Analysis of proteins with the `hot dog' fold: Prediction of function and identification of catalytic residues of hypothetical proteins

Background: The hot dog fold has been found in more than sixty proteins since the first report of its existence about a decade ago. The fold appears to have a strong association with fatty acid biosynthesis, its regulation and metabolism, as the proteins with this fold are predominantly coenzyme A-binding enzymes with a variety of substrates located at their active sites. Results: We have analyzed the structural features and sequences of proteins having the hot dog fold. This study reveals that though the basic architecture of the fold is well conserved in these proteins, significant differences exist in their sequence, nature of substrate and oligomerization. Segments with certain conserved sequence motifs seem to play crucial structural and functional roles in various classes of these proteins. Conclusion: The analysis led to predictions regarding the functional classification and identification of possible catalytic residues of a number of hot dog fold-containing hypothetical proteins whose structures were determined in high throughput structural genomics projects.

Fluctuation Theory Of The Specific-Heat Of Normal Liquid-3He

The measured specific heat of normal liquid 3He shows a plateau for 0.15<1 K; below 0.15 K and above 1 K, it rises linearly with temperature. However, the slope on the high-temperature side is very much reduced compared with the free-Fermi-gas value. We explain these features through a microscopic, thermal spin- and density-fluctuation model. The plateau is due to spin fluctuations which have a low characteristic energy in 3He. Because of the low compressibility, the density fluctuations are highly suppressed; this leads to a reduced slope for CV(T) for high temperatures.

Information theory and resistance fluctuations in one-dimensional disordered conductors

A novel method is proposed to treat the problem of the random resistance of a strictly one-dimensional conductor with static disorder. For the probability distribution of the transfer matrix R of the conductor we propose a distribution of maximum information entropy, constrained by the following physical requirements: (1) flux conservation, (2) time-reversal invariance, and (3) scaling with the length of the conductor of the two lowest cumulants of ω, where R=exp(iω→⋅Jbhat). The preliminary results discussed in the text are in qualitative agreement with those obtained by sophisticated microscopic theories.

Theory of freezing in simple systems

The transition parameters for the freezing of two one-component liquids into crystalline solids are evaluated by two theoretical approaches. The first system considered is liquid sodium which crystallizes into a body-centered-cubic (bcc) lattice; the second system is the freezing of adhesive hard spheres into a face-centered-cubic (fcc) lattice. Two related theoretical techniques are used in this evaluation: One is based upon a recently developed bifurcation analysis; the other is based upon the theory of freezing developed by Ramakrishnan and Yussouff. For liquid sodium, where experimental information is available, the predictions of the two theories agree well with experiment and each other. The adhesive-hard-sphere system, which displays a triple point and can be used to fit some liquids accurately, shows a temperature dependence of the freezing parameters which is similar to Lennard-Jones systems. At very low temperature, the fractional density change on freezing shows a dramatic increase as a function of temperature indicating the importance of all the contributions due to the triplet direction correlation function. Also, we consider the freezing of a one-component liquid into a simple-cubic (sc) lattice by bifurcation analysis and show that this transition is highly unfavorable, independent of interatomic potential choice. The bifurcation diagrams for the three lattices considered are compared and found to be strikingly different. Finally, a new stability analysis of the bifurcation diagrams is presented.

Prediction of Compressibility of Overconsolidated Uncemented Soils

Overconsolidated soils exhibit a bilinear e-log p relationship. During virgin compression, microstructural units form larger stable groups, thereby reducing the operating specific surface and, in turn, net osmotic repulsive forces in the soil. The rebound portion of the e-log p curve is consequently flatter. The generalized relationship for compressibility of uncemented soils in the overconsolidated state has been developed in the form of e/eL = 1.122 = 0.188 log pc - 0.0463 log p in which e/eL is the generalized soil state parameter, pc is the preconsolidation pressure in kPa, p is the effective overburden pressure in kPa, e is the in situ void ratio, and eL is the void ratio corresponding to the liquid limit water content (wLG). This relationship can be usefully employed to predict both the preconsolidation pressure and compressibility responses of overconsolidated uncemented soils.

Prediction of Breakdown Voltages of Binary Gas Mixtures in Uniform Electric Fields

A simple equation to predict the breakdown voltages for binary mixtures (Vmix) of electronegative gases (SF6, CCl2F2) and buffer gases (N2, N2O, CO2, air) under uniform electric field has been proposed. Values of Vmix evaluated using this equation for mixtures of SF6-N2, SF6-air, SF6-N2O, SF6-CO2 and CCl2F2-N2 over a wide range of pd show an excellent agreement with the experimentally measured data available in the literature.

