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Comparing interfacial dynamics in protein-protein complexes: an elastic network approach
No full textBackground: The transient, or permanent, association of proteins to form organized complexes is one of the most common mechanisms of regulation of biological processes. Systematic physico-chemical studies of the binding interfaces have previously shown that a key mechanism for the formation/stabilization of dimers is the steric and chemical complementarity of the two semi-interfaces. The role of the fluctuation dynamics at the interface of the interacting subunits, although expectedly important, proved more elusive to characterize. The aim of the present computational study is to gain insight into salient dynamics-based aspects of protein-protein interfaces. Results: The interface dynamics was characterized by means of an elastic network model for 22 representative dimers covering three main interface types. The three groups gather dimers sharing the same interface but with good (type I) or poor (type II) similarity of the overall fold, or dimers sharing only one of the semi-interfaces (type III). The set comprises obligate dimers, which are complexes for which no structural representative of the free form (s) is available. Considerations were accordingly limited to bound and unbound forms of the monomeric subunits of the dimers. We proceeded by first computing the mobility of amino acids at the interface of the bound forms and compare it with the mobility of (i) other surface amino acids (ii) interface amino acids in the unbound forms. In both cases different dynamic patterns were observed across interface types and depending on whether the interface belongs to an obligate or non-obligate complex.
Conclusions: The comparative investigation indicated that the mobility of amino acids at the dimeric interface is generally lower than for other amino acids at the protein surface. The change in interfacial mobility upon removing "in silico" the partner monomer (unbound form) was next found to be correlated with the interface type, size and obligate nature of the complex. In particular, going from the unbound to the bound forms, the interfacial mobility is noticeably reduced for dimers with type I interfaces, while it is largely unchanged for type II ones. The results suggest that these structurally-and biologically-different types of interfaces are stabilized by different balancing mechanisms between enthalpy and conformational entropy
Modeling and experimental observation of parametric processes in segmented KTiOPO4 channel waveguides
No full textThis letter presents a modeling technique for quasiphase-matched parametric processes in segmented channel waveguides and the results of measurements of infrared parametric fluorescence in segmented KTiOPO4 channel waveguides. We demonstrate both theoretically and experimentally a strong dependence of optical parametric oscillator tuning curves and parametric conversion efficiency (parametric gain) on the segmentation duty cycle. We show that the optimum conversion efficiency for parametric interactions in segmented waveguides is obtained for duty cycles greater than 50%. Our results validate the use of an effective continuous waveguide model for segmented channel waveguide calculations over a wide range of wavelengths and duty cycles. (C) 1999 American Institute of Physics. [S0003-6951(99)02812-0]
Reviewed work: İstanbul 1910–2010 kent, yapılı çevre ve mimarlık kültürü sergisi / City, built environment and architectural culture exhibition
No full textFuzzy framework for unsupervised video content characterization and shot classification
No full textIn this paper we present a fuzzy framework for domain-dependent analysis of video sequences. Fuzzy clustering and cluster validation methods are first employed to determine the number of distinct shot patterns and construct a reference model for a program or video domain of interest, using an appropriate training set. This model is subsequently utilized to assign new input data to the available classes by a fuzzy minimum-distance classifier. Additional domain-specific information can be introduced after classification to further enhance the annotations associated with every shot. The main advantage of the approach is that it builds a model for the input video automatically from training data, and thus eliminates the need for extensive user supervision. The fuzzy representation method improves the interpretability of the results, and reduces the number of erroneous classifications, since the continuous class affiliations of each input sample provide a confidence measure for the final assignments. The proposed approach presents a computationally efficient, unsupervised method for building browsable semantic descriptions of video sequences. Specifically, the algorithm can be used to generate various components of an MPEG-7-compliant description. © 2001 SPIE and IS&T
Modelling and analysis of a network organization for cooperation of manufacturers on production capacity
No full textWe present an analytical model to analyze the operation of a productive cooperation network where producers cooperate on production capacity. Producers have limited capacity and have access to subcontractors at a higher cost. A single-unit auction-based allocation mechanism is proposed to allocate an arriving order based on the producers' cost structures and their current loads to maximize the total profit. We show that when the costs are private information, producers are willing to cooperate in order to increase their expected profit. Furthermore, it is shown that there is an equilibrium where producers bid their actual costs. The cooperation can also generate extra profit to cover a part of its operating expenses with this allocation mechanism. A continuous-time Markov chain model is utilized to evaluate the performance of the allocation mechanism where producers submit their myopic best response bids. The cooperation case is also compared with the no-cooperation case and also with the centralized operation of producers
