A method to identify protein sequences that fold into a known three-dimensional structure

The inverse protein folding problem, the problem of finding which amino acid sequences fold into a known three-dimensional (3D) structure, can be effectively attacked by finding sequences that are most compatible with the environments of the residues in the 3D structure. The environments are described by: (i) the area of the residue buried in the protein and inaccessible to solvent; (ii) the fraction of side-chain area that is covered by polar atoms (O and N); and (iii) the local secondary structure. Examples of this 3D profile method are presented for four families of proteins: the globins, cyclic AMP (adenosine 3',5'-monophosphate) receptor-like proteins, the periplasmic binding proteins, and the actins. This method is able to detect the structural similarity of the actins and 70- kilodalton heat shock proteins, even though these protein families share no detectable sequence similarity.     

A room-temperature molecular/organic-based magnet

The reaction of bis(benzene)vanadium with tetracyanoethylene, TCNE, affords an insoluble amorphous black solid that exhibits field-dependent magnetization and hysteresis at room temperature. The critical temperature could not be estimated as it exceeds 350 kelvin, the thermal decomposition temperature of the sample. The empirical composition of the reported material is V(TCNE)x.Y(CH(2)Cl(2)) with x approximately 2 and Y approximately 1/2. On the basis of the available magnetic and infrared data, threedimensional antiferromagnetic exchange of the donor and acceptor spins resulting in ferrimagnetic behavior appears to be the mode of magnetic coupling.     

Quantum annealing of a disordered magnet

Traditional simulated annealing uses thermal fluctuations for convergence in optimization problems. Quantum tunneling provides a different mechanism for moving between states, with the potential for reduced time scales. Thermal and quantum annealing are compared in a model disordered magnet, where the effects of quantum mechanics can be tuned by varying an applied magnetic field. The results indicate that quantum annealing hastens convergence to the optimum state.     

Coherent spin oscillations in a disordered magnet

Most materials freeze when cooled to sufficiently low temperature. We find that magnetic dipoles randomly distributed in a solid matrix condense into a spin liquid with spectral properties on cooling that are the diametric opposite of those for conventional glasses. Measurements of the nonlinear magnetic dynamics in the low-temperature liquid reveal the presence of coherent spin oscillations composed of hundreds of spins with lifetimes of up to 10 seconds. These excitations can be labeled by frequency and manipulated by the magnetic fields from a loop of wire and can permit the encoding of information at multiple frequencies simultaneously.     

基于三维模型的不同树龄苹果树冠层结构评价

【目的】对高纺锤形苹果树的冠层生长规律进行研究,为苹果高纺锤形树形的生长管理提供参考。【方法】以M26中间砧短枝富士为试材,选择4,8,12年生3个树龄的果树作为3个处理,人工测量和统计各树龄冠层基本信息及枝组结构,构建3个树龄果树的虚拟树体模型,比较实际树体照片与虚拟树体,基于构建的三维模型计算果树冠层总叶面积（total leaf area,TLA）、照射叶面积（projected leaf area,PLA）、光截获效率（silhouette to total leaf area ratio,STAR）、叶面积指数（Leaf Area Index,LAI）等指标,建立3个树龄果树的虚拟果园,并模拟计算其中单株果树的光截获效率,用LAI-2000冠层分析仪测定各树龄冠层的LAI,并与三维模型计算结果进行比较和验证。【结果】数字化得到的果树冠层基本信息及枝组结构与人工测量统计结果均无显著差异,但数字化得到的枝组结构更为准确。与实际树体照片相比,虚拟树体图像整体上能够展示树体实际生长情况。3个树龄果树冠层的TLA与PLA分别为6.41,11.60,19.69 m²和2.38,3.88,5.77 m²,随树龄的增长而显著上升;STAR值分别为0.37,0.33和0.29,随树龄增长而下降,但三者之间差异并不显著,LAI分别为1.78,3.87和3.28;在虚拟果园中,模拟计算得到的4,8和12年生果树的STAR值分别为0.30,0.18和0.19,其中4年生与8,12年生果树之间有显著差异。冠层叶面积指数实测值与三维模型模拟值的均方根误差（RMSE）为0.171,可知模型的精准度高。【结论】高纺锤形富士苹果树幼树有较好的光截获效率,随树龄增长单株果树的光截获效率有所下降。且相较于低龄果园,高龄果园中果树冠层光截获效率下降明显,建议果园管理中应注意合理控制种植密度和枝叶密度,以改善高龄果园冠层的光照分布。     

Quantum phase transition of a magnet in a spin bath

The excitation spectrum of a model magnetic system, LiHoF4, was studied with the use of neutron spectroscopy as the system was tuned to its quantum critical point by an applied magnetic field. The electronic mode softening expected for a quantum phase transition was forestalled by hyperfine coupling to the nuclear spins. We found that interactions with the nuclear spin bath controlled the length scale over which the excitations could be entangled. This generic result places a limit on our ability to observe intrinsic electronic quantum criticality.     

