The stretching of single poly-ubiquitin molecules: Static versus dynamic disorder in the non-exponential kinetics of chain unfolding

Static disorder has recently been implicated in the non-exponential kinetics of the unfolding of single molecules of poly-ubiquitin under a constant force Kuo, Garcia-Manyes, Li, Barel, Lu, Berne, Urbakh, Klafter, and Fernandez, Proc. Natl. Acad. Sci. U. S. A. 107, 11336 (2010)]. In the present paper, it is suggested that dynamic disorder may provide a plausible, alternative description of the experimental observations. This suggestion is made on the basis of a model in which the barrier to chain unfolding is assumed to be modulated by a control parameter r that evolves in a parabolic potential under the action of fractional Gaussian noise according to a generalized Langevin equation. The treatment of dynamic disorder within this model is pursued using Zwanzig's indirect approach to noise averaging Acc. Chem. Res. 23, 148 (1990)]. In conjunction with a self-consistent closure scheme developed by Wilemski and Fixman J. Chem. Phys. 58, 4009 (1973); ibid. 60, 866 (1974)], this approach eventually leads to an expression for the chain unfolding probability that can be made to fit the corresponding experimental data very closely. (C) 2011 American Institute of Physics.

Generation of an eight node brick element using Papcovitch-Neuber functions

Some conventional finite elements suffer from drawbacks, such as shear locking, membrane locking, etc. To overcome them researchers have developed various techniques, termed as tricks by some and variational crimes by others. Many attempts have been made, but satisfactory explanations for why some of these techniques work have not been obtained, especially in the case of solid elements. This paper attempts a simple non-conforming solid element using assumed displacement fields which satisfy the Navier equation exactly. Its behaviour under simple loadings like bending, torsion and tension is examined and comparisons are made with existing elements.

Geometrically Simple Logarithmic Weir

This paper discusses the design and experimental verification of a geometrically simple logarithmic weir. The weir consists of an inward trapezoidal weir of slope 1 horizontal to n vertical, or 1 in n, over two sectors of a circle of radius R and depth d, separated by a distance 2t. The weir parameters are optimized using a numerical optimization algorithm. The discharge through this weir is proportional to the logarithm of head measured above a fixed reference plane for all heads in the range 0.23R less than or equal to h less than or equal to 3.65R within a maximum deviation of +/-2% from the theoretical discharge. Experiments with two weirs show excellent agreement with the theory by giving a constant average coefficient of discharge of 0.62. The application of this weir to the field of irrigation, environmental, and chemical engineering is highlighted.

Uniform algebras generated by holomorphic and close-to-harmonic functions

The initial motivation for this paper is to discuss a more concrete approach to an approximation theorem of Axler and Shields, which says that the uniform algebra on the closed unit disc (D) over bar generated by z and h, where h is a nowhere-holomorphic harmonic function on D that is continuous up to partial derivative D, equals C((D) over bar). The abstract tools used by Axler and Shields make harmonicity of h an essential condition for their result. We use the concepts of plurisubharmonicity and polynomial convexity to show that, in fact, the same conclusion is reached if h is replaced by h + R, where R is a non-harmonic perturbation whose Laplacian is ``small'' in a certain sense.

Violin string shape functions for finite element analysis of rotating Timoshenko beams

Violin strings are relatively short and stiff and are well modeled by Timoshenko beam theory. We use the static part of the homogeneous differential equation of violin strings to obtain new shape functions for the finite element analysis of rotating Timoshenko beams. For deriving the shape functions, the rotating beam is considered as a sequence of violin strings. The violin string shape functions depend on rotation speed and element position along the beam length and account for centrifugal stiffening effects as well as rotary inertia and shear deformation on dynamic characteristics of rotating Timoshenko beams. Numerical results show that the violin string basis functions perform much better than the conventional polynomials at high rotation speeds and are thus useful for turbo machine applications. (C) 2011 Elsevier B.V. All rights reserved.

