Structural dissimilarity sampling with dynamically self‐guiding selection

Structural dissimilarity sampling (SDS) has been proposed as an enhanced conformational sampling method for reproducing the structural transitions of a given protein. SDS consists of cycles of two steps: (1) Selections of initial structures with structural dissimilarities by referring to a measure. (2) Conformational resampling by restarting short‐time molecular dynamics (MD) simulations from the initial structures. In the present study, an efficient measure is proposed as a dynamically self‐guiding selection to accelerate the structural transitions from a reactant state to a product state as an extension to the original SDS. In the extended SDS, the inner product (IP ) between the reactant and the snapshots generated by short‐time MD simulations are evaluated and ranked according to the IP s at every cycle. Then, the snapshots with low IP s are selected as initial structures for the short‐time MD simulations. This scheme enables one to choose dissimilar and distant initial structures from the reactant, and thus the initial structures dynamically head towards the product, promoting structural transitions from the reactant. To confirm the conformational sampling efficiency, the extended SDS was applied to maltodextrin binding protein (MBP), and we successfully reproduced the structural transition from the open to closed states with submicrosecond‐order simulation times. However, a conventional long‐time MD simulation failed to reproduce the same structural transition. We also compared the performance with that obtained by the ordinary SDS and other sampling techniques that have been developed by us to characterize the possible utility of the extended SDS for actual applications. © 2017 Wiley Periodicals, Inc.     

Adaptive‐numerical‐bias metadynamics

A metadynamics scheme is presented in which the free energy surface is filled with progressively adding adaptive biasing potentials, obtained from the accumulated probability distribution of the collective variables. Instead of adding Gaussians with assigned height and width in conventional metadynamics method, here we add a more realistic adaptive biasing potential to the Hamiltonian of the system. The shape of the adaptive biasing potential is adjusted on the fly by sampling over the visited states. As the top of the barrier is approached, the biasing potentials become wider. This decreases the problem of trapping the system in the niches, introduced by the addition of Gaussians of fixed height in metadynamics. Our results for the free energy profiles of three test systems show that this method is more accurate and converges more quickly than the conventional metadynamics, and is quite comparable (in accuracy and convergence rate) with the well‐tempered metadynamics method. © 2017 Wiley Periodicals, Inc.     

On Conditional Independence,Mixing, and Association

Abstract

This is a follow-up to a recent article by Prakasa Rao [15 Prakasa Rao , B.L.S. 2008 . Conditional independence, conditional mixing and association . Annals of the Institute of Statistical Mathematics AISM , doi: 10.1007/S10463-007-0152-2 . [Google Scholar]] on conditional independence, conditional mixing and conditional association. The purpose of this article is to derive rigorously some results following from conditioning. To this end, a brief review is presented of the concepts of conditional independence of events, classes of events, and random variables, followed by a conditional version of a factorization theorem, as well as a first installment of some basic results. Next, the concepts of conditional covariance and variance are introduced, and a second installment of basic results follows. Furthermore, a certain representation of the covariance is established in detail, followed by a conditional version of it, as well as a generalization. The concept of the conditional characteristic function is also recalled, and a certain inequality is established. Finally, the concept of conditional positive (negative) quadrant dependence, as well as that of conditional positive (negative) association are introduced. The article concludes with the derivation of the conditional versions of some known results, regarding positive (negative) association. This is done anticipating that conditional association (and also conditional mixing) will prove to be of significant applicability.     

Modeling host-parasitoid interactions with correlated events

In this paper, we present a host-parasitoid model with correlated events. We apply a block-structured state-dependent (BSDE) approach that provides a methodological tool to model state-dependent Markovian transitions operating in the presence of phases. A particularly appealing feature of the resulting BSDE host-parasitoid model is that it allows us to deal with non-exponential distributional assumptions on a host birth, a parasitoid death, and parasitism, but keeping the dimensionality of the underlying block-structured Markov chain tractable. Numerical examples are presented to illustrate the effects of the correlation structure on the expected extinction times and the extinction probabilities.     

Students’ Reasoning About One-Object Stochastic Phenomena in an ICT-Environment

This paper focuses on the different ways in which students in lower secondary school (14–16 year olds) experience compound random events, presented to them in the form of combined junctions. A carefully designed ICT environment was developed enabling the students to interact with different representations of such structures. Data for the analysis was gathered from two interview sessions. The analysis of the interaction is based on constructivist principles on learning; i.e. we adopted a student-oriented perspective, taking into consideration the different ways students try to make sense of chance encounters. Our results show how some students give priority to geometrical and physical concerns, and we discuss how seeking causal explanations of random phenomena may have encouraged this. With respect to numerically oriented models a division strategy appears to stand out as the preferred one.     

一个风险模型的研究

研究了索赔到达过程为平稳无后效流,保单到达过程为平稳无后效流,并带扩散扰动项的盈余过程．讨论了该盈余过程的马尔科夫性和鞅性．然后用鞅方法得到其破产概率的表达式及其相应的Lundberg不等式．     

二参数有限随机事件流

本文讨论二参数无后效有限随机事件流的鞅性和各种二参数Ｍａｒｋｏｖ性。     

基于CSA-SQP的预测控制器参数整定研究

针对预测控制器参数整定困难, 提出了一种基于克隆选择和序列二次规划的预测控制器参数整定算法, 建立了一个基于免疫原理和序列二次规划算法进行控制器参数整定的机制, 并给出了参数整定问题中的抗原、抗体及亲和力的定义. 在此基础上, 针对系统的不确定性干扰, 构造了基于事件触发的参数调整框架. 最后, 将算法应用于仿真实验, 通过与设定值控制结果的对比, 证明所提出的预测控制器参数整定方法是有效的.     

高能强子在铁中的衰减

利用强子探测效率高的厚型甘巴拉山铁乳胶室,观测了能量大于4TeV强子流的衰减长度.分别对无伴随的单个强子、ΣE_γ>500TeV、100TeV≤ΣE_γ≤500TeV和30TeV≤ΣE_γ<100TeV的族事例中的强子作了测量. 初步结果表明,四种情况的衰减长度是有差异的,对此作了讨论.     

Extreme fluxes in solar energetic particle events: Methodological and physical limitations

In this study, all available data on the largest solar proton events (SPEs), or extreme solar energetic particle (SEP) events, for the period from 1561 up to now are analyzed. Under consideration are the observational, methodological and physical problems of energy-spectrum presentation for SEP fluxes (fluences) near the Earth's orbit. Special attention is paid to the study of the distribution function for extreme fluences of SEPs by their sizes. The authors present advances in at least three aspects: 1) a form of the distribution function that was previously obtained from the data for three cycles of solar activity has been completely confirmed by the data for 41 solar cycles; 2) early estimates of extremely large fluences in the past have been critically revised, and their values were found to be overestimated; and 3) extremely large SEP fluxes are shown to obey a probabilistic distribution, so the concept of an “upper limit flux” does not carry any strict physical sense although it serves as an important empirical restriction. SEP fluxes may only be characterized by the relative probabilities of their appearance, and there is a sharp break in the spectrum in the range of large fluences (or low probabilities). It is emphasized that modern observational data and methods of investigation do not allow, for the present, the precise resolution of the problem of the spectrum break or the estimation of the maximum potentialities of solar accelerator(s). This limitation considerably restricts the extrapolation of the obtained results to the past and future for application to the epochs with different levels of solar activity.