Macromolecular crystallography research at Trombay

Neutron diffraction studies of hydrogen positions in small molecules of biological interest at Trombay have provided valuable information that has been used in protein and enzyme structure model-building and in developing hydrogen bond potential functions. The new R-5 reactor is expected to provide higher neutron fluxes and also make possible smallangle neutron scattering studies of large biomolecules and bio-aggregates. In the last few years infrastructure facilities have also been established for macromolecular x-ray crystallography research. Meanwhile, the refinement of carbonic hydrases’ and lysozyme structures have been carried out and interesting results obtained on protein dynamics and structure-function relationships. Some interesting presynaptic toxin phospholipases have also been taken up for study.     

An Analytical Study of Molecular Transport in a Zeolite Crystallite Bed

Analytical solutions of the diffusion equations to obtain the diffusant concentrations in the macro- and micropores which constitute the pore system of a zeolite bed are presented. The parameter which determines the influence of each pore type on the evolution of the adsorbate/adsorbant system towards the equilibrium state is described. Examples are given to illustrate a qualitative and quantitative study based on the curves obtained from these equations.     

INTRAPARTICLE DIFFUSION EFFECTS IN FISCHER-TROPSCH SYNTHESIS Ⅰ. MODELING OF DIFFUSION AND REACTION

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Pion absorption by16O using realistic interactions—II: Free pion absorption followed by emission of proton

Matrix element of the Gallilean invariant nonrelativistic reduction of the pseudoscalar-pseudovector interaction has been calculated for free pion absorption by a single nucleon inside the nucleus of¹⁶O. The Hartree-Fock wavefunctions obtained with the unitary-model-operator approach starting with the hard-core nucleon-nucleon interaction have been used for the π-capturing nucleon in the initial state. The initial pion distortion in the presence of nuclear field of the absorbing nucleus prior to its absorption together with the Coulomb interaction with the finite nuclear size has been taken into account. The distortion of the emitted proton in the field of the residual nucleus has also been considered. The differential cross-sections have been obtained and calculated results are compared with the previous experimental and theoretical work.     

The Mathematical Theory of Ito Diffusions on Hypersurfaces, with Applications to NMR Relaxation Problems

A mathematical framework for translational Brownian motion on hypersurfaces is presented, using an imbedding of the surface and Ito diffusions in the ambient space. This includes a survey of Ito calculus and differential geometry. Computational methods for time correlation functions relevant to spin relaxation studies on curved interfaces are given, and explicit calculations of time correlation functions and order parameters for a Rippled surface are presented.     

Diffusion of Cesium Ions in Agar Gel Containing Alkali Metal Bromides

The present paper gives an account of different aspects of the tracer diffusion of Cs⁺ ions in alkali metal bromides. We have measured the diffusion coefficients, D, of cesium ions in 1% agar gel medium at 25 ^∘C using a zone-diffusion technique over a concentration range of 5 × 10⁻⁵ to 0.1 mol,dm⁻³. The values of the diffusion coefficients were found to deviate from theory, which are explained on the basis of different types of interactions occurring in the ion-gel-water system. The study is also focused on the effect of alkali metal bromides on the obstruction effect and activation energy for the tracer-diffusion of cesium ions in agar gel medium. It is observed that both parameters, extent of obstruction, ∝, and activation energy, E, decrease with increasing charge density of the cation of the supporting electrolyte. The influence of these trends is explained on the basis of competitive hydration between the ions and agar molecules, and the relative distortion in the water structure that is brought about by these different ions and agar molecules.     

A critical reappraisal of recent communications on the hydrodynamic characterization of silica (aerosil) hydrosols

Different results from recent communications on the hydrodynamic characterization of ultrasonicated silica (®Aerosil) hydrosols led to a critical reappraisal of the data.It can be concluded that the degree of dispersion achievable in pyrogenic (Aerosil) hydrosols by ultrasonication is highly sensitive to the detailed parameters of the dispersion process. Characterization in terms ofabsolute numbers of a limiting particle morphology, corresponding to minima of aggregate size, porosity and number of primary particles in the aggregate is not possible.The most straightforward approach for hydrodynamic characterization seems to be a combination of sedimentation and diffusion data.Other approaches using a combination of sedimentation and viscosity data underestimate the particle dimensions. Moreover, they are quite arbitrary since the final result depends upon the proper choice between several equations for fitting the viscosity concentration dependence; the most rigorous approach seems to be an extended Einstein equation which has recently been adapted to particle aggregates.     

Monte Carlo simulation of phase separation and clustering in the ABV model

As a model for a binary alloy undergoing an unmixing phase transition, we consider a square lattice where each site can be either taken by an A atom, a B atom, or a vacancy (V), and there exists a repulsive interaction between AB nearest neighbor pairs. Starting from a random initial configuration, unmixing proceeds via random jumps of A atoms or B atoms to nearest neighbor vacant sites. In the absence of any interaction, these jumps occur at jump rates _A and _B, respectively. For a small concentration of vacancies (c _v=0.04) the dynamics of the structure factorS(k,t) and its first two momentsk ₁(t),k ₂ ² (t) is studied during the early stages of phase separation, for several choices of concentrationc _B of B atoms. Forc _B=0.18 also the time evolution of the cluster size distribution is studied. Apart from very early times, the mean cluster sizel(t) as well as the moments of the structure function depend on timet and the ratio of the jump rates (= _B/ _A) only via a scaled timet/(). Qualitatively, the behavior is very similar to the direct exchange model containing no vacancies. Consequences for phase separation of real alloys are briefly discussed.     

Quantum qualitative dynamics

We describe our work on qualitative methods for visualizing the quantum eigenstates of systems with nonlinear classical dynamics. For two-degree-of-freedom systems, our approach is based on the use of generalized coherent states, and allows systems with nonoscillator kinematics to be investigated. The general approach is illustrated with two examples involving vibration-rotation interaction in polyatomic molecules. We apply the coherent states of the Lie groupH ₄SU(2) to define quantum surfaces of section for a model involving centrifugal coupling of a harmonic bend with molecular rotation, andSU(2)SU(2) coherent states to study two harmonic normal modes coupled to overall molecular rotation through coriolis interaction. In both systems, quantum states are visualized on the rotational surface of section and compared with the corresponding classical phase space structure. Striking classical-quantum correspondence is observed. We then describe recent results on the quantum states of (N 3)-dimensional systems of coupled nonlinear oscillators, which reveal a quantum delocalization that is reminiscent of classical Arnold diffusion.     

Computer simulation of the steady state currents at enzyme doped carbon paste electrodes

The plate-gap model of porous enzyme doped electrode has been proposed and analyzed. It was suggested that reaction diffusion conditions in pores of bulk electrode resemble particular conditions in thin gap between parallel conducting plates. The model is based on the diffusion equations containing a nonlinear term related to the Michaelis–Menten kinetic of the enzymatic reaction inside gap. Steady state current was calculated for the wide range of given parameters and substrate concentrations. All dependences of current on substrate concentration were approximated by hyperbolas in order to obtain “apparent” parameters (maximal currents and apparent Michaelis constants) of modelled biosensors. Simple approximate relationships between given and apparent parameters were derived. The applicability of theoretical plate-gap model was tested for the case of carbon paste electrodes which were doped with PQQ – dependent glucose dehydrogenase. It was found, that soluble glucose dehydrogenase based biosensors exhibit characteristic features of the theoretical plate-gap biosensors.