Modes of binding of 2'-AMP to RNase T1. A computer modeling study

The modes of binding of adenosine 2'-monophosphate (2'-AMP) to the enzyme ribonuclease (RNase) T1 were determined by computer modelling studies. The phosphate moiety of 2'-AMP binds at the primary phosphate binding site. However, adenine can occupy two distinct sites--(1) The primary base binding site where the guanine of 2'-GMP binds and (2) The subsite close to the N1 subsite for the base on the 3'-side of guanine in a guanyl dinucleotide. The minimum energy conformers corresponding to the two modes of binding of 2'-AMP to RNase T1 were found to be of nearly the same energy implying that in solution 2'-AMP binds to the enzyme in both modes. The conformation of the inhibitor and the predicted hydrogen bonding scheme for the RNase T1-2'-AMP complex in the second binding mode (S) agrees well with the reported x-ray crystallographic study. The existence of the first mode of binding explains the experimental observations that RNase T1 catalyses the hydrolysis of phosphodiester bonds adjacent to adenosine at high enzyme concentrations. A comparison of the interactions of 2'-AMP and 2'-GMP with RNase T1 reveals that Glu58 and Asn98 at the phosphate binding site and Glu46 at the base binding site preferentially stabilise the enzyme-2'-GMP complex.

Modes of binding of α(1–2) linked manno-oligosaccharides to concanavalin A

Three-dimensional structures of the complexes of concanavalin A (ConA) with alpha(1-2) linked mannobiose, triose and tetraose have been generated with the X-ray crystal structure data on native ConA using the CCEM (contact criteria and energy minimization) method. All the constituting mannose residues of the oligosaccharide can reach the primary binding site of ConA (where methyl-alpha-D-mannopyranose binds). However, in all the energetically favoured complexes, either the non-reducing end or middle mannose residues of the oligosaccharide occupy the primary binding site. The middle mannose residues have marginally higher preference over the non-reducing end residue. The sugar binding site of ConA is extended and accommodates at least three alpha(1-2) linked mannose residues. Based on the present calculations two mechanisms have been proposed for the binding of alpha(1-2) linked mannotriose and tetraose to ConA.

Topological phases, Majorana modes and quench dynamics in a spin ladder system

We explore the salient features of the `Kitaev ladder', a two-legged ladder version of the spin-1/2 Kitaev model on a honeycomb lattice, by mapping it to a one-dimensional fermionic p-wave superconducting system. We examine the connections between spin phases and topologically non-trivial phases of non-interacting fermionic systems, demonstrating the equivalence between the spontaneous breaking of global Z(2) symmetry in spin systems and the existence of isolated Majorana modes. In the Kitaev ladder, we investigate topological properties of the system in different sectors characterized by the presence or absence of a vortex in each plaquette of the ladder. We show that vortex patterns can yield a rich parameter space for tuning into topologically non-trivial phases. We introduce and employ a new topological invariant for explicitly determining the presence of zero energy Majorana modes at the boundaries of such phases. Finally, we discuss dynamic quenching between topologically non-trivial phases in the Kitaev ladder and, in particular, the post-quench dynamics governed by tuning through a quantum critical point.

Phase diagram of a two-species lattice model with a linear instability

We discuss the properties of a one-dimensional lattice model of a driven system with two species of particles in which the mobility of one species depends on the density of the other. This model was introduced by Lahiri and Ramaswamy (Phys. Rev. Lett., 79, 1150 (1997)) in the context of sedimenting colloidal crystals, and its continuum version was shown to exhibit an instability arising from linear gradient couplings. In this paper we review recent progress in understanding the full phase diagram of the model. There are three phases. In the first, the steady state can be determined exactly along a representative locus using the condition of detailed balance. The system shows phase separation of an exceptionally robust sort, termed strong phase separation, which survives at all temperatures. The second phase arises in the threshold case where the first species evolves independently of the second, but the fluctuations of the first influence the evolution of the second, as in the passive scalar problem. The second species then shows phase separation of a delicate sort, in which long-range order coexists with fluctuations which do not damp down in the large-size limit. This fluctuation-dominated phase ordering is associated with power law decays in cluster size distributions and a breakdown of the Porod law. The third phase is one with a uniform overall density, and along a representative locus the steady state is shown to have product measure form. Density fluctuations are transported by two kinematic waves, each involving both species and coupled at the nonlinear level. Their dissipation properties are governed by the symmetries of these couplings, which depend on the overall densities. In the most interesting case,, the dissipation of the two modes is characterized by different critical exponents, despite the nonlinear coupling.