The effect of temperature on the surface tension and adsorption functions of the Fe-S-O melts - an analysis based on interaction parameters

The present investigation analyses the thermodynamic behaviour of the surfaces and adsorption as a function of temperature and composition in the Fe-S-O melts based on the Butler's equations. The calculated-values of the surface tensions exhibit an elevation or depression depending on the type of the added solute at a concentration which coincides with that already present in the system. Generally, the desorption of the solutes as a function of temperature results in an initial increase followed by a decrease in the values of the surface tension. The observations are analyzed based on the surface interaction parameters which are derived in the present research.

Lithium ion transport in Li2SO4-Li2O-B2O3 glasses

Electrical conductivity and dielectric relaxation studies with a wide range of compositions of lithium ion conducting glasses belonging to the ternary glass system Li2SO4-Li2O-B2-O3- have been carried out over the temperature range 150-450 K and between 10 - 10(7) Hz. DC conductivities exhibit two different activation regions. This seems to suggest the presence of a cluster tissue texture in these glasses with weakly ordered clusters of Li2SO4 and lithium berates being held together by a truly amorphous tissue of the same average composition as clusters. AC conductivity behaviour of these glasses has been analysed using both power law and stretched exponential relaxation functions. The variation of the power law exponent s and the stretched exponent beta with temperature seems to be consistent with the presence of a cluster tissue texture in these glasses.

Efficient algorithms for learning kernels from multiple similarity matrices with general convex loss functions

In this paper we consider the problem of learning an n × n kernel matrix from m(1) similarity matrices under general convex loss. Past research have extensively studied the m = 1 case and have derived several algorithms which require sophisticated techniques like ACCP, SOCP, etc. The existing algorithms do not apply if one uses arbitrary losses and often can not handle m > 1 case. We present several provably convergent iterative algorithms, where each iteration requires either an SVM or a Multiple Kernel Learning (MKL) solver for m > 1 case. One of the major contributions of the paper is to extend the well knownMirror Descent(MD) framework to handle Cartesian product of psd matrices. This novel extension leads to an algorithm, called EMKL, which solves the problem in O(m2 log n 2) iterations; in each iteration one solves an MKL involving m kernels and m eigen-decomposition of n × n matrices. By suitably defining a restriction on the objective function, a faster version of EMKL is proposed, called REKL,which avoids the eigen-decomposition. An alternative to both EMKL and REKL is also suggested which requires only an SVMsolver. Experimental results on real world protein data set involving several similarity matrices illustrate the efficacy of the proposed algorithms.

Exact spectral functions of a non-Fermi liquid in one dimension

We study the exact one-electron propagator and spectral function of a solvable model of interacting electrons due to Schulz and Shastry. The solution previously found for the energies and wave functions is extended to give spectral functions that turn out to be computable, interesting, and nontrivial. They provide one of the few examples of cases where the spectral functions are known asymptotically as well as exactly.

Quadratic Lyapunov functions for linear systems Journal

The paper deals with the existence of a quadratic Lyapunov function V = x′P(t)x for an exponentially stable linear system with varying coefficients described by the vector differential equation S0305004100044777_inline1 The derivative dV/dt is allowed to be strictly semi-(F) and the locus dV/dt = 0 does not contain any arc of the system trajectory. It is then shown that the coefficient matrix A(t) of the exponentially stable sy

Acquisition time improvement of PLLs using some aiding functions

Analytical studies are carried out to minimize acquisition time in phase-lock loop (PLL) applications using aiding functions. A second order aided PLL is realized with the help of the quasi-stationary approach to verify the acquisition behavior in the absence of noise. Time acquisition is measured both from the study of the LPF output transient and by employing a lock detecting and indicating circuit to crosscheck experimental and analytical results. A closed form solution is obtained for the evaluation of the time acquisition using different aiding functions. The aiding signal is simple and economical and can be used with state of the art hardware.