C80-C90富勒烯结构与稳定性的理论研究

本文结合分子力学、半经验PM3和密度泛函(DFT)B3LYP方法对C80-C90的非分离五元环异构体和所有分离五元环异构体进行了理论研究。计算得到的B3LYP／6-31G的最低能量结构与文献报道一致。而且,对于C80-C90,并不存在一个特别稳定的非分离五元环异构体,分离五元环规则仍适用于富勒烯C80-C90。     

Relative stability of ordered phases in bcc Cu-Al-Zn

The relative stability of the short range ordered and different long range ordered structures in body centered cubic Cu-Al-Zn is studied by means of the Cluster Variation Method in the Irregular Tetrahedron approximation (IT-CVM). The energetic parameters (constant pair interchange energies for first and second neighbor pairs) used in our calculations have been extracted from experimental order-disorder transition temperatures. It is shown that the use of constant pair interchange energies allows accurate reproduction of the experimental transition temperatures in the binary subsystems Cu-Al and Cu-Zn. Several isothermal sections of the ternary system at temperatures between 600 and 900 K have been calculated. The two-phase field for compositions around Cu₃Al in the ternary system was determined: It was found that such region extends to around 15 at.% Zn in the pseudo-binary Cu_0.76-0.5x-Al_0.24-0.5x-Zn_x.     

论(Cl_2BN_3)_n(n=1-4)簇合物

用密度泛函论B3LYP/6-311+G*法,计算(C1_2BN_3)_n(n=1-4)簇合物的结构和性质.发现,多聚体(C1_2BN_3)_n(n=2-4)的优化构型原来是由不同子体系的叠氮基α-N和B原子相连而形成的环状结构。几何参数的比较分析还发现N_α-B、N_α-N_β、N_β-N_Υ和B-Cl的键长与聚合度密切相关,环状构型中B-N_α-B键角总比N_α-B-N_α大。同时计算所有优化构型的振动频率,将其IR谱归类.通过热力学计算,发现簇合物的稳定性为3A>3B;4A>4B.由焓变可知,从单体形成二聚体于热力学不利,而形成最稳定三聚体和四聚体的温度分别达800K和500K仍是有利的.     

Antipole tree indexing to support range search and k-nearest neighbor search in metric spaces

Range and k-nearest neighbor searching are core problems in pattern recognition. Given a database S of objects in a metric space M and a query object q in M, in a range searching problem the goal is to find the objects of S within some threshold distance to g, whereas in a k-nearest neighbor searching problem, the k elements of S closest to q must be produced. These problems can obviously be solved with a linear number of distance calculations, by comparing the query object against every object in the database. However, the goal is to solve such problems much faster. We combine and extend ideas from the M-tree, the multivantage point structure, and the FQ-tree to create a new structure in the "bisector tree" class, called the Antipole tree. Bisection is based on the proximity to an "Antipole" pair of elements generated by a suitable linear randomized tournament. The final winners a, b of such a tournament is far enough apart to approximate the diameter of the splitting set. If dist(a, b) is larger than the chosen cluster diameter threshold, then the cluster is split. The proposed data structure is an indexing scheme suitable for (exact and approximate) best match searching on generic metric spaces. The Antipole tree outperforms by a factor of approximately two existing structures such as list of clusters, M-trees, and others and, in many cases, it achieves better clustering properties.     

