A perspective of biological supramolecular electron transfer

Electron transfer is an essential activity in biological systems. The migrating electron originates from water-oxygen in photosynthesis and reverts to dioxygen in respiration. In this cycle two metal porphyrin complexes possessing circular conjugated system and macrocyclic pi-clouds, chlorophyll and hems, play a decisive role in mobilising electrons for travel over biological structures as extraneous electrons. Transport of electrons within proteins (as in cytochromes) and within DNA (during oxidative damage and repair) is known to occur. Initial evaluations did not favour formation of semiconducting pathways of delocalized electrons of the peptide bonds in proteins and of the bases in nucleic acids. Direct measurement of conductivity of bulk material and quantum chemical calculations of their polymeric structures also did not support electron transfer in both proteins and nucleic acids. New experimental approaches have revived interest in the process of charge transfer through DNA duplex. The fluorescence on photoexcitation of Ru-complex was found to be quenched by Rh-complex, when both were tethered to DNA and intercalated in the base stack. Similar experiments showed that damage to G-bases and repair of T-T dimers in DNA can occur by possible long range electron transfer through the base stack. The novelty of this phenomenon prompted the apt name, chemistry at a distance. Based on experiments with ruthenium modified proteins, intramolecular electron transfer in proteins is now proposed to use pathways that include C-C sigma-bonds and surprisingly hydrogen bonds which remained out of favour for a long time. In support of this, some experimental evidence is now available showing that hydrogen bond-bridges facilitate transfer of electrons between metal-porphyrin complexes. By molecular orbital calculations over 20 years ago. we found that "delocalization of an extraneous electron is pronounced when it enters low-lying virtual orbitals of the electronic structures of peptide units linked by hydrogen bonds". This review focuses on supramolecular electron transfer pathways that can emerge on interlinking by hydrogen bonds and metal coordination of some unnoticed structures with pi-clouds in proteins and nucleic acids, potentially useful in catalysis and energy missions.

Absolute Entropy and Energy of Carbon Dioxide Using the Two-Phase Thermodynamic Model

The two-phase thermodynamic (2PT) model is used to determine the absolute entropy and energy of carbon dioxide over a wide range of conditions from molecular dynamics trajectories. The 2PT method determines the thermodynamic properties by applying the proper statistical mechanical partition function to the normal modes of a fluid. The vibrational density of state (DoS), obtained from the Fourier transform of the velocity autocorrelation function, converges quickly, allowing the free energy, entropy, and other thermodynamic properties to be determined from short 20-ps MD trajectories. The anharmonic effects in the vibrations are accounted for by the broadening of the normal modes into bands from sampling the velocities over the trajectory. The low frequency diffusive modes, which lead to finite DoS at zero frequency, are accounted for by considering the DoS as a superposition of gas-phase and solid-phase components (two phases). The analytical decomposition of the DoS allows for an evaluation of properties contributed by different types of molecular motions. We show that this 2PT analysis leads to accurate predictions of entropy and energy of CO2 over a wide range of conditions (from the triple point to the critical point of both the vapor and the liquid phases along the saturation line). This allows the equation of state of CO2 to be determined, which is limited only by the accuracy of the force field. We also validated that the 2PT entropy agrees with that determined from thermodynamic integration, but 2PT requires only a fraction of the time. A complication for CO2 is that its equilibrium configuration is linear, which would have only two rotational modes, but during the dynamics it is never exactly linear, so that there is a third mode from rotational about the axis. In this work, we show how to treat such linear molecules in the 2PT framework.

Sliding wear of copper against alumina

OFHC copper pins with 10 ppm oxygen were slid against alumina at a load of 50 N and sliding speeds of 0.1 ms(-1) to 4.0 ms(-1) The wear characteristics of copper were related to the strain rate response of copper under uniaxial compression between strain rates of 0.1 s(-1) and 100 s(-1) and temperatures in the range of 298 K to 673 K. It is seen that copper undergoes flow banding at strain rates of 1 s(-1) up to a temperature of 523 K, which is the major instability in the region tested. These flow bands are regions of crack nucleation. The strain rates and temperatures existing in the subsurface of copper slid against alumina are estimated and superimposed on the strain rate response map of copper. The superposition shows that the subsurface of copper slid at low velocities is likely to exhibit flow band instability induced cracking. It is suggested that this is the,reason for the observed high wear rate at low velocities. The subsurface deformation with increasing velocity becomes more homogeneous. This reduces the wear rate. At velocities >2 ms(-1) there is homogenous flow and extrusion of thin (10 mu m) bands of material out of the trailing edge. This results in the gradual increase of wear rate with increasing velocity above 2.0 ms(-1).

