Dynamic coupling between the LID and NMP domain motions in the catalytic conversion of ATP and AMP to ADP by adenylate kinase

The catalytic conversion of adenosine triphosphate (ATP) and adenosine monophosphate (AMP) to adenosine diphosphate (ADP) by adenylate kinase (ADK) involves large amplitude, ligand induced domain motions, involving the opening and the closing of ATP binding domain (LID) and AMP binding domain (NMP) domains, during the repeated catalytic cycle. We discover and analyze an interesting dynamical coupling between the motion of the two domains during the opening, using large scale atomistic molecular dynamics trajectory analysis, covariance analysis, and multidimensional free energy calculations with explicit water. Initially, the LID domain must open by a certain amount before the NMP domain can begin to open. Dynamical correlation map shows interesting cross-peak between LID and NMP domain which suggests the presence of correlated motion between them. This is also reflected in our calculated two-dimensional free energy surface contour diagram which has an interesting elliptic shape, revealing a strong correlation between the opening of the LID domain and that of the NMP domain. Our free energy surface of the LID domain motion is rugged due to interaction with water and the signature of ruggedness is evident in the observed root mean square deviation variation and its fluctuation time correlation functions. We develop a correlated dynamical disorder-type theoretical model to explain the observed dynamic coupling between the motion of the two domains in ADK. Our model correctly reproduces several features of the cross-correlation observed in simulations. (C) 2011 American Institute of Physics. doi:10.1063/1.3516588]

Theory of the non-Fermi-liquid transition point in the two-impurity Kondo model

We present an explicit solution of the problem of two coupled spin-1/2 impurities, interacting with a band of conduction electrons. We obtain an exact effective bosonized Hamiltonian, which is then treated by two different methods (low-energy theory and mean-field approach). Scale invariance is explicitly shown at the quantum critical point. The staggered susceptibility behaves like ln(T(K)/T) at low T, whereas the magnetic susceptibility and [S1.S2] are well behaved at the transition. The divergence of C(T)/T when approaching the transition point is also studied. The non-Fermi-liquid (actually marginal-Fermi-liquid) critical point is shown to arise because of the existence of anomalous correlations, which lead to degeneracies between bosonic and fermionic states of the system. The methods developed in this paper are of interest for studying more physically relevant models, for instance, for high-T(c) cuprates.

A non-cooperative game-theoretic approach to channel assignment in multi-channel multi-radio wireless networks

Channel assignment in multi-channel multi-radio wireless networks poses a significant challenge due to scarcity of number of channels available in the wireless spectrum. Further, additional care has to be taken to consider the interference characteristics of the nodes in the network especially when nodes are in different collision domains. This work views the problem of channel assignment in multi-channel multi-radio networks with multiple collision domains as a non-cooperative game where the objective of the players is to maximize their individual utility by minimizing its interference. Necessary and sufficient conditions are derived for the channel assignment to be a Nash Equilibrium (NE) and efficiency of the NE is analyzed by deriving the lower bound of the price of anarchy of this game. A new fairness measure in multiple collision domain context is proposed and necessary and sufficient conditions for NE outcomes to be fair are derived. The equilibrium conditions are then applied to solve the channel assignment problem by proposing three algorithms, based on perfect/imperfect information, which rely on explicit communication between the players for arriving at an NE. A no-regret learning algorithm known as Freund and Schapire Informed algorithm, which has an additional advantage of low overhead in terms of information exchange, is proposed and its convergence to the stabilizing outcomes is studied. New performance metrics are proposed and extensive simulations are done using Matlab to obtain a thorough understanding of the performance of these algorithms on various topologies with respect to these metrics. It was observed that the algorithms proposed were able to achieve good convergence to NE resulting in efficient channel assignment strategies.

Constitutive modeling of ice in the high strain rate regime

The objective of the present work is to propose a constitutive model for ice by considering the influence of important parameters such as strain rate dependence and pressure sensitivity on the response of the material. In this regard, the constitutive model proposed by Carney et al. (2006) is considered as a starting basis and subsequently modified to incorporate the effect of brittle cracking within a continuum damage mechanics framework. The damage is taken to occur in the form of distributed cracking within the material during impact which is consistent with experimental observations. At the point of failure, the material is assumed to be fluid-like with deviatoric stress almost dropping down to zero. The constitutive model is implemented in a general purpose finite element code using an explicit formulation. Several single element tests under uniaxial tension and compression, as well as biaxial loading are conducted in order to understand the performance of the model. Few large size simulations are also performed to understand the capability of the model to predict brittle damage evolution in un-notched and notched three point bend specimens. The proposed model predicts lower strength under tensile loading as compared to compressive loading which is in tune with experimental observations. Further the model also asserts the strain rate dependency of the strength behavior under both compressive as well as tensile loading, which also corroborates well with experimental results. (C) 2010 Elsevier Ltd. All rights reserved.