基于特征点的抗几何攻击零水印

提出了最小偏离度的概念,根据IPR库中的特征点信息和待测图像自身的特征点信息分别构造Delaunay三角网,并以此计算两张三角网中三角形的最小偏离度值。若该值低于预先设定的阈值,则可以确认待测图像的版权归属。实验表明,该算法对各种几何攻击甚至是组合几何攻击均具有较强的鲁棒性。     

Barnase thermal titration via molecular dynamics simulations: detection of early denaturation sites

The thermal stability of barnase has been studied using constant pressure and temperature (CPT) molecular dynamics at different temperatures. Barnase X-ray coordinates were obtained from the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB code:1rnb). Simulations were performed at 285, 295, 300, 335, 345, and 395 K in explicit water under periodic boundary conditions for 280 ps. For each simulation, conformations were saved every 0.2 ps. Root mean square deviation (RMSD) values were calculated relative to the starting structure at 300 K and at time t = 0. Root mean square fluctuation (RMSF) values were calculated relative to the average structure obtained from the 300K simulation. Both root mean square deviation and fluctuation analysis indicated the presence of discrete regions of hyper-sensitivity along the barnase polypeptide chain. These regions exhibited spikes in flexibility prior to any global structural changes. The specific changes in barnase backbone flexibility are accompanied by increased phi/psi angle fluctuations. These results suggest the presence of early denaturation sites or denaturation nuclei whose local structure is disrupted prior to global structure disruption. Identification of denaturation nuclei suggests that appropriate amino acid replacements at these sites may lead to the design and development of more stable barnase mutants. This strategy of identifying denaturation nuclei in protein structures may represent a first step in the design of more stable protein structures.     

Computing the relative gas-phase populations of C60 and C70: beyond the traditional delta H(fo),298 scale

Computations and experiments have shown that the relative heat of formation (i.e., the heat of formation per carbon atom) of C70 is lower than of C60. Moreover, various computations suggest that this is actually a general trend among fullerene cages. The relationship is particularly important for gas-phase fullerenes. Experiments have shown that C60 is typically more populated than C70 when produced in high-temperature gas-phase synthesis. It is not immediately obvious how to reconcile those two terms, or whether the relative heats of formation and the relative populations are in conflict or in agreement. This article deals with this problem, treating it as a general task of relative stabilities of gas-phase clusters of different dimensions (i.e., nonisomeric clusters) under different types of thermodynamic equilibria. The results are then applied to C60 and C70 and point out that the conventional standard pressure of 1 atm is considerably different from actual fullerene-synthesis conditions. Apparently, we should expect considerably lower cluster pressures in carbon-arc synthesis. At 1 atm, C70 is more populated than C60, but at the conditions of a saturated carbon vapor the stability order is reversed in favor of C60 so that an agreement with experiment is obtained already within the thermodynamic treatment. The pressure effects are modeled using the MNDO, AM1, PM3, and SAM1 quantum-chemical semi-empirical methods as well as the available experimental data. The computations consistently show that, if the pressure effects are considered, C60 becomes more populated than C70. Relationships of the thermodynamic treatment to more sophisticated but impractical kinetic analysis are also discussed.     

Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations

The brevity of molecular dynamics simulations often limits their utility in developing and evaluating structural models of proteins. The duration of simulations can be increased greatly using discrete molecular dynamics (DMD). However, the trade off is that coarse graining, implicit solvent, and other time-saving procedures reduce the accuracy of DMD simulations. Here we address some of these issues by comparing results of DMD and conventional all atom MD simulations on proteins of known structure and misfolded proteins. DMD simulations were performed at a range of temperatures to identify a 'physiological' temperature for DMD that mimicked molecular motions of conventional MD simulations at 310K. We also compared results obtained with a new implicit solvent model developed here based on Miyazawa-Jernigan interaction pair potential to those obtained with a previously used model based on Kyte-Doolittle hydropathy scale. We compared DMD and all atom molecular dynamics with explicit water by simulating both correctly and incorrectly folded structures, and monomeric and dimeric α β-barrel structures to analyze the ability of these procedures to distinguish between good and bad models. Deviations from the correct structures were substantially greater with DMD, as would be expected from coarse-graining and longer simulation time. Deviations were smallest for β-strands and greatest for coiled loops. Structures of the incorrectly folded models were very poorly preserved during the DMD simulations; but both methods were able to distinguish between the correct and the incorrect structures based on differences in the magnitudes of the root mean squared deviation (RMSD) from the starting conformation.     