Pricing a Shared Access Link for Fair and Efficient Operation with Variable User Data Rates

The literature on pricing implicitly assumes an "infinite data" model, in which sources can sustain any data rate indefinitely. We assume a more realistic "finite data" model, in which sources occasionally run out of data; this leads to variable user data rates. Further, we assume that users have contracts with the service provider, specifying the rates at which they can inject traffic into the network. Our objective is to study how prices can be set such that a single link can be shared efficiently and fairly among users in a dynamically changing scenario where a subset of users occasionally has little data to send. User preferences are modelled by concave increasing utility functions. Further, we introduce two additional elements: a convex increasing disutility function and a convex increasing multiplicative congestion-penally function. The disutility function takes the shortfall (contracted rate minus present rate) as its argument, and essentially encourages users to send traffic at their contracted rates, while the congestion-penalty function discourages heavy users from sending excess data when the link is congested. We obtain simple necessary and sufficient conditions on prices for fair and efficient link sharing; moreover, we show that a single price for all users achieves this. We illustrate the ideas using a simple experiment.

Application of composition gradient solid electrolytes in sensors and thermodynamic measurements

New compos~tiong radient solid electrolytes are developed which have application in high temperature solid state galvanic sensors and provide a new tool for thermodynamic measurements. The electrolyte consists oi a solid solution between two ionic conductors with a common mobile ion and spatial variation in composition of otber coxup nents. Incorporation of the composite electrolyte in sensors permits the use oi dissimilar gas electrodes. It is demonsuated, both experimentall y and theoretically, that the composition gradient of the relativeiy immobile species does not give rise to a diffusion potential.The emi of a cell is determined by the activity of the mobile species at the two eiectrodes. The thermodynamic properties of solid solutions can be measured using the gradient solid electrolyte. The experimental stuay is based on model systems A?(COj)x(S04)l-x (A=Na,K),where S \.aria across the electrolyte. The functionally gradient solid electrolytes used for activity measurements consist of pure carbonate at one ena and the solid solution under stuav at the other. The identical vaiues of activity, obtained h m t hree different modes of operation of the ceil. indicate unit transport number for the ddi metal ion in the graciient electrolyte. Tlle activities in the solid solutions exhibit moderate positive deviations from Raoult 's law.

Bypass operation in bridge convertors for high-voltage d.c. transmission

Bypass operation with the aid of a special bypass valve is an important part of present-day schemes of protection for h.v. d.c. transmission systems. In this paper, the possibility of using two valves connected to any phase in the bridge convertor for the purpose of bypass operation is studied. The scheme is based on the use of logic circuits in conjunction with modified methods of fault detection. Analysis of the faults in a d.c. transmission system is carried out with the object of determining the requirements of such a logic-circuit control system. An outline of the scheme for the logic-circuit control of the bypass operation for both rectifier and invertor bridges is then given. Finally, conclusions are drawn regarding the advantages of such a system, which include reduction in the number of valves, prevention of severe faults and fast clearance of faults, in addition to the immediate location of the fault and its nature.

Exciting forces due to interaction of water waves with a submerged sphere in an ice-covered two-layer fluid of finite depth

Scattering of water waves by a sphere in a two-layer fluid, where the upper layer has an ice-cover modelled as an elastic plate of very small thickness, while the lower one has a rigid horizontal bottom surface, is investigated within the framework of linearized water wave theory. The effects of surface tension at the surface of separation is neglected. There exist two modes of time-harmonic waves - the one with lower wave number propagating along the ice-cover and the one with higher wave number along the interface. Method of multipole expansions is used to find the particular solution for the problem of wave scattering by a submerged sphere placed in either of the layers. The exciting forces for vertical and horizontal directions are derived and plotted against different values of the wave number for different submersion depths of the sphere and flexural rigidity of the ice-cover. When the flexural rigidity and the density of the ice-cover are taken to be zero, the numerical results for the exciting forces for the problem with free surface are recovered as particular cases. (C) 2011 Elsevier Ltd. All rights reserved.

