面心立方晶体外延膜沉积生长中失配位错的结构与形成过程

用分子动力学方法对5%负失配条件下面心立方晶体铝薄膜的原子沉积外延生长进行了三维模拟.铝原子间的相互作用采用嵌入原子法(EAM)多体势计算.模拟结果再现了失配位错的形成现象.分析表明，失配位错在形成之初即呈现为Shockley扩展位错，即由两个伯格斯矢量为〈211〉/6的部分位错和其间的堆垛层错组成，两个部分位错的间距、即层错宽度为1.8 nm,与理论计算结果一致；外延晶体薄膜沉积生长中，位错对会发生滑移，但其间距保持稳定.进一步观察发现，该扩展位错产生于一种类似于“局部熔融-重结晶”的表层局部无序紊乱- 关键词： 失配位错 外延生长 薄膜 分子动力学 铝     

FFT-based algorithms for the string matching with mismatches problem

The string matching with mismatches problem requires finding the Hamming distance between a pattern P of length m and every length m substring of text T with length n. Fischer and Paterson's FFT-based algorithm solves the problem without error in O(σnlogm), where σ is the size of the alphabet Σ [SIAM–AMS Proc. 7 (1973) 113–125]. However, this in the worst case reduces to O(nmlogm). Atallah, Chyzak and Dumas used the idea of randomly mapping the letters of the alphabet to complex roots of unity to estimate the score vector in time O(nlogm) [Algorithmica 29 (2001) 468–486]. We show that the algorithm's score variance can be substantially lowered by using a bijective mapping, and specifically to zero in the case of binary and ternary alphabets. This result is extended via alphabet remappings to deterministically solve the string matching with mismatches problem with a constant factor of 2 improvement over Fischer–Paterson's method.     

Bit-parallel approximate string matching algorithms with transposition

Using bit-parallelism has resulted in fast and practical algorithms for approximate string matching under Levenshtein edit distance, which permits a single edit operation to insert, delete or substitute a character. Depending on the parameters of the search, currently the fastest non-filtering algorithms in practice are the O(km/wn) algorithm of Wu and Manber, the O((k+2)(m−k)/wn) algorithm of Baeza-Yates and Navarro, and the O(m/wn) algorithm of Myers, where m is the pattern length, n is the text length, k is the error threshold and w is the computer word size. In this paper we discuss a uniform way of modifying each of these algorithms to permit also a fourth type of edit operation: transposing two adjacent characters in the pattern. This type of edit distance is also known as Damerau edit distance. In the end we also present an experimental comparison of the resulting algorithms.     

Cu~+、Ag~+、Au~+与乙硫醇的气相化学反应

利用激光溅射 分子束的技术 ,结合反射飞行时间质谱计 ,研究了Cu+、Ag+、Au+与乙硫醇的气相化学反应。结果显示这三种金属离子与 (CH3 CH2 SH) n 反应形成一系列团簇离子M+(CH3 CH2 SH) n,且团簇离子尺寸不一样。Ag+、Au+与乙硫醇的反应还生成了 (CH3 CH2 SH) +n ,由此推测Cu+、Ag+、Au+与乙硫醇团簇的反应存在两种通道 ,一种通道是生成M+(CH3 CH2 SH) n,另一种是生成 (CH3 CH2 SH) +n 。Cu+、Au+与乙硫醇的反应还生成了M+(H2 S) (M =Cu、Au) ,但是实验中没有观察到Ag+(H2 S) ,理论计算表明Ag+(H2 S)很不稳定。另外 ,分析产物离子M+(CH3 CH2 SH) n 的强度发现 ,n =1～ 2之间存在明显的强度突变现象     

基于MMD算法的HMM参数重估计的矩阵表示

本文提出的MMD算法用于提高模型区别错误信息和正确信息的能力．利用该算法在对模型的参数进行重估计时．涉及到复杂的目标函数的梯度运算．击运用矩阵运算使得梯度运算变得简单明了，因此本文给出了MMD算法下的HMM参数重估计的矩阵表示形式并给出了证明．     

Rotational analysis ofA 1Π-X 1Σ+ bands of P14N and P15N: Perturbatio studies in theA 1Π state

The ultraviolet band systemsA ¹Π-X ¹Σ⁺ of P¹⁴N and P¹⁵N were excited in an electrodeless tube containing traces of phosphorus specpure nitrogen and neon using a microwave discharge (2450 MHz). Bands of the isotopic species, P¹⁵N, were obtained using¹⁵N₂ enriched to 95.5%. Rotational analyses of eleven bands of P¹⁴N and sixteen bands of P¹⁵N were carried out. Three perturbing statese ³Σ⁻,d ³Δ andb ³Π, arising from the lower valence configurations were identified from the observed perturbations in thev′=0–4 levels of theA ¹Π state. Deperturbation studies led to the determination of molecular constants of the perturbing states. Vibrational assignments of the perturbing states were made from isotope shift studies.     