Ambient Temperature Effects on Paired Associate Learning∗

Male college students learned and later recalled a paired associate list (word-number pairs) in one of five air (dry bulb) temperatures (52, 62, 72. 82, or 92°F), with wet bulb temperature held constant. They learned and recalled best at 72°F, with performance declining at successively lower and higher air temperatures. In a second experiment, dry and wet bulb temperatures were varied from 52-82°F, in 5° increments, with relative humidity held constant. Other male students learned equally well in these effective temperatures. It was concluded that rote verbal learning may not be impaired even by quite low air temperatures, if relative humidity is controlled appropriately.     

Gallium arsenide suspended microheater for MEMS sensor arrays

This work describes the design, simulation, fabrication and characterization of a TiN/Pt microheater prepared on a GaAs micromechanical structure as a prospective device for micro-electro-mechanical system (MEMS) sensor arrays. Electro-thermal simulation was employed to verify the properties of the designed microstructure, which confirmed achievement of the operating temperatures in the range from 470 to 600 K with a heating power less than 25 mW. The average temperature gradient in the active area does not exceed 0.6 K/μm. Fabrication of GaAs suspended membranes was demonstrated, realized in two steps by combination of surface and bulk micromachining. Development and characterization of a microheater on a GaAs membrane is described. The mechanical stability of the heated multilayer membrane structure was tested and satisfactory mechanical stability of the hotplate was confirmed. The power consumption at an operating temperature of approximately 550 K is about 30 mW which is in good agreement with the value of about 22 mW obtained from electro-thermal simulation. The achieved thermal resistance value is 8.43 K/mW.     

Evaluating the phase stability of binary titanium alloy Ti-X (X = Mo,Nb, Al,and Zr) using first-principles calculations and a Debye model

To realize bottom-up design of alloys based on theoretical calculations, the thermodynamic stabilities of phases in Ti binary alloys were estimated by a combination of density functional theory calculations for the internal enthalpy energy, the Bragg-Williams approximation for the mixing entropy contribution, the Debye model for the vibrational free energy, and the Sommerfeld model for the electronic excitation entropy. The special quasirandom structure (SQS) model was used to describe the disordered distribution of the alloying element in the solid solution state. We focused on Ti–Mo, Ti–Nb, Ti–Al, and Ti–Zr binary alloys, which have different phases, such as the α phase in the hexagonal close-packed (hcp) structure and the β phase in the body-centered cubic (bcc) structure, depending on the temperature and alloying element fraction. The elastic constants, bulk modulus, and Poisson's ratios were calculated using a strain energy method. Excitations from the vibrational contribution to the quasi-harmonic Debye approximation were added to the 0 K free energy originally derived from ab initio calculations. The effect of temperature up to 1000 K on phase stability was analyzed. Furthermore, to compare phase stabilities, the free energies of formation were calculated using the ground states of the constituent phases as references. The calculated elastic property indicated the mechanical instability of most bcc Ti–Al and bcc Ti–Zr alloys, hcp Ti–Mo and hcp Ti–Nb at high fraction range. The SQS supercell models showed good agreement in elastic constant, bulk modulus, and Poisson's ratio compared to the previous experimental and theoretical results. Free energy results showed that Mo and Nb are β-phase stabilizers, Al is an α-phase stabilizer, and Zr is a neutral element. As the fraction of the alloying element changed, stabilizing or destabilizing effects were observed under different temperatures. Moreover, the linear relationship between the filling of the d band and phase stability was identified in low temperature range. For the β phase, Mo had a stronger stabilizing effect than Nb; both Mo and Nb destabilized the α phase at low temperatures, whereas high temperatures increased the stability of the α phase and the temperature effect became more significant than the element effect. In the examined temperature range, the α phase Ti–Al alloys were stable at all Al fractions, where the thermal effect was negligible. All the α Ti–Zr alloys in this study had similar stabilities to their constituent phases (hcp Ti and hcp Zr) over a wide temperature range.     