Higher spin quasinormal modes and one-loop determinants in the BTZ black hole

We solve the wave equations of arbitrary integer spin fields in the BTZ black hole background and obtain exact expressions for their quasinormal modes. We show that these quasinormal modes precisely agree with the location of the poles of the corresponding two point function in the dual conformal field theory as predicted by the AdS/CFT correspondence. We then use these quasinormal modes to construct the one-loop determinant of the higher spin field in the thermal BTZ background. This is shown to agree with that obtained from the corresponding heat kernel constructed recently by group theoretic methods.

Loop Heat Pipes: A Review of Fundamentals, Operation, and Design

The loop heat pipe (LHP) is a passive two-phase heat transport device that is gaining importance as a part of spacecraft thermal control systems and also in applications such as in avionics cooling and submarines. A major advantage of a loop heat pipe is that the porous wick structure is confuned to the evaporator section, and connection between the evaporator and condenser sections is by smooth tubes, thus minimizing pressure drop. A brief overview of loop heat pipes with respect to basic fundamentals, construction details, operating principles, and typical operating characteristics is presented in this paper. Finally, the paper presents the current developments in modeling of thermohydraulics and design methodologies of LHPs.

Unstable m=1 modes of counter-rotating Keplerian discs

We study the linear m= 1 counter-rotating instability in a two-component, nearly Keplerian disc. Our goal is to understand these slow modes in discs orbiting massive black holes in galactic nuclei. They are of interest not only because they are of large spatial scale and can hence dominate observations but also because they can be growing modes that are readily excited by accretion events. Self-gravity being non-local, the eigenvalue problem results in a pair of coupled integral equations, which we derive for a two-component softened gravity disc. We solve this integral eigenvalue problem numerically for various values of mass fraction in the counter-rotating component. The eigenvalues are in general complex, being real only in the absence of the counter-rotating component, or imaginary when both components have identical surface density profiles. Our main results are as follows: (i) the pattern speed appears to be non-negative, with the growth (or damping) rate being larger for larger values of the pattern speed; (ii) for a given value of the pattern speed, the growth (or damping) rate increases as the mass in the counter-rotating component increases; (iii) the number of nodes of the eigenfunctions decreases with increasing pattern speed and growth rate. Observations of lopsided brightness distributions would then be dominated by modes with the least number of nodes, which also possess the largest pattern speeds and growth rates.

LOCAL TWO-DIMENSIONAL PARTICLE-IN-CELL SIMULATIONS OF THE COLLISIONLESS MAGNETOROTATIONAL INSTABILITY

The magnetorotational instability (MRI) is a crucial mechanism of angular momentum transport in a variety of astrophysical accretion disks. In systems accreting at well below the Eddington rate, such as the central black hole in the Milky Way (Sgr A*), the plasma in the disk is essentially collisionless. We present a nonlinear study of the collisionless MRI using first-principles particle-in-cell plasma simulations. We focus on local two-dimensional (axisymmetric) simulations, deferring more realistic three-dimensional simulations to future work. For simulations with net vertical magnetic flux, the MRI continuously amplifies the magnetic field, B, until the Alfven velocity, v(A), is comparable to the speed of light, c (independent of the initial value of v(A)/c). This is consistent with the lack of saturation of MRI channel modes in analogous axisymmetric MHD simulations. The amplification of the magnetic field by the MRI generates a significant pressure anisotropy in the plasma (with the pressure perpendicular to B being larger than the parallel pressure). We find that this pressure anisotropy in turn excites mirror modes and that the volume-averaged pressure anisotropy remains near the threshold for mirror mode excitation. Particle energization is due to both reconnection and viscous heating associated with the pressure anisotropy. Reconnection produces a distinctive power-law component in the energy distribution function of the particles, indicating the likelihood of non-thermal ion and electron acceleration in collisionless accretion disks. This has important implications for interpreting the observed emission-from the radio to the gamma-rays-of systems such as Sgr A*.

