Inferring topological features of proteins from amino acid residue networks

Topological properties of native folds are obtained from statistical analysis of 160 low homology proteins covering the four structural classes. This is done analyzing one, two and three-vertex joint distribution of quantities related to the corresponding network of amino acid residues. Emphasis on the amino acid residue hydrophobicity leads to the definition of their center of mass as vertices in this contact network model with interactions represented by edges. The network analysis helps us to interpret experimental results such as hydrophobic scales and fraction of buried accessible surface area in terms of the network connectivity. Moreover, those networks show assortative mixing by degree. To explore the vertex-type dependent correlations, we build a network of hydrophobic and polar vertices. This procedure presents the wiring diagram of the topological structure of globular proteins leading to the following attachment probabilities between hydrophobic–hydrophobic 0.424(5), hydrophobic-polar 0.419(2) and polar–polar 0.157(3) residues.     

Interface control of emergent ferroic order in Ruddlesden-Popper Sr(n+1)Ti(n)O(3n+1)

We discovered from first principles an unusual polar state in the low n Sr(n+1)Ti(n)O(3n+1) Ruddlesden-Popper (RP) layered perovskites in which ferroelectricity is nearly degenerate with antiferroelectricity, a relatively rare form of ferroic order. We show that epitaxial strain plays a key role in tuning the "perpendicular coherence length" of the ferroelectric mode, and does not induce ferroelectricity in these low-dimensional RP materials as is well known to occur in SrTiO(3). These systems present an opportunity to manipulate the coherence length of a ferroic distortion in a controlled way, without disorder or a free surface.     

Effect of Sb substitution on the superconductivity of Bi2(Ca,Sr) n+1Cu n O4n+2 (n=1, 2 and 3) systems

Effect of incorporation of Sb in place of Bi in the bismuth cuprate superconductors has been examined. The nominal compositions studied are MCa_1·5Sr_1·5Cu₂O_8+δ and MCa₂Sr₂Cu₃O_10+δ, whereM=Bi_2−x Sb _x or Bi_1·5−x Sb _x Pb_0·5. Different preparative routes such as the ceramic method, the matrix route as well as the melt route were employed to prepare the materials. No indication of either Sb entering the lattice or enhancement ofT _c is noted from resistivity, magnetic susceptibility and microwave absorption measurements. Communication No. 162 from Materials Research Centre.     

Pressure-tuned collapse of the Mott-like state in Ca(n+1)Ru(n)O(3n+1) (n=1,2): Raman spectroscopic studies

We report a Raman scattering study of the pressure-induced collapse of the Mott-like phases of Ca3Ru2O7 (T(N)=56 K) and Ca2RuO4 (T(N)=110 K). The pressure dependence of the phonon and two-magnon excitations in these materials indicate (i) a T approximately 0 pressure-induced collapse of the antiferromagnetic (AF) insulating phase above P(*) approximately 55 kbar in Ca3Ru2O7 and P(*) approximately 5-10 kbar in Ca2RuO4, (ii) a remarkable insensitivity of the exchange interaction to pressure in both systems, and (iii) evidence for persistent AF correlations above the critical pressure of Ca2RuO4, suggestive of phase separation involving AF insulator and ferromagnetic metal phases.     

Crystal chemistry of the Tl2−xBa2Ca n Cu n+1O2n+6 (n=0, 1, 2) high-T c superconductors

We report on a comparative crystal chemical study of the Tl_2–xBa₂Ca _n Cu _n+1O_2n+6(n=0, 1, 2) high-T _c superconductors. Superconducting properties were determined by DC-conductivity and-susceptibility measurements. An X-ray diffraction analysis reveals the nonstoichiometry of the compounds as a link between structural and superconducting behavior. A comparison of the different structures gives evidence that T1 deficiency in the TlO double layers increases with increasingn; this deficiency causes apparent Cu valences larger than 2+in the superconducting phases thus maintaining the charge balance. By extracting appropriate chemical formulas and performing a bond strength calculation we obtained the mixed-valent oxidation state of copper for the superconducting tetragonal phases as being 2.17+(n=0), 2.25+(n=1) and 2.31+(n=2) respectively; for the non-superconducting orthorhombic phase Tl_2–xBa₂CuO_6–y a Cu valence of about 2+is suggested.     

