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Akinori Kidera - One of the best experts on this subject based on the ideXlab platform.
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linear Response Theory in dihedral angle space for protein structural change upon ligand binding
Journal of Computational Chemistry, 2009Co-Authors: Satoshi Omori, Mitsunori Ikeguchi, Sotaro Fuchigami, Akinori KideraAbstract:Coupling between proteins motion and ligand binding can be well explained by the linear Response Theory (Ikeguchi, M.; Ueno, J.; Sato, M.; Kidera, A. Phys Rev Lett 2005, 94, 078102.), in which the structural change is treated as a Response to ligand binding. The prediction accuracy of structural change upon ligand binding has been improved by replacing the variables in the linear Response Theory from Cartesian coordinates to dihedral angles. The dihedral angle Theory can more accurately describe the rotational motions of protein domains compared with the Cartesian Theory, which tends to shift the coordinate to the tangential direction of the domain rotation. In this study, the ligand-bound form of Ferric-binding protein was predicted from its ligand-free form using the dihedral linear Response Theory. When the variance-covariance matrix, the key component in the linear Response Theory, was derived by linear conversion from Cartesian coordinates to dihedral angles, the dihedral linear Response Theory gave an improvement in the prediction. Therefore, the description of the rotational motion by dihedral angles is crucial for accurate prediction of protein structural change.
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protein structural change upon ligand binding linear Response Theory
Physical Review Letters, 2005Co-Authors: Mitsunori Ikeguchi, Jiro Ueno, Miwa Sato, Akinori KideraAbstract:A simple formula based on linear Response Theory is proposed to explain and predict the structural change of proteins upon ligand binding. By regarding ligand binding as an external perturbation, the structural change as a Response is described by atomic fluctuations in the ligand-free form and the protein-ligand interactions. The results for three protein systems of various sizes are consistent with the observations in the crystal structures, confirming the validity of the linear relationship between the equilibrium fluctuations and the structural change upon ligand binding.
Sandip Sinharay - One of the best experts on this subject based on the ideXlab platform.
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assessment of fit of item Response Theory models used in large scale educational survey assessments
Large-scale Assessments in Education, 2016Co-Authors: Peter W Van Rijn, Sandip Sinharay, Shelby J Haberman, Matthew S JohnsonAbstract:Latent regression models are used for score-reporting purposes in large-scale educational survey assessments such as the National Assessment of Educational Progress (NAEP) and Trends in International Mathematics and Science Study (TIMSS). One component of these models is based on item Response Theory. While there exists some research on assessment of fit of item Response Theory models in the context of large-scale assessments, there is a scope of further research on the topic. We suggest two types of residuals to assess the fit of item Response Theory models in the context of large-scale assessments. The Type I error rates and power of the residuals are computed from simulated data. The residuals are computed using data from four NAEP assessments. Misfit was found for all data sets for both types of residuals, but the practical significance of the misfit was minimal.
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posterior predictive assessment of item Response Theory models
Applied Psychological Measurement, 2006Co-Authors: Sandip Sinharay, M. Johnson, Hal S. SternAbstract:Model checking in item Response Theory (IRT) is an underdeveloped area. There is no universally accepted tool for checking IRT models. The posterior predictive model-checking method is a popular Bayesian model-checking tool because it has intuitive appeal, is simple to apply, has a strong theoretical basis, and can provide graphical or numerical evidence about model misfit. An important issue with the application of the posterior predictive model-checking method is the choice of a discrepancy measure (which plays a role like that of a test statistic in traditional hypothesis tests). This article examines the performance of a number of discrepancy measures for assessing different aspects of fit of the common IRT models and makes specific recommendations about what measures are most useful in assessing model fit. Graphical summaries of model-checking results are demonstrated to provide useful insights about model fit.
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posterior predictive model checking for multidimensionality in item Response Theory
Posterior predictive model checking for multidimensionality in item response theory, 2006Co-Authors: Roy Levy, Robert J Mislevy, Sandip SinharayAbstract:If data exhibit multidimensionality, key conditional independence assumptions of unidimensional models do not hold. The current work pursues posterior predictive model checking, a flexible family of model-checking procedures, as a tool for criticizing models due to unaccounted for dimensions in the context of item Response Theory. Factors hypothesized to influence dimensionality and dimensionality assessment are couched in conditional covariance Theory and conveyed via geometric representations of multidimensionality. A simulation study investigates the performance of the model-checking tools for dichotomous observables. Key findings include support for the hypothesized effects of the manipulated factors with regard to their influence on dimensionality assessment and the superiority of certain discrepancy measures for conducting posterior predictive model checking for dimensionality assessment.
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assessing fit of unidimensional item Response Theory models using a bayesian approach
Journal of Educational Measurement, 2005Co-Authors: Sandip SinharayAbstract:Even though Bayesian estimation has recently become quite popular in item Response Theory (IRT), there is a lack of works on model checking from a Bayesian perspective. This paper applies the posterior predictive model checking (PPMC) method (Guttman, 1967; Rubin, 1984), a popular Bayesian model checking tool, to a number of real applications of unidimensional IRT models. The applications demonstrate how to exploit the flexibility of the posterior predictive checks to meet the need of the researcher. This paper also examines practical consequences of misfit, an area often ignored in educational measurement literature while assessing model fit.
S Prunet - One of the best experts on this subject based on the ideXlab platform.
