Enhancements of the Gaussian network model in describing nucleotide residue fluctuations for RNA

Gaussian network model (GNM) is an efficient method to investigate the structural dynamics of biomolecules. However, the application of GNM on RNAs is not as good as that on proteins, and there is still room to improve the model. In this study, two novel approaches, named the weighted GNM (wGNM) and the force-constant-decayed GNM (fcdGNM), were proposed to enhance the performance of ENM in investigating the structural dynamics of RNAs. In wGNM, the force constant for each spring is weighted by the number of interacting heavy atom pairs between two nucleotides. In fcdGNM, all the pairwise nucleotides were connected by springs and the force constant decayed exponentially with the separate distance of the nucleotide pairs. The performance of these two proposed models was evaluated by using a non-redundant RNA structure database composed of 51 RNA molecules. The calculation results show that both the proposed models outperform the conventional GNM in reproducing the experimental B-factors of RNA structures. Compared with the conventional GNM, the Pearson correlation coefficient between the predicted and experimental B-factors was improved by 9.85% and 6.76% for wGNM and fcdGNM, respectively. Our studies provide two candidate methods for better revealing the dynamical properties encoded in RNA structures.     

Mechanism of defect evolution in H+ and He+ implanted InP

The defect evolution in InP with the 75 keV H⁺ and 115 keV He⁺ implantation at room temperature after subsequent annealing has been investigated in detail. With the same ion implantation fluence, the He⁺ implantation caused much broader damage distribution accompanied by much higher out-of-plane strain with respect to the H⁺ implanted InP. After annealing, the H⁺ implanted InP did not show any blistering or exfoliation on the surface even at the high fluence and the H₂ molecules were stored in the heterogeneously oriented platelet defects. However, the He molecules were stored into the large bubbles which relaxed toward the free surface, creating blisters at the high fluence.     

基于PCA-BP神经网络的光谱消光法颗粒粒径反演算法研究

光谱消光法广泛应用于颗粒粒径测量领域,在利用光谱消光法对颗粒粒径进行反演的过程中,由于颗粒的消光系数存在理论复杂、计算繁琐、收敛速度慢以及求解不稳定等问题,很大程度上影响了整个反演过程的快速性和准确性。且在众多波长的消光数据中,存在较多重复冗余的信息,也很大程度上增加了反演算法的时间。针对光谱消光法粒径反演算法计算繁琐、反演效率低的问题,提出了基于主成分分析（PCA）和BP神经网络的光谱消光颗粒粒径分析方法。基于Mie散射理论对不同粒径、不同波长下的光谱消光值进行了仿真计算,通过对光谱消光数据集的主成分分析及各个波长综合载荷系数的计算,实现了最优特征波长的选取,利用降维后的光谱消光数据训练了PCA-BP神经网络模型,并利用该网络模型计算了粒径颗粒分布。通过仿真计算,比较了PCA-BP神经网络模型与传统的BP神经网络模型的预测精度,并分析了波长数目对两种神经网络模型预测结果的影响。针对训练得到的PCA-BP神经网络模型开展光谱消光法粒径参数反演算法的验证实验,搭建了光谱消光法颗粒粒径参数测量实验系统,测量了粒径范围在0.5～9.7 μm内的6种不同粒径参数的聚苯乙烯标准颗粒。仿真和实验结果表明：基于主成分分析方法可确定各个波长向量之间的相关性,利用综合载荷系数选取最优特征波长对应的消光值对整体的光谱数据具有较好的代表性,可实现光谱数据的降维。相比传统的BP神经网络模型,基于PCA-BP神经网络模型的颗粒粒径分布的分析方法预测精度更高,对于较分散颗粒系的分布参数的预测有更加明显的优势。而且,被选取的波长数较少时,PCA-BP神经网络模型依然有较高的预测精度。利用训练好的PCA-BP神经网络模型对颗粒粒径参数进行实验验证,预测结果可瞬时输出,颗粒粒径分布误差在5%以内,验证了该算法的可行性。     

基于精确时间协议的HL-2M装置定时同步网络研究

基于HL-2M装置对时序精度的要求,参考ITER的设计方案,设计了基于精确时间协议(PTP)的HL-2M分布式时间通讯网络,使HL-2M装置的时钟同步和事件触发的精度从微秒级提高到亚微秒级,最终优于100ns.     

复杂网络上的意见动力学对谣言传播的影响

通过在SIR(susceptible-infected-recovered)模型中引入抑制者对谣言的辟谣机制研究了在线社交网络上的意见动力学对谣言传播的影响.在这一模型中,节点可以与自身的邻居组成1个群,传播者可以通过该群传播信息,抑制者也可以在此群中对信息发表意见进行辟谣.辟谣机制在降低未知者对于谣言的接受概率的同时也可以促使传播者向抑制者转变.本文采用ER(Erd?s-Rényi)随机网络、无标度网络以及真实的社交网络研究了抑制者的沉默概率对于谣言传播范围的影响.首先发现,谣言传播的过程以传播者的峰值为界可以分为两个阶段,即谣言自由传播的前期以及抑制者和传播者互相制衡的后期;其次,谣言的传播会随着抑制者的沉默概率的增大而突然暴发.在谣言暴发阈值之下,沉默概率的增大不会导致谣言传播范围显著增大,这是由于未知者在感知到谣言并转变为传播者后又迅速转变为抑制者;而当沉默概率达到谣言暴发阈值时,抑制者将不能控制传播者对谣言的传播从而导致抑制者的降低和谣言的暴发;最后,无标度上的谣言自由传播的前期阶段比随机网络持续的时间更短,从而使无标度上的谣言更难以暴发.本文的模型综合考虑了意见动力学和谣言传播的相互作用,更加真实地模拟了真实世界社交网络中的谣言传播过程.为谣言传播的控制和干预提供了一些有用的思路和见解.     