Thermodynamic scaling theory for the two-impurity Anderson model

We present results of a study of the two-impurity Anderson model using a thermodynamic scaling theory developed recently. The model is characterized by the Coulomb energy U, the orbital energy epsilond, the d-level width Gamma, and the separation between impurities R. If Gamma<<−epsilond<~Gamma. Here we find that the single-impurity physics dominates the low-temperature behavior, and impurity-impurity interactions are perturbative. The qualitative features of the temperature-dependent susceptibility are discussed. Journal of Applied Physics is copyrighted by The American Institute of Physics.

Critical-point Properties of Liquids and the Born-Green Theory

Recent work of Jones et al. giving the long-range behaviour of the pair correlation function is used to confirm that the critical ratio Pc/nckBTc = 1/2 in the Born-Green theory. This deviates from experimental results on simple insulating liquids by more than the predictions of the van der Waals equation of state. A brief discussion of conditions for thermodynamic consistency, which the Born-Green theory violates, is then given. Finally, the approach of the Ornstein-Zernike correlation function to its critical point behaviour is discussed within the Born-Green theory.

Coupled amplitude theory of nonlinear surface acoustic waves

The nonlinear propagation characteristics of surface acoustic waves on an isotropic elastic solid have been studied in this paper. The solution of the harmonic boundary value problem for Rayleigh waves is obtained as a generalized Fourier series whose coefficients are proportional to the slowly varying amplitudes of the various harmonics. The infinite set of coupled equations for the amplitudes when solved exhibit an oscillatory slow variation signifying a continuous transfer of energy back and forth among the various harmonics. A conservation relation is derived among all the harmonic amplitudes.

Prediction of frequency and amplitude of foundations at resonance

This note presents the statistical analysis carried out on some of the available experimental results to predict the resonant frequency and maximum displacement amplitude of a machine foundation – soil system under vertical vibration as a function of the size and weight of the foundation and of the excitation level. A total of 442 experimental results of Fry, Novak, and Raman have been analysed using nonlinear regression analysis. The results obtained compared well with predictions obtained from the popular theoretical models, and the coefficient of correlation obtained from the analysis was satisfactory in most of the cases.

On the propagation of a weak shock front: Theory and application

In this paper the kinematics of a weak shock front governed by a hyperbolic system of conservation laws is studied. This is used to develop a method for solving problems, involving the propagation of nonlinear unimodal waves. It consists of first solving the nonlinear wave problem by moving along the bicharacteristics of the system and then fitting the shock into this solution field, so that it satisfies the necessary jump conditions. The kinematics of the shock leads in a natural way to the definition of ldquoshock-raysrdquo, which play the same role as the ldquoraysrdquo in a continuous flow. A special case of a circular cylinder introduced suddenly in a constant streaming flow is studied in detail. The shock fitted in the upstream region propagates with a velocity which is the mean of the velocities of the linear and the nonlinear wave fronts. In the downstream the solution is given by an expansion wave.

Non-Abelian monopoles break color. II. Field theory and quantum mechanics

Many grand unified theories (GUT's) predict non-Abelian monopoles which are sources of non-Abelian (and Abelian) magnetic flux. In the preceding paper, we discussed in detail the topological obstructions to the global implementation of the action of the "unbroken symmetry group" H on a classical test particle in the field of such a monopole. In this paper, the existence of similar topological obstructions to the definition of H action on the fields in such a monopole sector, as well as on the states of a quantum-mechanical test particle in the presence of such fields, are shown in detail. Some subgroups of H which can be globally realized as groups of automorphisms are identified. We also discuss the application of our analysis to the SU(5) GUT and show in particular that the non-Abelian monopoles of that theory break color and electroweak symmetries.

A Fredholm-type theory for third-kind linear integral equations

The third-kind linear integral equation Image where g(t) vanishes at a finite number of points in (a, b), is considered. In general, the Fredholm Alternative theory [[5.]] does not hold good for this type of integral equation. However, imposing certain conditions on g(t) and K(t, t′), the above integral equation was shown [[1.], 49–57] to obey a Fredholm-type theory, except for a certain class of kernels for which the question was left open. In this note a theory is presented for the equation under consideration with some additional assumptions on such kernels.

A semi-empirical theory of molten salts

A semi-empirical model is presented for describing the interionic interactions in molten salts using the experimentally available structure data. An extension of Bertaut's method of non-overlapping charges is used to estimate the electrostatic interaction energy in ionic melts. It is shown, in agreement with earlier computer simulation studies, that this energy increases when an ionic salt melts. The repulsion between ions is described using a compressible ion theory which uses structure-independent parameters. The van der Waals interactions and the thermal free energy are also included in the total energy, which is minimised with respect to isostructural volume variations to calculate the equilibrium density. Detailed results are presented for three molten systems, NaCl, CaCl2 and ZnCl2, and are shown to be in satisfactory agreement with experiments. With reliable structural data now being reported for several other molten salts, the present study gains relevance.