding to A and B without requiring the Cartesian map and the localisation process. Research on animals has revealed how insects are able to exploit very limited computational and memory resources to successfully navigate to a desired destination without computing Cartesian positions. For example, a honeybee balances the left and right optical flows to navigate in a nar- row corridor. Unlike many other ants, Cataglyphis bicolor does not secrete pheromone trails in order to find its way home but instead uses the sun as a compass to keep track of its home direction vector. The home vector can be inaccurate, so the ant also uses landmark recognition. More precisely, it takes snapshots and compass headings of some landmarks. To return home, the ant tries to line up the landmarks exactly as they were before it started wandering. This thesis introduces a navigation method based on reflex actions in sensor space. The sensor vector is made of the bearings of some landmarks, and the reflex action is a gradient descent with respect to the distance in sensor space between the current sensor vector and the target sensor vec- tor. Our theoretical analysis shows that except for some fully characterized pathological cases, any point is reachable from any other point by reflex action in the bearing sensor space provided the environment contains three landmarks and is free of obstacles. The trajectories of a robot using reflex navigation, like other image- based visual control strategies, do not correspond necessarily to the shortest paths on the ground, because the sensor error is minimized, not the moving distance on the ground. However, we show that the use of a sequence of waypoints in sensor space can address this problem. In order to identify relevant waypoints, we train a Self Organising Map (SOM) from a set of observations uniformly distributed with respect to the ground. This SOM provides a sense of location to the robot, and allows a form of path planning in sensor space. The navigation proposed system is analysed theoretically, and evaluated both in simulation and with experiments on a real robot.

Numerical study of two ill-posed one-phase Stefan problems

We treat two related moving boundary problems. The first is the ill-posed Stefan problem for melting a superheated solid in one Cartesian coordinate. Mathematically, this is the same problem as that for freezing a supercooled liquid, with applications to crystal growth. By applying a front-fixing technique with finite differences, we reproduce existing numerical results in the literature, concentrating on solutions that break down in finite time. This sort of finite-time blow-up is characterised by the speed of the moving boundary becoming unbounded in the blow-up limit. The second problem, which is an extension of the first, is proposed to simulate aspects of a particular two-phase Stefan problem with surface tension. We study this novel moving boundary problem numerically, and provide results that support the hypothesis that it exhibits a similar type of finite-time blow-up as the more complicated two-phase problem. The results are unusual in the sense that it appears the addition of surface tension transforms a well-posed problem into an ill-posed one.

Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state

Enzyme is a dynamic entity with diverse time scales, ranging from picoseconds to seconds or even longer. Here we develop a rate theory for enzyme catalysis that includes conformational dynamics as cycling on a two-dimensional (2D) reaction free energy surface involving an intrinsic reaction coordinate (X) and an enzyme conformational coordinate (Q). The validity of Michaelis-Menten (MM) equation, i.e., substrate concentration dependence of enzymatic velocity, is examined under a nonequilibrium steady state. Under certain conditions, the classic MM equation holds but with generalized microscopic interpretations of kinetic parameters. However, under other conditions, our rate theory predicts either positive (sigmoidal-like) or negative (biphasic-like) kinetic cooperativity due to the modified effective 2D reaction pathway on X-Q surface, which can explain non-MM dependence previously observed on many monomeric enzymes that involve slow or hysteretic conformational transitions. Furthermore, we find that a slow conformational relaxation during product release could retain the enzyme in a favorable configuration, such that enzymatic turnover is dynamically accelerated at high substrate concentrations. The effect of such conformation retainment in a nonequilibrium steady state is evaluated.

Computer modelling studies of ribonuclease A-pyrimidine nucleotide complexes

Different modes of binding of pyrimidine monophosphates 2'-UMP, 3'-UMP, 2'-CMP and 3'-CMP to ribonuclease (RNase) A are studied by energy minimization in torsion angle and subsequently in Cartesian coordinate space. The results are analysed in the light of primary binding sites. The hydrogen bonding pattern brings out roles for amino acids such as Asn44 and Ser123 apart from the well known active site residues viz., His12,Lys41,Thr45 and His119. Amino acid segments 43-45 and 119-121 seem to be guiding the ligand binding by forming a pocket. Many of the active site charged residues display considerable movement upon nucleotide binding.

Obliquely incident water waves against a vertical cliff

Utilizing the commutativity property of the Cartesian coordinate differential operators arising in the boundary conditions associated with the propagation of surface water waves against a vertical cliff, under the assumptions of linearized theory, the problem of obliquely incident surface waves is considered for solution. The case of normal incidence, handled by previous workers follow as a particular limiting case of the present problem, which exhibits a source/sink type behavior of the velocity potential at the shore-line. An independent method of attack is also presented to handle the case of normal incidence.