Molecular dynamics and information on possible sites of interaction of intramyocellular metabolites in vivo from resolved dipolar couplings in localized H NMR spectra

Proton NMR resonances of the endogenous metabolites creatine and phosphocreatine ((P)Cr), taurine (Tau), and carnosine (Cs, β-alanyl-l-histidine) were studied with regard to residual dipolar couplings and molecular mobility. We present an analysis of the direct ¹H–¹H interaction that provides information on motional reorientation of subgroups in these molecules in vivo. For this purpose, localized ¹H NMR experiments were performed on m. gastrocnemius of healthy volunteers using a 1.5-T clinical whole-body MR scanner. We evaluated the observable dipolar coupling strength SD₀ (S = order parameter) of the (P)Cr-methyl triplet and the Tau-methylene doublet by means of the apparent line splitting. These were compared to the dipolar coupling strength of the (P)Cr-methylene doublet. In contrast to the aliphatic protons of (P)Cr and Tau, the aromatic H2 (δ = 8 ppm) and H4 (δ = 7 ppm) protons of the imidazole ring of Cs exhibit second-order spectra at 1.5 T. This effect is the consequence of incomplete transition from Zeeman to Paschen-Back regime and allows a determination of SD₀ from H2 and H4 of Cs as an alternative to evaluating the multiplet splitting which can be measured directly in high-resolution ¹H NMR spectra. Experimental data showed striking differences in the mobility of the metabolites when the dipolar coupling constant D₀ (calculated with the internuclear distance known from molecular geometry in the case of complete absence of molecular dynamics and motion) is used for comparison. The aliphatic signals involve very small order parameters S ≈ (1.4 − 3) × 10⁻⁴ indicating rapid reorientation of the corresponding subgroups in these metabolites. In contrast, analysis of the Cs resonances yielded S ≈ (113 − 137) × 10⁻⁴. Thus, the immobilization of the Cs imidazole ring owing to an anisotropic cellular substructure in human m. gastrocnemius is much more effective than for (P)Cr and Tau subgroups. Furthermore, ¹H NMR experiments on aqueous model solutions of histidine and N-acetyl-l-aspartate (NAA) enabled the assignment of an additional signal component at δ = 8 ppm of Cs in vivo to the amide group at the peptide bond. The visibility of this proton could result from hydrogen bonding which would agree with the anticipated stronger motional restriction of Cs. Referring to the observation that all dipolar-coupled multiplets resolved in localized in vivo ¹H NMR spectra of human m. gastrocnemius collapse simultaneously when the fibre structure is tilted towards the magic angle (θ ≈ 55°), a common model for molecular confinement in muscle tissue is proposed on the basis of an interaction of the studied metabolites with myocellular membrane phospholipids.     

Biopolymers for biocatalysis: Structure and catalytic mechanism of hydroxynitrile lyases

Hydroxynitrile lyases catalyze the reversible cleavage of α-cyanohydrins to yield hydrocyanic acid and the corresponding aldehyde or ketone. Besides its biological interest, this class of enzymes is also of relevance in industrial biocatalysis for the enantioselective condensation of HCN with a variety of aldehydes and ketones. Several distinctly different types of hydroxynitrile lyases (HNLs) are known, which must have originated through convergent evolution from different ancestral proteins. Three-dimensional structural data are known for three classes of hydroxynitrile lyases. Insights into the reaction mechanisms emerged from a combination of structural, enzyme kinetic, spectroscopic, and molecular modeling data. For all three types of HNLs, mechanisms involving acid–base catalysis were proposed. In members belonging to the α,β-hydrolase type, the amino acid residues of the catalytic triad presumably act as general acid/base, whereas for flavine adenine dinucleotide (FAD)-dependent HNLs a single histidine residue fulfills this function. In the third type of HNL—which is related to carboxypeptidase—acid–base catalysis involves the carboxylate of the C-terminal residue. The catalytic relevance of a positive electrostatic potential in the active site was suggested in some of the mechanistic proposals. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 479–486, 2004