Protein fold recognition score functions: Unusual construction strategies

We describe two ways of optimizing score functions for protein sequence to structure threading. The first method adjusts parameters to improve sequence to structure alignment. The second adjusts parameters so as to improve a score function's ability to rank alignments calculated in the first score function. Unlike those functions known as knowledge-based force fields, the resulting parameter sets do not rely on Boltzmann statistics, have no claim to representing free energies and are purely constructions for recognizing protein folds. The methods give a small improvement, but suggest that functions can be profitably optimized for very specific aspects of protein fold recognition, Proteins 1999;36:454-461. (C) 1999 Wiley-Liss, Inc.

Two-dimensional nonlinear dynamics of evanescent-wave guided atoms in a hollow fiber

We describe the classical and quantum two-dimensional nonlinear dynamics of large blue-detuned evanescent-wave guiding cold atoms in hollow fiber. We show that chaotic dynamics exists for classic dynamics, when the intensity of the beam is periodically modulated. The two-dimensional distributions of atoms in (x,y) plane are simulated. We show that the atoms will accumulate on several annular regions when the system enters a regime of global chaos. Our simulation shows that, when the atomic flux is very small, a similar distribution will be obtained if we detect the atomic distribution once each the modulation period and integrate the signals. For quantum dynamics, quantum collapses, and revivals appear. For periodically modulated optical potential, the variance of atomic position will be suppressed compared to the no modulation case. The atomic angular momentum will influence the evolution of wave function in two-dimensional quantum system of hollow fiber.

U-q[(sl(2)over-cap vertical bar 1)] vertex operators, screen currents, and correlation functions at an arbitrary level

Bosonized q-vertex operators related to the four-dimensional evaluation modules of the quantum affine superalgebra U-q[sl((2) over cap\1)] are constructed for arbitrary level k=alpha, where alpha not equal 0,-1 is a complex parameter appearing in the four-dimensional evaluation representations. They are intertwiners among the level-alpha highest weight Fock-Wakimoto modules. Screen currents which commute with the action of U-q[sl((2) over cap/1)] up to total differences are presented. Integral formulas for N-point functions of type I and type II q-vertex operators are proposed. (C) 2000 American Institute of Physics. [S0022-2488(00)00608-3].

Water wave-driven seepage in marine sediments

The action of water waves moving over a porous seabed drives a seepage flux into and out of the marine sediments. The volume of fluid exchange per wave cycle may affect the rate of contaminant transport in the sediments. In this paper, the dynamic response of the seabed to ocean waves is treated analytically on the basis of pore-elastic theory applied to a porous seabed. The seabed is modelled as a semi-infinite, isotropic, homogeneous material. Most previous investigations on the wave-seabed interaction problem have assumed quasi-static conditions within the seabed, although dynamic behaviour often occurs in natural environments. Furthermore, wave pressures used in the previous approaches were obtained from conventional ocean wave theories: which are based on the assumption of an impermeable rigid seabed. By introducing a complex wave number, we derive a new wave dispersion equation, which includes the seabed characteristics (such as soil permeability, shear modulus, etc.). Based on the new closed-form analytical solution, the relative differences of the wave-induced seabed response under dynamic and quasi-static conditions are examined. The effects of wave and soil parameters on the seepage flux per wave cycle are also discussed in detail. (C) 2000 Elsevier Science Ltd. All rights reserved.

Atoms in an amplitude-modulated standing wave - dynamics and pathways to quantum chaos

Cold rubidium atoms are subjected to an amplitude-modulated far-detuned standing wave of light to form a quantum-driven pendulum. Here we discuss the dynamics of these atoms. Phase space resonances and chaotic transients of the system exhibit dynamics which can be useful in many atom optics applications as they can be utilized as means for phase space state preparation. We explain the occurrence of distinct peaks in the atomic momentum distribution, analyse them in detail and give evidence for the importance of the system for quantum chaos and decoherence studies.

The human papillomavirus E7 protein is able to inhibit the antiviral and anti-growth functions of interferon-alpha

It is now well recognized that cervical cancer is caused by infection with certain human papillomavirus (HPV) subtypes and while interferon-alpha (IFN-alpha) is used to treat HPV-infected lesions, HPV appears to have developed a means to avoid the effects of IFN-alpha. Clinically, resistance appears to be associated with the expression of the E7 oncoprotein. Here we investigated the effects of expression in cells of the E7 protein from high- and low-risk papillomavirus subtypes on a range of responses to IFN-alpha. 2fTGH, a cell line dependent on IFN-alpha for growth in selection medium, grew significantly less well in the presence of E7, and the antiproliferative effects of IFN-alpha upon epithelial cells was lost upon E7 expression. The antiviral effects of IFN-alpha were abrogated in E7-expressing cells. Loss of response to IFN-alpha was found to occur in both high- and low-risk papillomaviruses. Finally, deletion of amino acids 21-24 of HPV type 16 E7 protein partially reversed repression. We conclude that E7 inhibits the functional effects of IFN-alpha and that this property is shared by all HPV subtypes tested. (C) 2000 Academic Press.