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linear Response Theory and damped modes of stellar clusters
Monthly Notices of the Royal Astronomical Society, 2021Co-Authors: Jeanbaptiste Fouvry, S PrunetAbstract:Because all stars contribute to its gravitational potential, stellar clusters amplify perturbations collectively. In the limit of small fluctuations, this is described through linear Response Theory, via the so-called Response matrix. While the evaluation of this matrix is somewhat straightforward for unstable modes (i.e. with a positive growth rate), it requires a careful analytic continuation for damped modes (i.e. with a negative growth rate). We present a generic method to perform such a calculation in spherically symmetric stellar clusters. When applied to an isotropic isochrone cluster, we recover the presence of a low-frequency weakly damped $\ell = 1$ mode. We finally use a set of direct $N$-body simulations to test explicitly this prediction through the statistics of the correlated random walk undergone by a cluster's density centre.
Anna I Krylov - One of the best experts on this subject based on the ideXlab platform.
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the orbital picture of the first dipole hyperpolarizability from many body Response Theory
Journal of Chemical Physics, 2021Co-Authors: Kaushik D Nanda, Anna I KrylovAbstract:We present an approach for obtaining a molecular orbital picture of the first dipole hyperpolarizability (β) from correlated many-body electronic structure methods. Ab initio calculations of β rely on quadratic Response Theory, which recasts the sum-over-all-states expression of β into a closed-form expression by calculating a handful of first- and second-order Response states; for resonantly enhanced β, damped Response Theory is used. These Response states are then used to construct second-order Response reduced one-particle density matrices (1PDMs), which, upon visualization in terms of natural orbitals (NOs), facilitate a rigorous and black-box mapping of the underlying electronic structure with β. We explain the interpretation of different components of the Response 1PDMs and the corresponding NOs within both the undamped and damped Response Theory framework. We illustrate the utility of this new tool by deconstructing β for cis-difluoroethene, para-nitroaniline, and hemibonded OH· + H2O complex, computed within the framework of coupled-cluster singles and doubles Response Theory, in terms of the underlying Response 1PDMs and NOs for a range of frequencies.
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a simple molecular orbital picture of rixs distilled from many body damped Response Theory
Journal of Chemical Physics, 2020Co-Authors: Kaushik D Nanda, Anna I KrylovAbstract:Ab initio calculations of resonant inelastic x-ray scattering (RIXS) often rely on damped Response Theory, which prevents the divergence of Response solutions in the resonant regime. Within the damped Response Theory formalism, RIXS moments are expressed as the sum over all electronic states of the system [sum-over-states (SOS) expressions]. By invoking resonance arguments, this expression can be reduced to a few terms, an approximation commonly exploited for the interpretation of computed cross sections. We present an alternative approach: a rigorous formalism for deriving a simple molecular orbital picture of the RIXS process from many-body calculations using the damped Response Theory. In practical implementations, the SOS expressions of RIXS moments are recast in terms of matrix elements between the zero-order wave functions and first-order frequency-dependent Response wave functions of the initial and final states such that the RIXS moments can be evaluated using complex Response one-particle transition density matrices (1PTDMs). Visualization of these 1PTDMs connects the RIXS process with the changes in electronic density. We demonstrate that the real and imaginary components of the Response 1PTDMs can be interpreted as contributions of the undamped off-resonance and damped near-resonance SOS terms, respectively. By analyzing these 1PTDMs in terms of natural transition orbitals, we derive a rigorous, black-box mapping of the RIXS process into a molecular orbital picture. We illustrate the utility of the new tool by analyzing RIXS transitions in the OH radical, benzene, para-nitroaniline, and 4-amino-4′-nitrostilbene. These examples highlight the significance of both the near-resonance and off-resonance channels.
Mitsunori Ikeguchi - One of the best experts on this subject based on the ideXlab platform.
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linear Response Theory in dihedral angle space for protein structural change upon ligand binding
Journal of Computational Chemistry, 2009Co-Authors: Satoshi Omori, Mitsunori Ikeguchi, Sotaro Fuchigami, Akinori KideraAbstract:Coupling between proteins motion and ligand binding can be well explained by the linear Response Theory (Ikeguchi, M.; Ueno, J.; Sato, M.; Kidera, A. Phys Rev Lett 2005, 94, 078102.), in which the structural change is treated as a Response to ligand binding. The prediction accuracy of structural change upon ligand binding has been improved by replacing the variables in the linear Response Theory from Cartesian coordinates to dihedral angles. The dihedral angle Theory can more accurately describe the rotational motions of protein domains compared with the Cartesian Theory, which tends to shift the coordinate to the tangential direction of the domain rotation. In this study, the ligand-bound form of Ferric-binding protein was predicted from its ligand-free form using the dihedral linear Response Theory. When the variance-covariance matrix, the key component in the linear Response Theory, was derived by linear conversion from Cartesian coordinates to dihedral angles, the dihedral linear Response Theory gave an improvement in the prediction. Therefore, the description of the rotational motion by dihedral angles is crucial for accurate prediction of protein structural change.
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protein structural change upon ligand binding linear Response Theory
Physical Review Letters, 2005Co-Authors: Mitsunori Ikeguchi, Jiro Ueno, Miwa Sato, Akinori KideraAbstract:A simple formula based on linear Response Theory is proposed to explain and predict the structural change of proteins upon ligand binding. By regarding ligand binding as an external perturbation, the structural change as a Response is described by atomic fluctuations in the ligand-free form and the protein-ligand interactions. The results for three protein systems of various sizes are consistent with the observations in the crystal structures, confirming the validity of the linear relationship between the equilibrium fluctuations and the structural change upon ligand binding.