Cumulus clouds and convective boundary layers: a tropical perspective on two turbulent shear flows

This paper is a review prepared for the second Marseille Colloquium on the mechanics of turbulence, held in 2011, 50 years after the first. The review covers recent developments in our understanding of the large-scale dynamics of cumulus cloud flows and of the atmospheric boundary layer in the low-wind convective regime that is often encountered in the tropics. It has recently been shown that a variety of cumulus cloud forms and life cycles can be experimentally realized in the laboratory, with the transient diabatic plume taken as the flow model for a cumulus cloud. The plume is subjected to diabatic heating scaled to be dynamically similar to heat release from phase changes in clouds. The experiments are complemented by exact numerical solutions of the Navier-Stokes-Boussinesq equations for plumes with scaled off-source heating. The results show that the Taylor entrainment coefficient first increases with heating, reaches a positive maximum and then drops rapidly to zero or even negative values. This reduction in entrainment is a consequence of structural changes in the flow, smoothing out the convoluted boundaries in the non-diabatic plume, including the tongues engulfing the ambient flow. This is accompanied by a greater degree of mixedness in the core flow because of lower dilution by the ambient fluid. The cloud forms generated depend strongly on the history of the diabatic heating profile in the vertical direction. The striking effects of heating on the flow are attributable to the operation of the baroclinic torque due to the temperature field. The mean baroclinic torque is shown to peak around a quasi-cylindrical sheet situated midway between the axis of the flow and the edges. This torque is shear-enhancing and folds down the engulfment tongues. The increase in mixedness can be traced to an explosive growth in the enstrophy, triggered by a strong fluctuating baroclinic torque that acts as a source, especially at the higher wave numbers, thus enhancing the mixedness. In convective boundary layers field measurements show that, under conditions prevailing in the tropics, the eddy fluxes of momentum and energy do not follow the Monin-Obukhov similarity. Instead, the eddy momentum flux is found to be linear in the wind speed at low winds; and the eddy heat flux is, to a first approximation, governed by free convection laws, with wind acting as a small perturbation on a regime of free convection. A new boundary layer code, based on heat flux scaling rather than wall-stress scaling, shows promising improvements in predictive skills of a general circulation model.

Effects of different modes of hot cross-rolling in 7010 aluminum alloy: part I. evolution of microstructure and texture

The current study describes the evolution of microstructure and texture in an Al-Zn-Mg-Cu-Zr-based 7010 aluminum alloy during different modes of hot cross-rolling. Processing of materials involves three different types of cross-rolling. The development of texture in the one-step cross-rolled specimen can be described by a typical beta-fiber having the maximum intensity near Copper (Cu) component. However, for the multi-step cross-rolled specimens, the as-rolled texture is mainly characterized by a strong rotated-Brass (Bs) component and a very weak rotated-cube component. Subsequent heat treatment leads to sharpening of the major texture component (i.e., rotated-Bs). Furthermore, the main texture components in all the specimens appear to be significantly rotated in a complex manner away from their ideal positions because of non-symmetric deformations in the two rolling directions. Detailed microstructural study indicates that dynamic recovery is the dominant restoration mechanism operating during the hot rolling. During subsequent heat treatment, static recovery dominates, while a combination of particle-stimulated nucleation (PSN) and strain-induced grain boundary migration (SIBM) causes partial recrystallization of the grain structure. The aforementioned restoration mechanisms play an important role in the development of texture components. The textural development in the current study could be attributed to the combined effects of (a) cross-rolling and inter-pass annealing that reduce the intensity of Cu component after each successive pass, (b) recrystallization resistance of Bs-oriented grains, (c) stability of Bs texture under cross-rolling, and (d) Zener pinning by Al3Zr dispersoids.

An integrated model for optimal reservoir operation for irrigation of multiple crops

An integratedm odel is developed,b asedo n seasonailn puts of reservoiri nflow and rainfall in the irrigated area, to determine the optimal reservoir release policies and irrigation allocationst o multiple crops.T he model is conceptuallym ade up of two modules. Module 1 is an intraseasonal allocation model to maximize the sum of relative yieldso f all crops,f or a givens tateo f the systemu, singl inear programming(L P). The module takes into account reservoir storage continuity, soil moisture balance, and crop root growthw ith time. Module 2 is a seasonaal llocationm odel to derive the steadys tate reservoiro peratingp olicyu sings tochastidc ynamicp rogramming(S DP). Reservoir storage, seasonal inflow, and seasonal rainfall are the state variables in the SDP. The objective in SDP is to maximize the expected sum of relative yields of all crops in a year.The resultso f module 1 and the transitionp robabilitieso f seasonailn flow and rainfall form the input for module 2. The use of seasonailn puts coupledw ith the LP-SDP solution strategy in the present formulation facilitates in relaxing the limitations of an earlier study,w hile affectinga dditionali mprovementsT. he model is applied to an existing reservoir in Karnataka State, India.