On the stability of linear composite systems with delays

It is shown that the stability of composite feedback control systems with delays both in the state and the input can be checked from the stabilities of the individual isolated subsystems, if the composite system matrix has a certain new structure called the GKK-structure; and if the numerators and denominators of the determinants of the overall system transfer matrix and of the isolated system transfer matrices contain some term of a certain expansion called the principal term. The GKK-structure includes diagonal dominance, the Hadamard (M-matrix) structure, and normality as special cases.     

Computation of thermodynamic mixing parameters for isostructural,binary crystalline solutions using solvus experimental data

FORTRAN IV subroutines are presented for calculating the mixing parameters of the two-parameter Margules, van Laar, and quasichemical solution models. For isostructural, binary crystalline solutions the mixing parameters of these models are calculated using experimental data on the compositions and equilibration temperatures (K) of the two phases in binary “solvus-pairs”. However, the equations used in the calculations are different for each model, and computational methods range from direct calculation (Margules and van Laar models), to solution of two simultaneous nonlinear equations (quasichemical model). Most of the subroutines have been written so that they can be incorporated easily into a user's linear least-squares regression program to compute equations relating a set of values for a parameter to temperature, or temperature and pressure.Crystal structure plays an important role in the calculation of mixing parameters for the three solution models. For solvi among phases of different structure, mixing-parameter values should be calculated using not only the compositions and equilibration temperatures of the two phases in solvus-pairs, but also the values for the differences in free energies of the crystal structures in the standard state. Some thermodynamic theory of mutual solubility among binary crystalline phases of like and unlike structure will be described in detail.     

多溴苊化合物的分子结构和热力学性质

多溴苊是一类潜在的有机污染物。本文采用密度泛函理论在B3LYP/6-311G**水平上优化35个多溴苊化合物的分子几何结构,并获得它们在理想气态的一些热力学性质的数值,研究这些性质与取代的溴原子数目和位置的关系,根据各异构体的标准生成Gibbs自由能的相对大小,求得它们的热力学稳定性顺序。计算结果表明:在大部分多溴苊分子中,除4个氢原子外的其他原子在同一平面上。多溴苊最稳定及最不稳定异构体的ΔfH及ΔfG,都随Br原子数目增加而逐渐增加。溴原子数目相同的多溴苊异构体的ΔfH和ΔfG与溴原子的取代位置有很大的关系,其相对稳定性主要由分子内的处在不同六元环上的邻近Br...Br核排斥作用决定。所有多溴苊化合物在热力学上都比其母体化合物苊相对较难形成。     

The stability of transition phases in Fe-Mn-Si based alloys

Various transition phases, featured by nH(n>2), are possible in the Fe-Mn-Si based alloys. Using the Chou-Model, their Gibbs free energies are calculated and their stabilities are ranked. The thermodynamical parameters of those structures were deduced from those of fcc and hcp structures which have been established based on the stacking fault energy (SFE) and the SF density. The results indicate that at the temperatures below thermal equilibrium (To) the stability of transition phases is in an order of 2H(hcp)>9H(9R)>4H>6H>fcc and in the reverse order when the temperature is above To, consistent with the experimental observations. In the case that an external stress field exists, the strain energy plays an important role on the phase stabilities and, therefore, their order would be modified.     