Exact-Solutions Of Linear Partial-Differential Equations With Variable-Coefficients

Backlund transformations relating the solutions of linear PDE with variable coefficients to those of PDE with constant coefficients are found, generalizing the study of Varley and Seymour [2]. Auto-Backlund transformations are also determined. To facilitate the generation of new solutions via Backlund transformation, explicit solutions of both classes of the PDE just mentioned are found using invariance properties of these equations and other methods. Some of these solutions are new.

Affine Hall-Littlewood Functions for A(1)((1)) And Some Constant Term Identities of Cherednik-Macdonald-Mehta Type

We study t-analogs of string functions for integrable highest weight representations of the affine Kac-Moody algebra A(1)((1)). We obtain closed form formulas for certain t-string functions of levels 2 and 4. As corollaries, we obtain explicit identities for the corresponding affine Hall-Littlewood functions, as well as higher level generalizations of Cherednik's Macdonald and Macdonald-Mehta constant term identities.

Accelerated gradient based diffuse optical tomographic image reconstruction

Purpose: Fast reconstruction of interior optical parameter distribution using a new approach called Broyden-based model iterative image reconstruction (BMOBIIR) and adjoint Broyden-based MOBIIR (ABMOBIIR) of a tissue and a tissue mimicking phantom from boundary measurement data in diffuse optical tomography (DOT). Methods: DOT is a nonlinear and ill-posed inverse problem. Newton-based MOBIIR algorithm, which is generally used, requires repeated evaluation of the Jacobian which consumes bulk of the computation time for reconstruction. In this study, we propose a Broyden approach-based accelerated scheme for Jacobian computation and it is combined with conjugate gradient scheme (CGS) for fast reconstruction. The method makes explicit use of secant and adjoint information that can be obtained from forward solution of the diffusion equation. This approach reduces the computational time many fold by approximating the system Jacobian successively through low-rank updates. Results: Simulation studies have been carried out with single as well as multiple inhomogeneities. Algorithms are validated using an experimental study carried out on a pork tissue with fat acting as an inhomogeneity. The results obtained through the proposed BMOBIIR and ABMOBIIR approaches are compared with those of Newton-based MOBIIR algorithm. The mean squared error and execution time are used as metrics for comparing the results of reconstruction. Conclusions: We have shown through experimental and simulation studies that Broyden-based MOBIIR and adjoint Broyden-based methods are capable of reconstructing single as well as multiple inhomogeneities in tissue and a tissue-mimicking phantom. Broyden MOBIIR and adjoint Broyden MOBIIR methods are computationally simple and they result in much faster implementations because they avoid direct evaluation of Jacobian. The image reconstructions have been carried out with different initial values using Newton, Broyden, and adjoint Broyden approaches. These algorithms work well when the initial guess is close to the true solution. However, when initial guess is far away from true solution, Newton-based MOBIIR gives better reconstructed images. The proposed methods are found to be stable with noisy measurement data. (C) 2011 American Association of Physicists in Medicine. DOI: 10.1118/1.3531572]

A Flexible Class of Regenerating Codes for Distributed Storage

In the distributed storage setting introduced by Dimakis et al., B units of data are stored across n nodes in the network in such a way that the data can be recovered by connecting to any k nodes. Additionally one can repair a failed node by connecting to any d nodes while downloading at most beta units of data from each node. In this paper, we introduce a flexible framework in which the data can be recovered by connecting to any number of nodes as long as the total amount of data downloaded is at least B. Similarly, regeneration of a failed node is possible if the new node connects to the network using links whose individual capacity is bounded above by beta(max) and whose sum capacity equals or exceeds a predetermined parameter gamma. In this flexible setting, we obtain the cut-set lower bound on the repair bandwidth along with a constructive proof for the existence of codes meeting this bound for all values of the parameters. An explicit code construction is provided which is optimal in certain parameter regimes.

A classification of homogeneous operators in the Cowen-Douglas class

An explicit construction of all the homogeneous holomorphic Hermitian vector bundles over the unit disc D is given. It is shown that every such vector bundle is a direct sum of irreducible ones. Among these irreducible homogeneous holomorphic Hermitian vector bundles over D, the ones corresponding to operators in the Cowen-Douglas class B-n(D) are identified. The classification of homogeneous operators in B-n(D) is completed using an explicit realization of these operators. We also show how the homogeneous operators in B-n(D) split into similarity classes. (C) 2011 Elsevier Inc. All rights reserved.

Exact free-surface flows for shallow-water equations .1. - the incompressible case

A comprehensive exact treatment of free surface flows governed by shallow water equations (in sigma variables) is given. Several new families of exact solutions of the governing PDEs are found and are shown to embed the well-known self-similar or traveling wave solutions which themselves are governed by reduced ODEs. The classes of solutions found here are explicit in contrast to those found earlier in an implicit form. The height of the free surface for each family of solutions is found explicitly. For the traveling or simple wave, the free surface is governed by a nonlinear wave equation, but is arbitrary otherwise. For other types of solutions, the height of the free surface is constant either on lines of constant acceleration or on lines of constant speed; in another case, the free surface is a horizontal plane while the flow underneath is a sine wave. The existence of simple waves on shear flows is analytically proved. The interaction of large amplitude progressive waves with shear flow is also studied.

