Modeling of pair distribution functions for XAFS in disordered systems

A commonly used expression for modeling the XAFS of highly disordered systems is shown to generate substantial systematic errors in the coordination number in many cases of practical interest. This expression is corrected and generalized. Further, a simpler and more flexible model distribution is proposed, and the corresponding XAFS expression is derived. Comparison with experimental and simulated data show that the new expressions are useful in cases of high disorder for which the cumulant expansion loses its utility, and they explicitly account for the k-dependence of the mean free path.     

颗粒流的动力学模型和实验研究进展

首先叙述了颗粒流研究的背景和基本概念,接着概述了颗粒流动力学研究的三种基本数学力学模型:颗粒动理论(kinetic theory)模型、摩擦塑性模型和离散元模拟模型.介绍了它们的基本原理,并分析了各个模型的优缺点和适用范围.随之,对颗粒流的实验研究情况作了简要的介绍,列举了研究中几种常用的试验方法和观测手段,以及观测到的一些典型现象.最后,我们简述了颗粒流研究的主要困难,并提出了某些有待解决的研究课题.      

Condensation and Crystal Nucleation in a Lattice Gas with a Realistic Phase Diagram

We reconsider model II of Orban et al. (J. Chem. Phys. 1968, 49, 1778–1783), a two-dimensional lattice-gas system featuring a crystalline phase and two distinct fluid phases (liquid and vapor). In this system, a particle prevents other particles from occupying sites up to third neighbors on the square lattice, while attracting (with decreasing strength) particles sitting at fourth- or fifth-neighbor sites. To make the model more realistic, we assume a finite repulsion at third-neighbor distance, with the result that a second crystalline phase appears at higher pressures. However, the similarity with real-world substances is only partial: Upon closer inspection, the alleged liquid–vapor transition turns out to be a continuous (albeit sharp) crossover, even near the putative triple point. Closer to the standard picture is instead the freezing transition, as we show by computing the free-energy barrier relative to crystal nucleation from the “liquid”.     

Reduction in Allergenicity and Induction of Oral Tolerance of Glycated Tropomyosin from Crab

Tropomyosin (TM) is an important crustacean (Scylla paramamosain) allergen. This study aimed to assess Maillard-reacted TM (TM-G) induction of allergenic responses with cell and mouse models. We analyzed the difference of sensitization and the ability to induce immune tolerance between TM and TM-G by in vitro and in vivo models, then we compared the relationship between glycation sites of TM-G and epitopes of TM. In the in vitro assay, we discovered that the sensitization of TM-G was lower than TM, and the ability to stimulate mast cell degranulation decreased from 55.07 ± 4.23% to 27.86 ± 3.21%. In the serum of sensitized Balb/c mice, the level of specific IgE produced by TM-G sensitized mice was significantly lower than TM, and the levels of interleukins 4 and interleukins 13 produced by Th2 cells in spleen lymphocytes decreased by 82.35 ± 5.88% and 83.64 ± 9.09%, respectively. In the oral tolerance model, the ratio of Th2/Th1 decreased from 4.05 ± 0.38 to 1.69 ± 0.19. Maillard reaction masked the B cell epitopes of TM and retained some T cell epitopes. Potentially, Maillard reaction products (MRPs) can be used as tolerance inducers for allergen-specific immunotherapy.     

Identification of Pharmacophoric Fragments of DYRK1A Inhibitors Using Machine Learning Classification Models

Dual-specific tyrosine phosphorylation regulated kinase 1 (DYRK1A) has been regarded as a potential therapeutic target of neurodegenerative diseases, and considerable progress has been made in the discovery of DYRK1A inhibitors. Identification of pharmacophoric fragments provides valuable information for structure- and fragment-based design of potent and selective DYRK1A inhibitors. In this study, seven machine learning methods along with five molecular fingerprints were employed to develop qualitative classification models of DYRK1A inhibitors, which were evaluated by cross-validation, test set, and external validation set with four performance indicators of predictive classification accuracy (CA), the area under receiver operating characteristic (AUC), Matthews correlation coefficient (MCC), and balanced accuracy (BA). The PubChem fingerprint-support vector machine model (CA = 0.909, AUC = 0.933, MCC = 0.717, BA = 0.855) and PubChem fingerprint along with the artificial neural model (CA = 0.862, AUC = 0.911, MCC = 0.705, BA = 0.870) were considered as the optimal modes for training set and test set, respectively. A hybrid data balancing method SMOTETL, a combination of synthetic minority over-sampling technique (SMOTE) and Tomek link (TL) algorithms, was applied to explore the impact of balanced learning on the performance of models. Based on the frequency analysis and information gain, pharmacophoric fragments related to DYRK1A inhibition were also identified. All the results will provide theoretical supports and clues for the screening and design of novel DYRK1A inhibitors.     