Velocity distribution for a dilute vibrated granular material

The velocity distribution for a vibrated granular material is determined in the dilute limit where the frequency of particle collisions with the vibrating surface is large compared to the frequency of binary collisions. The particle motion is driven by the source of energy due to particle collisions with the vibrating surface, and two dissipation mechanisms-inelastic collisions and air drag-are considered. In the latter case, a general form for the drag force is assumed. First, the distribution function for the vertical velocity for a single particle colliding with a vibrating surface is determined in the limit where the dissipation during a collision due to inelasticity or between successive collisions due to drag is small compared to the energy of a particle. In addition, two types of amplitude functions for the velocity of the surface, symmetric and asymmetric about zero velocity, are considered. In all cases, differential equations for the distribution of velocities at the vibrating surface are obtained using a flux balance condition in velocity space, and these are solved to determine the distribution function. It is found that the distribution function is a Gaussian distribution when the dissipation is due to inelastic collisions and the amplitude function is symmetric, and the mean square velocity scales as [[U-2](s)/(1 - e(2))], where [U-2](s) is the mean square velocity of the vibrating surface and e is the coefficient of restitution. The distribution function is very different from a Gaussian when the dissipation is due to air drag and the amplitude function is symmetric, and the mean square velocity scales as ([U-2](s)g/mu(m))(1/(m+2)) when the acceleration due to the fluid drag is -mu(m)u(y)\u(y)\(m-1), where g is the acceleration due to gravity. For an asymmetric amplitude function, the distribution function at the vibrating surface is found to be sharply peaked around [+/-2[U](s)/(1-e)] when the dissipation is due to inelastic collisions, and around +/-[(m +2)[U](s)g/mu(m)](1/(m+1)) when the dissipation is due to fluid drag, where [U](s) is the mean velocity of the surface. The distribution functions are compared with numerical simulations of a particle colliding with a vibrating surface, and excellent agreement is found with no adjustable parameters. The distribution function for a two-dimensional vibrated granular material that includes the first effect of binary collisions is determined for the system with dissipation due to inelastic collisions and the amplitude function for the velocity of the vibrating surface is symmetric in the limit delta(I)=(2nr)/(1 - e)much less than 1. Here, n is the number of particles per unit width and r is the particle radius. In this Limit, an asymptotic analysis is used about the Limit where there are no binary collisions. It is found that the distribution function has a power-law divergence proportional to \u(x)\((c delta l-1)) in the limit u(x)-->0, where u(x) is the horizontal velocity. The constant c and the moments of the distribution function are evaluated from the conservation equation in velocity space. It is found that the mean square velocity in the horizontal direction scales as O(delta(I)T), and the nontrivial third moments of the velocity distribution scale as O(delta(I)epsilon(I)T(3/2)) where epsilon(I) = (1 - e)(1/2). Here, T = [2[U2](s)/(1 - e)] is the mean square velocity of the particles.

Ab initio studies of solvent effect on conformational equilibria and vibrational spectra of dipropionamide

Systematic ab initio molecular orbital studies of the conformational equilibria and vibrational spectra of dipropionamide using the basis sets 6-31g(d) and 6-31++G(d,p) have been carried out. The vibrational spectra of dipropionamide have been satisfactorily interpreted taking into account the agreement between the calculated frequencies, infrared and Raman band intensities and the shifts in the spectra of deuterated molecules with those observed. The previous assignments of most of the vibrational bands are well confirmed, a few bands need reassignment, however. The solvent effects were investigated by self-consistent reaction field theory using dipole and self-consistent isodensity polarized continuum model methods. The introduction of a dielectric medium has only a marginal effect on the conformational equilibria and vibrational spectra. However, the calculated changes in geometry and vibrational spectra on going from the gas phase to the solution phase are in accord with the increasing weight of the dipolar resonance structure in polar solvents. (C) 2002 Elsevier Science B.V. All rights reserved.