Exact N-Wave Solutions for the Non-Planar Burgers Equation

An exact representation of N-wave solutions for the non-planar Burgers equation u(t) + uu(x) + 1/2ju/t = 1/2deltau(xx), j = m/n, m < 2n, where m and n are positive integers with no common factors, is given. This solution is asymptotic to the inviscid solution for Absolute value of x < square-root (2Q0 t), where Q0 is a function of the initial lobe area, as lobe Reynolds number tends to infinity, and is also asymptotic to the old age linear solution, as t tends to infinity; the formulae for the lobe Reynolds numbers are shown to have the correct behaviour in these limits. The general results apply to all j = m/n, m < 2n, and are rather involved; explicit results are written out for j = 0, 1, 1/2, 1/3 and 1/4. The case of spherical symmetry j = 2 is found to be 'singular' and the general approach set forth here does not work; an alternative approach for this case gives the large time behaviour in two different time regimes. The results of this study are compared with those of Crighton & Scott (1979).

CM defect and Hilbert functions of monomial curves

In this article we consider a semigroup ring R = KGamma] of a numerical semigroup Gamma and study the Cohen- Macaulayness of the associated graded ring G(Gamma) := gr(m), (R) := circle plus(n is an element of N) m(n)/m(n+1) and the behaviour of the Hilbert function H-R of R. We define a certain (finite) subset B(Gamma) subset of F and prove that G(Gamma) is Cohen-Macaulay if and only if B(Gamma) = empty set. Therefore the subset B(Gamma) is called the Cohen-Macaulay defect of G(Gamma). Further, we prove that if the degree sequence of elements of the standard basis of is non-decreasing, then B(F) = empty set and hence G(Gamma) is Cohen-Macaulay. We consider a class of numerical semigroups Gamma = Sigma(3)(i=0) Nm(i) generated by 4 elements m(0), m(1), m(2), m(3) such that m(1) + m(2) = mo m3-so called ``balanced semigroups''. We study the structure of the Cohen-Macaulay defect B(Gamma) of Gamma and particularly we give an estimate on the cardinality |B(Gamma, r)| for every r is an element of N. We use these estimates to prove that the Hilbert function of R is non-decreasing. Further, we prove that every balanced ``unitary'' semigroup Gamma is ``2-good'' and is not ``1-good'', in particular, in this case, c(r) is not Cohen-Macaulay. We consider a certain special subclass of balanced semigroups Gamma. For this subclass we try to determine the Cohen-Macaulay defect B(Gamma) using the explicit description of the standard basis of Gamma; in particular, we prove that these balanced semigroups are 2-good and determine when exactly G(Gamma) is Cohen-Macaulay. (C) 2011 Published by Elsevier B.V.

Molecular interpretation of the linear relationship between the entropy and the enthalpy of activation of charge transfer reactions in polar liquids

The well-known linear relationship (T?S# =??H# +?, where 1 >? > 0,? > 0) between the entropy (?S#) and the enthalpy (?H#) of activation for reactions in polar liquids is investigated by using a molecular theory. An explicit derivation of this linear relation from first principles is presented for an outersphere charge transfer reaction. The derivation offers microscopic interpretation for the quantities? and?. It has also been possible to make connection with and justify the arguments of Bell put forward many years ago.

Knowledge-based clustering

In the knowledge-based clustering approaches reported in the literature, explicit know ledge, typically in the form of a set of concepts, is used in computing similarity or conceptual cohesiveness between objects and in grouping them. We propose a knowledge-based clustering approach in which the domain knowledge is also used in the pattern representation phase of clustering. We argue that such a knowledge-based pattern representation scheme reduces the complexity of similarity computation and grouping phases. We present a knowledge-based clustering algorithm for grouping hooks in a library.

The sputtering temperature of a cooling cylindrical rod without and with an insulated core in a two-fluid medium

Utilising Jones' method associated with the Wiener-Hopf technique, explicit solutions are obtained for the temperature distributions on the surface of a cylindrical rod without an insulated core as well as that inside a cylindrical rod with an insulated inner core when the rod, in either of the two cases, is allowed to enter, with a uniform speed, into two different layers of fluid with different cooling abilities. Simple expressions are derived for the values of the sputtering temperatures of the rod at the points of entry into the respective layers, assuming the upper layer of the fluid to be of finite depth and the lower of infinite extent. Both the problems are solved through a three-part Wiener-Hopf problem of special type and the numerical results under certain special circumstances are obtained and presented in tabular forms.