Application of torsion angle molecular dynamics for efficient sampling of protein conformations

We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A "projection" approach (Katritch et al. J Comput Chem 2003, 24, 254-265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone phi/psi and side chain chi1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency.     

态射的广义Moore—Penrose逆

本文定义了态射的广义Ｍｏｏｒｅ－Ｐｅｎｒｏｓｅ逆，给出了它存在的一些充要条件，确定了它的一些表达式，推广了关于态射的Ｍｏｏｒｅ－Ｐｅｎｒｏｓｅ逆的相应结果。     

On the construction of periodic solutions of kaplan-yorke type for some differential delay equations

In this paper we point out the main idea to yield periodic solutions of Kaplan-Yorke type of differential delay equations. Some new sufficient conditions for the existence of Kaplan-Yorke type periodic solutions have been given. Many interesting examples are also disscused.     

Likelihood Inference under Generalized Hybrid Censoring Scheme with Comp eting Risks

Statistical inference is developed for the analysis of generalized type-II hybrid censoring data under exponential competing risks model. In order to solve the problem that approximate methods make unsatisfactory performances in the case of small sample size, we establish the exact conditional distributions of estimators for parameters by conditional moment generating function(CMGF). Furthermore, confidence intervals(CIs) are constructed by exact distributions, approximate distributions as well as bootstrap method respectively, and their performances are evaluated by Monte Carlo simulations. And finally, a real data set is analyzed to illustrate all the methods developed here.     

Strong Convergence Theorems for the Generalized Viscosity Implicit Rules of Asymptotically Nonexpansive Mappings in the Intermediate Sense in Hilbert Spaces

Abstract

The aim of this paper is to introduce the generalized viscosity implicit rules of one asymptotically nonexpansive mapping in the intermediate sense in Hilbert spaces. We obtain some strong convergence theorems under certain assumptions imposed on the parameters. We also give a numerical example to support our main results. The results obtained in this paper improve and extend many recent ones in this culture.     

Fisher Information of Free-Electron Landau States

An electron in a constant magnetic field has energy levels, known as the Landau levels. One can obtain the corresponding radial wavefunction of free-electron Landau states in cylindrical polar coordinates. However, this system has not been explored so far in terms of an information-theoretical viewpoint. Here, we focus on Fisher information associated with these Landau states specified by the two quantum numbers. Fisher information provides a useful measure of the electronic structure in quantum systems, such as hydrogen-like atoms and under some potentials. By numerically evaluating the generalized Laguerre polynomials in the radial densities, we report that Fisher information increases linearly with the principal quantum number that specifies energy levels, but decreases monotonically with the azimuthal quantum number m. We also present relative Fisher information of the Landau states against the reference density with m=0, which is proportional to the principal quantum number. We compare it with the case when the lowest Landau level state is set as the reference.     

Intensity‐based estimation of extreme loss event probability and value at risk

We develop a methodology for the estimation of extreme loss event probability and the value at risk, which takes into account both the magnitudes and the intensity of the extreme losses. Specifically, the extreme loss magnitudes are modeled with a generalized Pareto distribution, whereas their intensity is captured by an autoregressive conditional duration model, a type of self‐exciting point process. This allows for an explicit interaction between the magnitude of the past losses and the intensity of future extreme losses. The intensity is further used in the estimation of extreme loss event probability. The method is illustrated and backtested on 10 assets and compared with the established and baseline methods. The results show that our method outperforms the baseline methods, competes with an established method, and provides additional insight and interpretation into the prediction of extreme loss event probability. Copyright © 2012 John Wiley & Sons, Ltd.     

Generalized vector variational-like inequalities and nonsmooth vector optimization problems

In this article, we establish some relationships between a solution of generalized vector variational-like inequalities and an efficient solution or a weakly efficient solution to the nonsmooth vector optimization problem under the assumptions of pseudoinvexity or invariant pseudomonotonicity. Our results extend and improve the corresponding results in the literature.     

Nonexistence of global solutions to new ordinary differential inequality and applications to nonlineardispersive equations

A new ordinary differential inequality without global solutions is proposed. Comparison with similar differential inequalities in the well‐known concavity method is performed. As an application, finite time blow up of the solutions to nonlinear Klein–Gordon equation and generalized Boussinesq equation is proven. The initial energy is arbitrary high positive. The structural conditions on the initial data generalize the assumptions used in the literature for the time being. Copyright © 2015 John Wiley & Sons, Ltd.