Transport coefficients for the shear dynamo problem at small Reynolds numbers

We build on the formulation developed in S. Sridhar and N. K. Singh J. Fluid Mech. 664, 265 (2010)] and present a theory of the shear dynamo problem for small magnetic and fluid Reynolds numbers, but for arbitrary values of the shear parameter. Specializing to the case of a mean magnetic field that is slowly varying in time, explicit expressions for the transport coefficients alpha(il) and eta(iml) are derived. We prove that when the velocity field is nonhelical, the transport coefficient alpha(il) vanishes. We then consider forced, stochastic dynamics for the incompressible velocity field at low Reynolds number. An exact, explicit solution for the velocity field is derived, and the velocity spectrum tensor is calculated in terms of the Galilean-invariant forcing statistics. We consider forcing statistics that are nonhelical, isotropic, and delta correlated in time, and specialize to the case when the mean field is a function only of the spatial coordinate X-3 and time tau; this reduction is necessary for comparison with the numerical experiments of A. Brandenburg, K. H. Radler, M. Rheinhardt, and P. J. Kapyla Astrophys. J. 676, 740 (2008)]. Explicit expressions are derived for all four components of the magnetic diffusivity tensor eta(ij) (tau). These are used to prove that the shear-current effect cannot be responsible for dynamo action at small Re and Rm, but for all values of the shear parameter.

An economical method for direct numerical simulation studies of transitional round jets

A pseudo-spectral method based on Fourier expansions in a Cartesian coordinate system is shown to be an economical method for direct numerical simulation studies of transitional round jets, Several characteristics of the solutions are presented to establish the validity of the solutions in spite of the unnatural choices. We show that neither periodicity, nor the use of a Cartesian system have adversely affected the simulations, Instead, there are benefits in terms of ease of computing and lack of the usual restrictions due to grid structure near the jet axis. By computing the simultaneous evolution of passive scalers, the process of reaction in round jet burners, between a fuel-laden jet and an ambient oxidizer, was also simulated. Some typical solutions are shown and then the results of analysis of these data are summarized. (C) 2001 Elsevier Science Ltd, All rights reserved.

Note on modelling directionality in piezoresistivity

When computing the change in electrical resistivity of a piezoresistive cubic material embedded in a deforming structure, the piezoresistive and the stress tensors should be in the same coordinate system. While the stress tensor is usually calculated in a coordinate system aligned with the principal axes of a regular structure, the specified piezoresistive coefficients may not be in that coordinate system. For instance, piezoresistive coefficients are usually given in an orthogonal cartesian coordinate system aligned with the <100> crystallographic directions and designers sometimes deliberately orient a crystallographic direction other than <100> along the principal directions of the structure to increase the gauge factor. In such structures, it is advantageous to calculate the piezoresistivity tensor in the coordinate system along which the stress tensors are known rather than the other way around. This is because the transformation of stress will have to be done at every point in the structure but piezoresistivity tensor needs to be transformed only once. Here, using tensor transformation relations, we show how to calculate the piezoresistive tensor along any arbitrary Cartesian coordinate system from the piezoresistive coefficients for the <100> coordinate system. Some of the software packages that simulate the piezoresistive effect do not have interfaces for calculation of the entire piezoresistive tensor for arbitrary directions. This warrants additional work for the user because not considering the complete piezoresisitive tensor can lead to large errors. This is illustrated with an example where the error is as high as 33%. Additionally, for elastic analysis, we used hybrid finite element formulation that estimates stresses more accurately than displacement-based formulation. Therefore, as shown in an example where the change in resistance can be calculated analytically, the percentage error of our piezoresistive program is an order of magnitude lower relative to displacement-based finite element method.

Mechanical modeling of grain boundary sliding of polycrystals

Using a variational method, a general three-dimensional solution to the problem of a sliding spherical inclusion embedded in an infinite anisotropic medium is presented in this paper. The inclusion itself is also a general anisotropic elastic medium. The interface is treated as a thin interface layer with interphase anisotropic properties. The displacements in the matrix and the inclusion are expressed as polynomial series of the cartesian coordinate components. Using the virtual work principle, a set of linear algebraic equations about unknown coefficients are obtained. Then the general sliding spherical inclusion problem is accurately solved. Based on this solution, a self-consistent method for sliding polycrystals is proposed. Combining this with a two-dimensional model of an aggregate polycrystal, a systematic analysis of the mechanical behaviour of sliding polycrystals is given in detail. Numerical results are given to show the significant effect of grain boundary sliding on the overall mechanical properties of aggregate polycrystals.