Network-Based Driving Force of National Economic Development: A Social Capital Perspective

Network science has been widely applied in theoretical and empirical studies of global value chain (GVC), and many related articles have emerged, forming many more mature and complete analytical frameworks. Among them, the GVC accounting method based on complex network theory is different from the mainstream economics in both research angle and content. In this paper, we build up global industrial value chain network (GIVCN) models based on World Input–Output Database, introduce the theoretical framework of Social Capital, and define the network-based indicators with economic meanings. Second, we follow the econometric framework to analyze the hypothesis and test whether it is true. Finally, we study how the three types of capital constituted by these indicators interact with each other, and discuss their impact on the social capital (economic development level, i.e., GDP). The results prove that the structural capital (industrial status) has a positive impact on the social capital; the relational capital (industrial correlation) has a positive impact on both social capital and structural capital; the cognitive capital (industrial structure) has a small impact on the social capital, structural capital, and relational capital.     

(Semi-)Automatically Parsing Private Protocols for In-Vehicle ECU Communications

In-vehicle electronic control unit (ECU) communications generally count on private protocols (defined by the manufacturers) under controller area network (CAN) specifications. Parsing the private protocols for a particular vehicle model would be of great significance in testing the vehicle’s resistance to various attacks, as well as in designing efficient intrusion detection and prevention systems (IDPS) for the vehicle. This paper proposes a suite of methods for parsing ECU private protocols on in-vehicle CAN network. These methods include an algorithm for parsing discrete variables (encoded in a discrete manner, e.g., gear state), an algorithm for parsing continuous variables (encoded in a continuous manner, e.g., vehicle speed), and a parsing method based on upper-layer protocols (e.g., OBD and UDS). Extensive verifications have been performed on five different brands of automobiles (including an electric vehicle) to demonstrate the universality and the correctness of these parsing algorithms. Some parsing tips and experiences are also presented. Our continuous-variables parsing algorithm could run in a semi-automatic manner and the parsing algorithm from upper-layer protocols could execute in a completely automatic manner. One might view the results obtained by our parsing algorithms as an important indicator of penetration testing on in-vehicle CAN network.     

Minimum Message Length in Hybrid ARMA and LSTM Model Forecasting

Modeling and analysis of time series are important in applications including economics, engineering, environmental science and social science. Selecting the best time series model with accurate parameters in forecasting is a challenging objective for scientists and academic researchers. Hybrid models combining neural networks and traditional Autoregressive Moving Average (ARMA) models are being used to improve the accuracy of modeling and forecasting time series. Most of the existing time series models are selected by information-theoretic approaches, such as AIC, BIC, and HQ. This paper revisits a model selection technique based on Minimum Message Length (MML) and investigates its use in hybrid time series analysis. MML is a Bayesian information-theoretic approach and has been used in selecting the best ARMA model. We utilize the long short-term memory (LSTM) approach to construct a hybrid ARMA-LSTM model and show that MML performs better than AIC, BIC, and HQ in selecting the model—both in the traditional ARMA models (without LSTM) and with hybrid ARMA-LSTM models. These results held on simulated data and both real-world datasets that we considered.We also develop a simple MML ARIMA model.     

Whether the Support Region of Three-Bit Uniform Quantizer Has a Strong Impact on Post-Training Quantization for MNIST Dataset?

Driven by the need for the compression of weights in neural networks (NNs), which is especially beneficial for edge devices with a constrained resource, and by the need to utilize the simplest possible quantization model, in this paper, we study the performance of three-bit post-training uniform quantization. The goal is to put various choices of the key parameter of the quantizer in question (support region threshold) in one place and provide a detailed overview of this choice’s impact on the performance of post-training quantization for the MNIST dataset. Specifically, we analyze whether it is possible to preserve the accuracy of the two NN models (MLP and CNN) to a great extent with the very simple three-bit uniform quantizer, regardless of the choice of the key parameter. Moreover, our goal is to answer the question of whether it is of the utmost importance in post-training three-bit uniform quantization, as it is in quantization, to determine the optimal support region threshold value of the quantizer to achieve some predefined accuracy of the quantized neural network (QNN). The results show that the choice of the support region threshold value of the three-bit uniform quantizer does not have such a strong impact on the accuracy of the QNNs, which is not the case with two-bit uniform post-training quantization, when applied in MLP for the same classification task. Accordingly, one can anticipate that due to this special property, the post-training quantization model in question can be greatly exploited.     

Airy加速光束的局域空间频率及其在光束设计中的应用

Airy加速光束是近年来备受关注的一种新型无衍射光束. 它所具有的自由加速、无衍射及自恢复特性使其在光学微操纵、非线性光学、 电子加速等诸多领域显示出重要的应用价值. 因此, 如何方便高效地生成加速光束成为近年来的一个热点研究内容. 本文对Airy加速光束复振幅分布的空间振荡特性进行了分析, 建立了利用局域空间频率描述其加速特性的理论. 提出了利用零点坐标计算加速光束局域空间频率的方法, 通过非线性拟合给出了可以精确描述Airy光束局域空间频率的解析公式; 确定了加速光束的局域空间频率函数与加速轨迹之间的定量关系, 给出了由给定加速轨迹计算相应的局域空间频率以及加速光束的纯相位函数的一种简单计算方法. 将上述分析结果用于设计产生具有给定加速轨迹的加速光束所需的相位函数, 成功求出了能够产生圆弧形加速轨迹的新型加速光束的纯相位函数的解析表达式. 基于该相位函数设计的纯相位衍射光学元件的模拟衍射结果证明了上述方法的可行性. 关键词： 衍射光学 加速光束 局域空间频率