空穴掺杂铱氧化物Srn+1IrnO3n+1 (n=1,2)的角分辨光电子能谱研究

近年来, 与铜氧化物高温超导体具有类似电子结构的5d 轨道 Ruddlesden-Popper 类型铱氧化物由于体系中库伦排斥和自旋轨道耦合之间的合作效应被人们广泛探究. 其中, 金属绝缘体转变的关键影响因素是该方向的核心研究问题, 该结果对推进掺杂莫特绝缘体体系的研究具有重要作用. 因为铱氧化物与铜氧化物在单能带哈伯德模型的次 近 邻 跃 迁 项 具 有 不 同 符 号, 因 此 空 穴 掺 杂 铱 氧 化 物 类 比 电 子 掺 杂 铜 氧 化 物. 我 们 将 空 穴 掺 杂Ruddlesden-Popper 类型铱氧 化 物 系 统 依 据 几 种 不 同 的 掺 杂 元 素 进 行 分 类, 分 别 介 绍 其 角 分 辨 光 电 子 能 谱(ARPES) 探测到的电子结构, 对其中金属绝缘体转变类型进行了总结, 并对该领域中的未来研究方向做出了展望.     

Charge states of atoms in the lattices of the high-temperature superconductors Tl2Ba2Ca n−1CunO2n+4 and Bi2Sr2Ca n−1CunO2n+4

To determine the charges of atoms in the lattices of the compounds Tl₂Ba₂Ca _n?1Cu_nO_2n+4 and Bi₂Sr₂Ca _n?1Cu_nO_2n+4 (n=1,2,3), the parameters of the electric field gradient tensor at the copper sites of the indicated lattices were found by emission Mössbauer spectroscopy on the isotopes ⁶¹Cu(⁶¹Ni) and ⁶⁷Cu(⁶⁷Zn), and a calculation of these parameters was performed in the point-charge approximation. A comparison of the resulting values and the published data on ⁶³Cu nuclear quadrupole resonance showed that agreement between the experimental and computed values of the parameters obtains for models in which the holes resulting from a reduction in the valence of some of the thallium (bismuth) atoms are localized predominantly at oxygen sites located in the same plane as the copper atoms (for the compounds Tl₂Ba₂Ca₂Cu₃O₁₀ and Bi_1.6Pb_0.4Sr₂Ca₂Cu₃O₁₀—at oxygen sites in the same plane as the Cu(2) atoms).     

The Embedding of Quantum Algebra U(gl(n+1)) in Irreducible Representations of U(gl(n+1))

Using a formula derived by Jimbo, we express the generators of U(gl(n+1)), the q-analogue of U(gl(n+1)) in an irreducible representation with Gel'fand basis, as functions of the generators of U(gl(n+1)).     

器件参数对GaN基n~+-GaN/i-Al_x Ga_(1-x)N/n~+-GaN结构紫外和红外双色探测器中紫外响应的影响

研究了AlGaN层参数对GaN基n+-GaN/i-AlxGa1-xN/n+-GaN结构紫外和红外双色探测器中紫外响应的影响规律及物理机制.模拟计算发现:降低AlGaN层本底载流子浓度会增加器件的量子效率,当本底载流子浓度不能进一步降低时,可以通过减小AlGaN层的厚度以保证器件的量子效率.在材料生长和器件工艺过程中都应减少界面态.外加较小的反向偏压能大幅度提高紫外量子效率,分析表明,GaN/AlGaN/GaN形成的两个背靠背、方向相反的异质结电场是出现这些现象的根本原因.在实际器件设计中,应该根据需要调节各结构参数,以保证器件的量子效率.     

SO q (n+1,n−1) as a real form of SO q (2n,ℂ)

Quantum pseudo-orthogonal groups SO _q (n+1,n–1) are defined as real forms of quantum orthogonal groups SO _q (n+1,n–1) by means of a suitable antilinear involution. In particular, the casen=2 gives a quantized Lorentz group.     

SL(n+1, C) strata and orbits in the solution space of Euclidean CP n models

We further study the action of SL(n+1, C) on the space of finite action solutions of the bidimensional Euclidean CP ⁿ models. We decompose the space of k-instantons into strata. Each stratum in characterized by an integer m with 0mmin(k, n) which can be calculated from the instanton by purely algebraic means. The k-instantons with m=n are called generic. Their stratum is shown to be dense in the space of k-instantons when kn. The isotropy subgroups for each stratum are identified.

---

Résumé Nous poursuivons l'étude de l'action de SL(n+1, C) sur l'espace des solutions à action finie du modèle CP ⁿ sur l'espace euclidien bi-dimensionnel. L'espace des k-instantons est décomposé en strates. Chaque strate est caractérisée par un entier m tel que 0 mmin(k, n) et qui peut être calculé à partir de l'instanton par des méthodes purement algébriques. Les k-instantons avec m=n sont dits génériques. Leur strate est dense dans l'espace des k-instantons (lorsque k n). Les sous-groupes d'isotropie de chacune des strates sont identifiés.

---

---

Supported in part by the Natural Sciences and Engineering Research Council of Canada and by the Fonds FCAR pour l'aide et le soutien à la recherche.     