Commentary: Using the convection-dispersion model and transit time density functions in the analysis of organ distribution kinetics

The convection-dispersion model and its extended form have been used to describe solute disposition in organs and to predict hepatic availabilities. A range of empirical transit-time density functions has also been used for a similar purpose. The use of the dispersion model with mixed boundary conditions and transit-time density functions has been queried recently by Hisaka and Sugiyanaa in this journal. We suggest that, consistent with soil science and chemical engineering literature, the mixed boundary conditions are appropriate providing concentrations are defined in terms of flux to ensure continuity at the boundaries and mass balance. It is suggested that the use of the inverse Gaussian or other functions as empirical transit-time densities is independent of any boundary condition consideration. The mixed boundary condition solutions of the convection-dispersion model are the easiest to use when linear kinetics applies. In contrast, the closed conditions are easier to apply in a numerical analysis of nonlinear disposition of solutes in organs. We therefore argue that the use of hepatic elimination models should be based on pragmatic considerations, giving emphasis to using the simplest or easiest solution that will give a sufficiently accurate prediction of hepatic pharmacokinetics for a particular application. (C) 2000 Wiley-Liss Inc. and the American Pharmaceutical Association J Pharm Sci 89:1579-1586, 2000.

Wave-induced seepage flux into anisotropic seabeds

Considerable effort has been devoted to quantifying the wave-induced soil response in a porous seabed in the last few decades. Most previous investigations have focused on the analysis of pore pressure and effective stresses within isotropic sediments, despite strong evidence of anisotropic soil behaviour reported in the literature. Furthermore, the seepage flux, which is important in the context of contaminant transport, has not been examined. In this paper, we focus on water wave-driven seepage in anisotropic marine sediments of finite thickness. The numerical results predict that the effects of hydraulic anisotropy and anisotropic soil behaviour on the wave-driven seepage in marine sediment are significant. Copyright (C) 2001 John Wiley & Sons, Ltd.

Determining complicated winding patterns for shim coils using stream functions and the target-field method

In a magnetic resonance imaging equipment, gradient and shim coils are needed to produce a spatially varying magnetic field throughout the sample being imaged. Such coils consist of turns of wire wound on the surface of a cylindrical tube. Shim coils in particular, must sometimes be designed to produce complicated magnetic fields to correct for impurities. Streamline patterns for shim coils are much more complicated than those for gradient coils, In this work we present a detailed analysis of streamline methods and their application to shim coil design, A method is presented for determining the winding patterns to generate these complicated fields. (C) 2002 John Wiley & Sons, Inc.

A method for the design of MRI radiofrequency coils based on triangular and pulse basis functions

This paper presents a numerical technique for the design of an RF coil for asymmetric magnetic resonance imaging (MRI) systems. The formulation is based on an inverse approach where the cylindrical surface currents are expressed in terms of a combination of sub-domain basis functions: triangular and pulse functions. With the homogeneous transverse magnetic field specified in a spherical region, a functional method is applied to obtain the unknown current coefficients. The current distribution is then transformed to a conductor pattern by use of a stream function technique. Preliminary MR images acquired using a prototype RF coil are presented and validate the design method. (C) 2002 Elsevier Science B.V. All rights reserved.

Group theory and quasiprobability integrals of Wigner functions

The integral of the Wigner function of a quantum-mechanical system over a region or its boundary in the classical phase plane, is called a quasiprobability integral. Unlike a true probability integral, its value may lie outside the interval [0, 1]. It is characterized by a corresponding selfadjoint operator, to be called a region or contour operator as appropriate, which is determined by the characteristic function of that region or contour. The spectral problem is studied for commuting families of region and contour operators associated with concentric discs and circles of given radius a. Their respective eigenvalues are determined as functions of a, in terms of the Gauss-Laguerre polynomials. These polynomials provide a basis of vectors in a Hilbert space carrying the positive discrete series representation of the algebra su(1, 1) approximate to so(2, 1). The explicit relation between the spectra of operators associated with discs and circles with proportional radii, is given in terms of the discrete variable Meixner polynomials.

Apparent strain localization and shear wave dispersion in elastic fault gouge with microrotations

Shear deformation of fault gouge or other particulate materials often results in observed strain localization, or more precisely, the localization of measured deformation gradients. In conventional elastic materials the strain localization cannot take place therefore this phenomenon is attributed to special types of non-elastic constitutive behaviour. For particulate materials however the Cosserat continuum which takes care of microrotations independent of displacements is a more appropriate model. In elastic Cosserat continuum the localization in displacement gradients is possible under some combinations of the generalized Cosserat elastic moduli. The same combinations of parameters also correspond to a considerable dispersion in shear wave propagation which can be used for independent experimental verification of the proposed mechanism of apparent strain localization in fault gouge.