Polarons in quantum chains with XY exchange and Dzyaloshinsky-Moriya interaction

Excitations of the polaron types are investigated in the spin-1/2 quantum chain with XY exchange and Dzyaloshinsky-Moriya interaction, both coupled to acoustic vibrations of the substrate lattice. The study is carried out via Jordan-Wigner transformation with the help of which the spin chain is mapped onto a chain of spinless fermions. From the resulting effective fermion-lattice Hamiltonian, the discrete equations of motion are derived. These equations are solved in the continuum limit for self-trapped states near the bottom of the fermion spectrum interacting with long-wavelength acoustic lattice modes. The associate polaron solution, which has a pulse shape, is shown to propagate bound to the induced lattice kink distortion by translation along the chain at a constant velocity v. The pair can also experience an additional acceleration ϑ₀ when the free fermion charge is excited above its groundstate. The polaron binding energy is strongly reduced, depending quadratically on the ratio D/J of the Dzyaloshinsky-Moriya interaction strength D to the isotropic XY exchange interaction J. It is also found that polaron parameters depend only on the XY spin-lattice coupling but not on the Dzyaloshinsky-Moriya contribution.     

Diffusion properties of Cu(0 0 1)-c(2 × 2)-Pd surface alloys

Structural and diffusion properties of a Cu(0 0 1)-c(2 × 2)-Pd surface and sub-surface ordered alloys are studied by using interaction potentials obtained from the embedded-atom method. The calculated diffusion energies are in agreement with observed kinetics of the surface alloy formation and confirm stability of the underlayer alloy. Activation energy of planar diffusion of palladium at the initial stage of the alloy formation as well as the activation energy of the overlayer-underlayer diffusion of the Pd atoms are in good agreement with those obtained by the scanning tunneling microscopy and low energy electron diffraction measurements, respectively.     

高斯波束在双负媒质中的传播特性分析

提出了一种基于Drude色散媒质模型的2维TM模时域有限差分法,数值模拟了高斯波束从自由空间垂直入射和斜入射到双负媒质(介电常数和磁导率同时为负)平板后的折射现象,并给出了平板内外的电场强度分布。模拟结果显示：垂直入射时,双负媒质平板对高斯波束具有汇聚作用,通过改变媒质的折射率,可以控制高斯波束通过组合平板的传播时间而不发生衰减;斜入射时,折射波束与入射波束均位于法线的同一侧,高斯波束在双负媒质与空气交界面处发生了负折射。     

Symbolic models for infinite networks of control systems: A compositional approach

This paper presents a compositional framework for the construction of symbolic models for a network composed of a countably infinite number of finite-dimensional discrete-time control subsystems. We refer to such a network as infinite network. The proposed approach is based on the notion of alternating simulation functions. This notion relates a concrete network to its symbolic model with guaranteed mismatch bounds between their output behaviors. We propose a compositional approach to construct a symbolic model for an infinite network, together with an alternating simulation function, by composing symbolic models and alternating simulation functions constructed for subsystems. Assuming that each subsystem is incrementally input-to-state stable and under some small-gain type conditions, we present an algorithm for orderly constructing local symbolic models with properly designed quantization parameters. In this way, the proposed compositional approach can provide us a guideline for constructing an overall symbolic model with any desired approximation accuracy. A compositional controller synthesis scheme is also provided to enforce safety properties on the infinite network in a decentralized fashion. The effectiveness of our result is illustrated through a road traffic network consisting of infinitely many road cells.     

Exact partition functions and correlation functions of multiple Hamiltonian walks on the Manhattan lattice

This is a general and exact study of multiple Hamiltonian walks (HAW) filling the two-dimensional (2D) Manhattan lattice. We generalize the original exact solution for a single HAW by Kasteleyn to a system ofmultiple closed walks, aimed at modeling a polymer melt. In 2D, two basic nonequivalent topological situations are distinguished. (1) the Hamiltonian loops are allrooted andcontractible to a point:adjacent one to another, and, on a torus,homotopic to zero. (2) the loops can encircle one another and, on a torus, canwind around it. Forcase 1, the grand canonical partition function and multiple correlation functions are calculated exactly as those of multiple rooted spanningtrees or of a massive 2Dfree field, critical at zero mass (zero fugacity). The conformally invariant continuum limit on a Manhattantorus is studied in detail. The melt entropy is calculated exactly. We also consider the relevant effect of free boundary conditions. The number of single HAWs on Manhattan lattices with other perimeter shapes (rectangular, Kagomé, triangular, and arbitrary) is studied and related to the spectral theory of the Dirichlet Laplacian. This allows the calculation of exact shape-dependent configuration exponents y. An exact surface critical exponent is obtained. Forcase 2, nested and winding Hamiltonian circuits are allowed. An exact equivalence to thecritical Q-state Potts model exists, whereQ ^1/2 is the walk fugacity. The Hamiltonian system is then always critical (forQ<-4). The exact critical exponents, in infinite numbers, are universal and identical to those of theO(n=Q ^1/2) model in its low-temperature phase, i.e. are those of dense polymers. The exact critical partition functions on the torus are given from conformai invariance theory. These models 1 and 2 yield the two first exactly solved models of polymer melts.