C40H2各种可能异构体芳香性的研究

用键共振能(BRE)和拓扑共振能(TRE)方法,对由从富勒烯C_(40)(D_(5d))产生的富勒烯氢化物C_(40)H_2H所有可能异构体的芳香性进行了研究。研究了氢原子加成位置和芳香性之间的关系。计算结果表明,氢原子的加成位置与C_(40)(D_(5d))中各键的键共振能直接有关。在C_(40)(D_(5d))中C3类碳原子具有最大的反应活性。大部分C_(40)H_2异构体的芳香性高于C_(40)。用拓扑共振能方法得到的C_(40)H_2异构体的稳定性顺序与AM1和PM3半经验方法得到的稳定性顺序是一致的,用键共振能和拓扑共振能方法同样地能预测富勒烯氢化物的稳定性。     

Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study

DNA within the living cells experiences a diverse range of temperature, ranging from freezing condition to hot spring water. How the structure, the mechanical properties of DNA, and the solvation dynamics around DNA changes with the temperature is important to understand the functionality of DNA under those acute temperature conditions. In that notion, we have carried out molecular dynamics simulations of a DNA oligomer, containing TATA-box sequence for three different temperatures (250 K, 300 K and 350 K). We observed that the structure of the DNA, in terms of backbone torsion angles, sugar pucker, base pair parameters, and base pair step parameters, did not show any unusual properties within the studied range of temperatures, but significant structural alteration was noticed between B_I and B_II forms at higher temperature. As expected, the flexibility of the DNA, in terms of the torsional rigidity and the bending rigidity is highly temperature dependent, confirming that flexibility increases with increase in temperature. Additionally, the groove widths of the studied DNA showed temperature sensitivity, specifically, the major groove width decreases and the minor groove width increases, respectively, with the increase in temperature. We observed that at higher temperature, water around both the major and the minor groove of the DNA is less structured. However, the water dynamics around the minor groove of the DNA is more restricted as compared to the water around the major groove throughout the studied range of temperatures, without any anomalous behavior.     

Study on component temperatures inversion using satellite remotely sensed data

Because of the low spatial resolution of MODIS data, it is important to decompose mixed pixels to retrieve component temperatures using thermal infrared bands. Grasslands with different coverage conditions are prominent in the area under study. Because of the simple vegetation structure, radiation is less influenced by vegetation shade. If the internal structure of the component parts of the mixed pixel is ignored, the total radiation emitted by the mixed pixel is approximately the sum of the radiation emitted by each component part of the pixel, weighted according to the percentage area of each component part. Vegetation/soil component temperatures based on the sub‐pixel scale are inverted using a constrained optimization algorithm—the genetic algorithm. The study not only broadens the application of the linear spectral mixing model but also develops a practical method for component temperatures retrieval from MODIS satellite data. The results provide more precise parameters for estimation of land surface energy balance and evapotranspiration.     

An Index Structure for Data Mining and Clustering

In this paper we present an index structure, called MetricMap, that takes a set of objects and a distance metric and then maps those objects to a k-dimensional space in such a way that the distances among objects are approximately preserved. The index structure is a useful tool for clustering and visualization in data-intensive applications, because it replaces expensive distance calculations by sum-of-square calculations. This can make clustering in large databases with expensive distance metrics practical. We compare the index structure with another data mining index structure, FastMap, recently proposed by Faloutsos and Lin, according to two criteria: relative error and clustering accuracy. For relative error, we show that (i) FastMap gives a lower relative error than MetricMap for Euclidean distances, (ii) MetricMap gives a lower relative error than FastMap for non-Euclidean distances (i.e., general distance metrics), and (iii) combining the two reduces the error yet further. A similar result is obtained when comparing the accuracy of clustering. These results hold for different data sizes. The main qualitative conclusion is that these two index structures capture complementary information about distance metrics and therefore can be used together to great benefit. The net effect is that multi-day computations can be done in minutes. Received February 1998 / Revised July 1999 / Accepted in revised form September 1999     

基于节点的线状图骨架提取算法研究

文中提出一种重视保留节点形位信息的线状图骨架提取算法,首先提出了截面序列的概念,光栅线索两侧的两个与线素走向近似垂直的轮廓点连线构成了一个截面,一组连续斋构成了一个截面序列,由不属于截面序列的轮廓点可计算出节点位置及拓扑结构关系;最后将通过同一节点并满足光滑性条件的截面序列归并为同源线索,并对其提取中心线得到的线状图骨架。