Letter: O(d + 1, d + n + 1)-Invariant Formulation of Stationary Heterotic String Theory

We present a pair of symmetric formulations of the matter sector of the stationary effective action of heterotic string theory that arises after the toroidal compactification of d dimensions. The first formulation is written in terms of a pair of matrix potentials Z ₁ and Z ₂ which exhibits a clear symmetry between them and can be used to generate new families of solutions on the basis of either Z ₁ or Z ₂; the second one is an O(d + 1, d + n + 1)-invariant formulation which is written in terms of a matrix vector W endowed with an O(d + 1, d + n + 1)-invariant scalar product which linearizes the action of the O(d + 1, d + n + 1)symmetry group on the coset space O(d + 1, d + n + 1)/[O(d + 1) × O(d + n + 1)]; this fact opens as well a simple solution-generating technique which can be applied on the basis of known solutions.     

Spin-parity analysis of the nπ+ system produced in the reaction π+p → π+π+n at 16GeV/c

A spin-parity analysis of the nπ⁺ system produced in the reaction π⁺p → π⁺π⁺n at 16 MeV/c has shown apart from the mass enhancements associated with the known resonances Δ⁺(1238), N¹(1520) and N¹(1688) there is an enhancement peaked at M(nπ⁺) ? 1.35 GeV, ∑0.2 GeV wide. For masses below M(nπ⁺) ? 1.35 GeV this enhancement is predominantly due to $\text{J}{}^{\mathrm{P}}\text{=}\text{1}\text{2}{}^{\mathrm{?}}$ states, predominate. The presence of $\text{J}{}^{\mathrm{P}}\text{=}\text{1}\text{2}{}^{\mathrm{?}}$ states indicates that the rule ΔP = (?1)^ΔJ is strongly violated in the diffractive process N → Nπ, and hence it cannot be considered a specific characteristic of all diffractive processes.     

Laser action ofnd 8(n + 1)s 2 −nd 9(n + 1)p transitions in HgIII,Cull and AgII

A mechanism of the laser action of 5d ⁸ 6s ² –5d ⁹ 6p HgIII transitions is proposed. The explanation is based on atomic constants of the transitions and the predominant role of direct electron excitation of the upper laser level. The kinetic models of electron beam and hollow cathode discharge sources are calculated. The theoretical estimations are compared with experimental data and possible laser transitions are also proposed. The role of electron impact excitation in the formation of inverse population for two-electron transitions in CuII and AgII obtained in hollow cathode discharges is discussed.     

Theoretical investigation on radiation tolerance of M_(n+1)AX_n phases

Ternary M_(n+1)AX_n phases with layered hexagonal structures, as candidate materials used for next-generation nuclear reactors, have shown great potential in tolerating radiation damage due to their unique combination of ceramic and metallic properties. However, M_(n+1)AX_n materials behave differently in amorphization when exposed to energetic neutron and ion irradiations in experiment. We first analyze the irradiation tolerances of different M_(n+1)AX_n(MAX) phases in terms of electronic structure, including the density of states(DOS) and charge density map. Then a new method based on the Bader analysis with the first-principle calculation is used to estimate the stabilities of MAX phases under irradiation. Our calculations show that the substitution of Cr/V/Ta/Nb by Ti and Si/Ge/Ga by Al can increase the ionicities of the bonds,thus strengthening the radiation tolerance. It is also shown that there is no obvious difference in radiation tolerance between M_(n+1)AC_n and M_(n+1)AN_n due to the similar charge transfer values of C and N atoms. In addition, the improved radiation tolerance from Ti_3AlC_2 to Ti_2AlC (Ti_3AlC_2 and Ti_2AlC have the same chemical elements), can be understood in terms of the increased Al/TiC layer ratio. Criteria based on the quantified charge transfer can be further used to explore other M_(n+1)AX_n phases with respect to their radiation tolerance, playing a critical role in choosing appropriate MAX phases before they are subjected to irradiation in experimental test for future nuclear reactors.     

幻数尺寸Li-n-1,Lin,Li+ n+1(n=20,40)团簇的几何结构、电子与光学性质的第一性原理研究

基于密度泛函理论,采用第一性原理分子动力学模拟退火方法,对Li^-_n-1,Li_n,Li⁺_n+1 (n=20,40)的最低能量结构进行了全局搜索. 发现锂团簇的生长模式是以单个或多个嵌套的正多面体为核心,其余原子以五角锥为基本单元围绕核心生长. 基于最低能量结构的第一性原理电子结构计算得到锂团簇的分子轨道能级分布与无结构凝胶模型给出的电子壳层完全一致. 在总电 关键词： 团簇 电子结构 极化率 光吸收