A differential geometric method for kinematic analysis of two- and three-degree-of-freedom rigid body motions

In this paper, we present a novel differential geometric characterization of two- and three-degree-of-freedom rigid body kinematics, using a metric defined on dual vectors. The instantaneous angular and linear velocities of a rigid body are expressed as a dual velocity vector, and dual inner product is defined on this dual vector, resulting in a positive semi-definite and symmetric dual matrix. We show that the maximum and minimum magnitude of the dual velocity vector, for a unit speed motion, can be obtained as eigenvalues of this dual matrix. Furthermore, we show that the tip of the dual velocity vector lies on a dual ellipse for a two-degree-of-freedom motion and on a dual ellipsoid for a three-degree-of-freedom motion. In this manner, the velocity distribution of a rigid body can be studied algebraically in terms of the eigenvalues of a dual matrix or geometrically with the dual ellipse and ellipsoid. The second-order properties of the two- and three-degree-of-freedom motions of a rigid body are also obtained from the derivatives of the elements of the dual matrix. This results in a definition of the geodesic motion of a rigid body. The theoretical results are illustrated with the help of a spatial 2R and a parallel three-degree-of-freedom manipulator.

A differential-geometric analysis of singularities of point trajectories of serial and parallel manipulators

In this paper, we present a differential-geometric approach to analyze the singularities of task space point trajectories of two and three-degree-of-freedom serial and parallel manipulators. At non-singular configurations, the first-order, local properties are characterized by metric coefficients, and, geometrically, by the shape and size of a velocity ellipse or an ellipsoid. At singular configurations, the determinant of the matrix of metric coefficients is zero and the velocity ellipsoid degenerates to an ellipse, a line or a point, and the area or the volume of the velocity ellipse or ellipsoid becomes zero. The degeneracies of the velocity ellipsoid or ellipse gives a simple geometric picture of the possible task space velocities at a singular configuration. To study the second-order properties at a singularity, we use the derivatives of the metric coefficients and the rate of change of area or volume. The derivatives are shown to be related to the possible task space accelerations at a singular configuration. In the case of parallel manipulators, singularities may lead to either loss or gain of one or more degrees-of-freedom. For loss of one or more degrees-of-freedom, ther possible velocities and accelerations are again obtained from a modified metric and derivatives of the metric coefficients. In the case of a gain of one or more degrees-of-freedom, the possible task space velocities can be pictured as growth to lines, ellipses, and ellipsoids. The theoretical results are illustrated with the help of a general spatial 2R manipulator and a three-degree-of-freedom RPSSPR-SPR parallel manipulator.

Structure and electrical properties of sputtered lithium cobaltite thin films

LixCoOy films with x < 1 and y > 2 have been prepared by radio-frequency (rf) sputtering from high temperature (HT) LiCoO2 targets. Their structures have been examined with high resolution electron microscopy. Conductivities have been studied between 77 and 400 K. The electrochemical behaviour of film electrodes have been investigated with Li/LiClO4-PC/LixCoOy cells. The annealed films consist of nanocrystalline domains with amorphous boundaries. Electrical conductivities appear to arise from variable-range hopping (VRH) of holes. The films form good electrodes with operating potentials between 2.7 and 3.8 V. The observations have been discussed on the basis of a tentative and heuristic molecular orbital based energy band diagram. (C) 2002 Published by Elsevier Science Ltd.

A cold model study of raceway hysteresis

The effect of a gas flow field on the size of raceway has been studied experimentally using a two-dimensional (2-D) cold model. It is observed that as the blast velocity from the tuyere increases, raceway size increases, and when the blast velocity is decreased from its highest value, raceway size does not change much until the velocity reaches a critical velocity. Below the critical velocity, raceway size decreases with decreasing velocity but is always larger than that for the same velocity when the velocity increased. This phenomenon is called "raceway hysteresis." Raceway hysteresis has been studied in the presence of different gas flow rates and different particle densities. Raceway hysteresis has been observed in all the experiments. The effect of liquid flow, with various superficial velocities, on raceway hysteresis has also been studied. A study of raceway size hysteresis shows that interparticle and particle-wall friction have a very large effect on raceway size. A hypothesis has been proposed to describe the hysteresis phenomenon in the packed beds. The relevance of hysteresis to blast furnace raceways has been discussed. Existing literature correlations for raceway size ignore the frictional effects. Therefore, their applicability to the ironmaking blast furnace is questionable.