Comparative performance analysis of 100% fill-factor microlens arrays fabricated by various methods
No full textFill-factor of microlens arrays (MLAs) is one of the most important performance criteria of microlens arrays (MLA), especially in imaging applications. Low fill-factor lenses suffer greatly from spurious light and diffraction affects and result in low contrast in a beam steering system. Contrast ratio of low fill-factor circular shaped microlens arrays is nearly one-fourth of that of the system with high fill-factor square shaped microlens arrays. In this study performance of various types of nearly 100% fill-factor spherical MLAs in beam steering applications are compared. Design and fabrication of the MLAs are studied. A new hybrid method for design and fabrication of 100% fill-factor MLAs -by combining refractive-diffractive lenses, is suggested and tested
Nonlinear frequency response of comb-driven microscanners
No full textAccurate prediction of the dynamic behavior of comb-driven MEMS microscanners is important to optimize the actuator and structure design. In this paper, a numerical and an analytical model for the dynamic analysis of comb-driven microscanners under different excitation schemes are presented. The numerical model is based on a second order nonlinear differential equation. Due to the nature of the torque function, this governing equation of motion is a parametric nonlinear ODE, which exhibits hysteretic frequency domain behavior and subharmonic oscillations.. Experimental results and approximate analytical expressions for this nonlinear torque function of the comb-drive are presented. Amplitude and phase relationship between the excitation signal and the resultant oscillations at different excitation frequencies are measured and we show that they are in close agreement with the numerical simulations. Analytical model uses perturbation methods to reach approximate close-form expressions for the dynamic behavior of the device in the first parametric resonance region. It is also utilized to predict the stability regions on the frequency-excitation voltage plane, where the device exhibit hysterical characteristics. Analytical and numerical modeling approaches proposed in this paper provides a simple yet powerful way to analyze the nonlinear frequency response of comb-driven actuators and simplify the design process for a microscanner based system
United we stand: the impact of buying groups on retailer productivity
No full textIn diverse industries, from grocery retailing to health care, retailers join buying groups to achieve better terms with suppliers. The authors track the buying group membership of Europe's largest grocery retailers over a 15-year period and evaluate why some buying groups are better than others in increasing retailer performance and why different members belonging to the same group do not always benefit equally from their membership. They find that, on average, buying groups indeed generate scale advantages for their members: group scale increases group members' productivity and sales and decreases their cost of goods sold. Still, bigger is not always better. Retailers benefit less from buying group scale when the group is more heterogeneous in terms of member size and when it extends its scope across too many markets. Moreover, the smaller a member is within the group and the more it overlaps with fellow members, the less it benefits
Pseudo-supersymmetric quantum mechanics and isospectral pseudo-Hermitian Hamiltonians
No full textWe examine the properties and consequences of pseudo-supersymmetry for quantum systems admitting a pseudo-Hermitian Hamiltonian. We explore the Witten index of pseudo-supersymmetry and show that every pair of diagonalizable (not necessarily Hermitian) Hamiltonians with discrete spectra and real or complex-conjugate pairs of eigenvalues are isospectral and have identical degeneracy structure except perhaps for the zero eigenvalue if and only if they are pseudo-supersymmetric partners. This implies that pseudo-supersymmetry is the basic framework for generating non-Hermitian PT-symmetric and non-P T-symmetric Hamiltonians with a real spectrum via a Darboux transformation, and shows that every diagonalizable Hamiltonian H with a discrete spectrum and real or complex-conjugate pairs of eigenvalues may be factored as H = (LL)-L-# where L is a linear operator with pseudo-adjoint L-#. In particular, this factorization applies to PT-symmetric and Hermitian Hamiltonians. The non-degenerate two-level systems provide a class of Hamiltonians that are pseudo-Hermitian. We demonstrate the implications of our general results for this class in some detail. (C) 2002 Elsevier Science B.V
Dualisation of the symmetric space sigma model with couplings
No full textThe first-order formulation of the G/K symmetric space sigma model of the scalar cosets of the supergravity theories is discussed when there is coupling of (m - 1)-form matter fields. The Lie superalgebra which enables the dualized coset formulation is constructed for a general scalar coset G/K with matter coupling where G is a non-compact real form of a semi-simple Lie group and K is its maximal compact subgroup. (C) 2004 Elsevier B.V. All rights reserved