Multipole moments in general relativity and dynamical perturbations of black-hole magnetospheres

This thesis consists of two parts. In Part I, we develop a multipole moment formalism in general relativity and use it to analyze the motion and precession of compact bodies. More specifically, the generic, vacuum, dynamical gravitational field of the exterior universe in the vicinity of a freely moving body is expanded in positive powers of the distance r away from the body's spatial origin (i.e., in the distance r from its timelike-geodesic world line). The expansion coefficients, called "external multipole moments,'' are defined covariantly in terms of the Riemann curvature tensor and its spatial derivatives evaluated on the body's central world line. In a carefully chosen class of de Donder coordinates, the expansion of the external field involves only integral powers of r ; no logarithmic terms occur. The expansion is used to derive higher-order corrections to previously known laws of motion and precession for black holes and other bodies. The resulting laws of motion and precession are expressed in terms of couplings of the time derivatives of the body's quadrupole and octopole moments to the external moments, i.e., to the external curvature and its gradient.

In part II, we study the interaction of magnetohydrodynamic (MHD) waves in a black-hole magnetosphere with the "dragging of inertial frames" effect of the hole's rotation - i.e., with the hole's "gravitomagnetic field." More specifically: we first rewrite the laws of perfect general relativistic magnetohydrodynamics (GRMHD) in 3+1 language in a general spacetime, in terms of quantities (magnetic field, flow velocity, ...) that would be measured by the ''fiducial observers” whose world lines are orthogonal to (arbitrarily chosen) hypersurfaces of constant time. We then specialize to a stationary spacetime and MHD flow with one arbitrary spatial symmetry (e.g., the stationary magnetosphere of a Kerr black hole); and for this spacetime we reduce the GRMHD equations to a set of algebraic equations. The general features of the resulting stationary, symmetric GRMHD magnetospheric solutions are discussed, including the Blandford-Znajek effect in which the gravitomagnetic field interacts with the magnetosphere to produce an outflowing jet. Then in a specific model spacetime with two spatial symmetries, which captures the key features of the Kerr geometry, we derive the GRMHD equations which govern weak, linealized perturbations of a stationary magnetosphere with outflowing jet. These perturbation equations are then Fourier analyzed in time t and in the symmetry coordinate x, and subsequently solved numerically. The numerical solutions describe the interaction of MHD waves with the gravitomagnetic field. It is found that, among other features, when an oscillatory external force is applied to the region of the magnetosphere where plasma (e⁺e^-) is being created, the magnetosphere responds especially strongly at a particular, resonant, driving frequency. The resonant frequency is that for which the perturbations appear to be stationary (time independent) in the common rest frame of the freshly created plasma and the rotating magnetic field lines. The magnetosphere of a rotating black hole, when buffeted by nonaxisymmetric magnetic fields anchored in a surrounding accretion disk, might exhibit an analogous resonance. If so then the hole's outflowing jet might be modulated at resonant frequencies ω=(m/2) Ω_H where m is an integer and Ω_H is the hole's angular velocity.

Long lasting phosphorescence, thermoluminescence and electron spin resonance property of Mn2+ activated ZnO-Al2O3SiO2 ceramic

The long lasting phosphorescence (LLP) phenomenon in Mn2+-doped ceramic based on ZnO-Al2O3-SiO2 (ZASM) is observed. After irradiation by a UVP standard mercury lamp peaking at 254 nm with a power of 0.6 mW/cm(2) for 15 min, the ceramic sample emits a bright green light peaking at 519 nm, which can be seen in the dark even 15 h after the removal of UVP standard mercury lamp by the naked eyes whose limit of light perception is 0.32 mcd/m(2). The initial afterglow intensity reaches about 1900 mcd/m(2), and the color coordinate (X, Y) is (0.2280, 0.5767) at about 10 s after stopping irradiation. The thermoluminescence (TL) spectra show that there are at least three kinds of trap centers with different trap levels while electron spin resonance (ESR) spectra indicate that there are electron- and hole-trapping centers induced after irradiation by a UVP standard mercury lamp. Based on these measurements, the LLP is considered to be due to the recombination of electrons and holes at trapping centers with different levels, which are firstly thermally released back to Mn2+ and then give rise to the bright green LLP at room temperature.