Particle dynamics in a turbulent particle–gas suspension at high Stokes number. Part 2. The fluctuating-force model

A fluctuating-force model is developed for representing the effect of the turbulent fluid velocity fluctuations on the particle phase in a turbulent gas–solid suspension in the limit of high Stokes number, where the particle relaxation time is large compared with the correlation time for the fluid velocity fluctuations. In the model, a fluctuating force is incorporated in the equation of motion for the particles, and the force distribution is assumed to be an anisotropic Gaussian white noise. It is shown that this is equivalent to incorporating a diffusion term in the Boltzmann equation for the particle velocity distribution functions. The variance of the force distribution, or equivalently the diffusion coefficient in the Boltzmann equation, is related to the time correlation functions for the fluid velocity fluctuations. The fluctuating-force model is applied to the specific case of a Couette flow of a turbulent particle–gas suspension, for which both the fluid and particle velocity distributions were evaluated using direct numerical simulations by Goswami & Kumaran (2010). It is found that the fluctuating-force simulation is able to quantitatively predict the concentration, mean velocity profiles and the mean square velocities, both at relatively low volume fractions, where the viscous relaxation time is small compared with the time between collisions, and at higher volume fractions, where the time between collisions is small compared with the viscous relaxation time. The simulations are also able to predict the velocity distributions in the centre of the Couette, even in cases in which the velocity distribution is very different from a Gaussian distribution.

Particle dynamics in a turbulent particle–gas suspension at high Stokes number. Part 1. Velocity and acceleration distributions

The effect of fluid velocity fluctuations on the dynamics of the particles in a turbulent gas–solid suspension is analysed in the low-Reynolds-number and high Stokes number limits, where the particle relaxation time is long compared with the correlation time for the fluid velocity fluctuations, and the drag force on the particles due to the fluid can be expressed by the modified Stokes law. The direct numerical simulation procedure is used for solving the Navier–Stokes equations for the fluid, the particles are modelled as hard spheres which undergo elastic collisions and a one-way coupling algorithm is used where the force exerted by the fluid on the particles is incorporated, but not the reverse force exerted by the particles on the fluid. The particle mean and root-mean-square (RMS) fluctuating velocities, as well as the probability distribution function for the particle velocity fluctuations and the distribution of acceleration of the particles in the central region of the Couette (where the velocity profile is linear and the RMS velocities are nearly constant), are examined. It is found that the distribution of particle velocities is very different from a Gaussian, especially in the spanwise and wall-normal directions. However, the distribution of the acceleration fluctuation on the particles is found to be close to a Gaussian, though the distribution is highly anisotropic and there is a correlation between the fluctuations in the flow and gradient directions. The non-Gaussian nature of the particle velocity fluctuations is found to be due to inter-particle collisions induced by the large particle velocity fluctuations in the flow direction. It is also found that the acceleration distribution on the particles is in very good agreement with the distribution that is calculated from the velocity fluctuations in the fluid, using the Stokes drag law, indicating that there is very little correlation between the fluid velocity fluctuations and the particle velocity fluctuations in the presence of one-way coupling. All of these results indicate that the effect of the turbulent fluid velocity fluctuations can be accurately represented by an anisotropic Gaussian white noise.

Quasicrystalline Coatings Through Laser Processing: A Study on Process Optimisation and Microstructure Evolution

Composite coatings containing quasicrystalline (QC) phases in Al-Cu-Fe alloys were prepared by laser cladding using a mixture of the elemental powders. Two substrates, namely pure aluminum and an Al-Si alloy were used. The clad layers were remelted at different scanning velocities to alter the growth conditions of different phases. The process parameters were optimized to produce quasicrystalline phases. The evolution of the microstructure in the coating layer was characterized by detailed microstructural investigation. The results indicate presence of quasicrystals in the aluminum substrate. However, only approximant phase could be observed in the substrate of Al-Si alloys. It is shown that there is a significant transport of Si atoms from the substrate to the clad layer during the cladding and remelting process. The hardness profiles of coatings on aluminum substrate indicate a very high hardness. The coating on Al-Si alloy, on the other hand, is ductile and soft. The fracture toughness of the hard coating on aluminum was obtained by nano-indentation technique. The K1C value was found to be 1.33 MPa m1/2 which is typical of brittle materials.

Two-channel Kondo physics in odd impurity chains

We study odd-membered chains of spin-1/2 impurities, with each end connected to its own metallic lead. For antiferromagnetic exchange coupling, universal two-channel Kondo (2CK) physics is shown to arise at low energies. Two overscreening mechanisms are found to occur depending on coupling strength, with distinct signatures in physical properties. For strong interimpurity coupling, a residual chain spin-1/2 moment experiences a renormalized effective coupling to the leads, while in the weak-coupling regime, Kondo coupling is mediated via incipient single-channel Kondo singlet formation. We also investigate models in which the leads are tunnel-coupled to the impurity chain, permitting variable dot filling under applied gate voltages. Effective low-energy models for each regime of filling are derived, and for even fillings where the chain ground state is a spin singlet, an orbital 2CK effect is found to be operative. Provided mirror symmetry is preserved, 2CK physics is shown to be wholly robust to variable dot filling; in particular, the single-particle spectrum at the Fermi level, and hence the low-temperature zero-bias conductance, is always pinned to half-unitarity. We derive a Friedel-Luttinger sum rule and from it show that, in contrast to a Fermi liquid, the Luttinger integral is nonzero and determined solely by the ``excess'' dot charge as controlled by gate voltage. The relevance of the work to real quantum dot devices, where interlead charge-transfer processes fatal to 2CK physics are present, is also discussed. Physical arguments and numerical renormalization-group techniques are used to obtain a detailed understanding of these problems.

Possible conversion of a neutron star to a quark star in the presence of high magnetic field

Recent results and data suggest that high magnetic fields in neutron stars (NS) strongly affect the characteristics (radius, mass) of the star. Such stars are even separated into a class known as magnetars, for which the surface magnetic field is greater than 10(14) G. In this work we discuss the effect of such a high magnetic field on the phase transition of a NS to a quark star (QS). We study the effect of magnetic field on the transition from NS to QS including the magnetic-field effect in the equation of state (EoS). The inclusion of the magnetic field increases the range of baryon number densities for which the flow velocities of the matter in the respective phase are finite. The magnetic field helps in initiation of the conversion process. The velocity of the conversion front, however, decreases due to the presence of the magnetic field, as the presence of the magnetic field reduces the effective pressure (P). The magnetic field of the star is decreased by the conversion process, and the resultant QS has lower magnetic field than the initial NS.

Axially homogeneous, zero mean flow buoyancy-driven turbulence in a vertical pipe

We report an experimental study of a new type of turbulent flow that is driven purely by buoyancy. The flow is due to an unstable density difference, created using brine and water, across the ends of a long (length/diameter=9) vertical pipe. The Schmidt number Sc is 670, and the Rayleigh number (Ra) based on the density gradient and diameter is about 108. Under these conditions the convection is turbulent, and the time-averaged velocity at any point is ‘zero’. The Reynolds number based on the Taylor microscale, Reλ, is about 65. The pipe is long enough for there to be an axially homogeneous region, with a linear density gradient, about 6–7 diameters long in the midlength of the pipe. In the absence of a mean flow and, therefore, mean shear, turbulence is sustained just by buoyancy. The flow can be thus considered to be an axially homogeneous turbulent natural convection driven by a constant (unstable) density gradient. We characterize the flow using flow visualization and particle image velocimetry (PIV). Measurements show that the mean velocities and the Reynolds shear stresses are zero across the cross-section; the root mean squared (r.m.s.) of the vertical velocity is larger than those of the lateral velocities (by about one and half times at the pipe axis). We identify some features of the turbulent flow using velocity correlation maps and the probability density functions of velocities and velocity differences. The flow away from the wall, affected mainly by buoyancy, consists of vertically moving fluid masses continually colliding and interacting, while the flow near the wall appears similar to that in wall-bound shear-free turbulence. The turbulence is anisotropic, with the anisotropy increasing to large values as the wall is approached. A mixing length model with the diameter of the pipe as the length scale predicts well the scalings for velocity fluctuations and the flux. This model implies that the Nusselt number would scale as Ra1/2Sc1/2, and the Reynolds number would scale as Ra1/2Sc−1/2. The velocity and the flux measurements appear to be consistent with the Ra1/2 scaling, although it must be pointed out that the Rayleigh number range was less than 10. The Schmidt number was not varied to check the Sc scaling. The fluxes and the Reynolds numbers obtained in the present configuration are much higher compared to what would be obtained in Rayleigh–Bénard (R–B) convection for similar density differences.