The three-dimensional structure of canine parvovirus and its functional implications

The three-dimensional atomic structure of a single-stranded DNA virus has been determined. Infectious virions of canine parvovirus contain 60 protein subunits that are predominantly VP-2. The central structural motif of VP-2 has the same topology (an eight-stranded antiparallel beta barrel) as has been found in many other icosahedral viruses but represents only about one-third of the capsid protein. There is a 22 angstrom (A) long protrusion on the threefold axes, a 15 A deep canyon circulating about each of the five cylindrical structures at the fivefold axes, and a 15 A deep depression at the twofold axes. By analogy with rhinoviruses, the canyon may be the site of receptor attachment. Residues related to the antigenic properties of the virus are found on the threefold protrusions. Some of the amino termini of VP-2 run to the exterior in full but not empty virions, which is consistent with the observation that some VP-2 polypeptides in full particles can be cleaved by trypsin. Eleven nucleotides are seen in each of 60 symmetry-related pockets on the interior surface of the capsid and together account for 13 percent of the genome.     

池塘鱼菜立体种养系统的微生物群落结构分析

为了解池塘鱼菜立体种养系统中微生物的群落结构特征, 探究池塘鱼菜立体种养系统不同组成之间的相互关系, 采用Illumina MiSeq高通量测序方法对系统不同组成的微生物16S rRNA V3～V4区进行测序,比较分析了水体、底泥、蕹菜Ipomoea aquatica Forsk根际与根表、暗纹东方鲀Takifugu ...     

池塘鱼菜立体种养系统的微生物群落结构分析

为了解池塘鱼菜立体种养系统中微生物的群落结构特征,探究池塘鱼菜立体种养系统不同组成之间的相互关系,采用Illumina MiSeq高通量测序方法对系统不同组成的微生物16S rRNA V3～V4区进行测序,比较分析了水体、底泥、蕹菜Ipomoea aquatica Forsk根际与根表、暗纹东方鲀Takifugu obscures肠道及凡纳滨对虾Litopenaeus vanname肠道微生物群落多样性及差异。结果表明:池塘鱼菜立体种养系统的6组样品细菌分布于62门1 503属,优势菌门包括变形菌门Proteobacteria (27.71%)、放线菌门Actinobacteria (16.37%)、蓝细菌门Cyanobacteria (16.05%)和拟杆菌门Bacteroidetes (10.07%),主要优势菌属包括红球菌属Rhodococcus、葡萄球菌属Staphylococcus、弓形杆菌属Arcobacter、红杆菌属Rhodobacter、硫杆菌属Thiobacillus和支原体属Mycoplasma;水体的优势菌门为放线菌门、变形菌门、蓝细菌门和拟杆菌门,底泥的优势菌门为变形菌门和拟杆菌门,蕹菜根际及根表的优势菌门为变形菌门、蓝细菌门和拟杆菌门,暗纹东方鲀肠道的优势菌门为厚壁菌门Firmicutes、Epsilonbacteraeota、蓝细菌门和拟杆菌门,凡纳滨对虾肠道的优势菌门为放线菌门和变形菌门;池塘鱼菜立体种养系统中的功能性细菌分布略有不同,蕹菜根表硝化细菌的相对丰度显著高于水体、鲀肠道和虾肠道(P<0.05),蕹菜根际反硝化细菌的相对丰度显著高于其他各组(P<0.05),水体和蕹菜根际固氮菌的相对丰度显著高于虾肠道、底泥和鲀肠道(P<0.05)。研究表明,池塘鱼菜立体种养系统的不同组成(底泥、水体、蕹菜根际与根表、养殖对象肠道)由于功能不同微生物群落结构存在较大差异,在蕹菜根际及根表包含有相对丰度较高的硝化细菌、反硝化细菌、固氮菌,有助于促进氮循环,提高系统中氮的利用率,而养殖对象肠道中既有有益菌也有致病菌属。     

Crystal structure of bee-venom phospholipase A2 in a complex with a transition-state analogue

The 2.0 angstroms crystal structure of a complex containing bee-venom phospholipase A2 (PLA2) and a phosphonate transition-state analogue was solved by multiple isomorphous replacement. The electron-density map is sufficiently detailed to visualize the proximal sugars of the enzyme's N-linked carbohydrate and a single molecule of the transition-state analogue bound ot its active center. Although bee-venom PLA2 does not belong to the large homologous Class I/II family that encompasses most other well-studied PLA2s, there is segmental sequence similarity and conservation of many functional substructures. Comparison of the bee-venom enzyme with other phospholipase structures provides compelling evidence for a common catalytic mechanism.     

Crystal structure of cobra-venom phospholipase A2 in a complex with a transition-state analogue

The crystal structure of a complex between a phosphonate transition-state analogue and the phospholipase A2 (PLA2) from Naja naja atra venom has been solved and refined to a resolution of 2.0 angstroms. The identical stereochemistry of the two complexes that comprise the crystal's asymmetric unit indicates both the manner in which the transition state is stabilized and how the hydrophobic fatty acyl chains of the substrate are accommodated by the enzyme during interfacial catalysis. The critical features that suggest the chemistry of binding and catalysis are the same as those seen in the crystal structure of a similar complex formed with the evolutionarily distant bee-venom PLA2.     

Structure of a three-dimensional, microporous molybdenum phosphate with large cavities

The synthesis, single-crystal x-ray structural characterization, and sorption properties of a microporous molybdenum phosphate, (Me(4)N)(1.3)(H(3)O)(0.7)[Mo(4)O(8)(PO(4))(2)] . 2H(2)O (Me, methyl), are presented. The three-dimensional framework is built up from Mo(4)O(8)(4+) cubes and PO(4)(3-) tetrahedra that are connected in such a way that large, cation-filled voids are generated; these voids constitute 25% of the volume of the solid. Absorption isotherms for water show the completely reversible uptake of 4 to 5 percent by weight water into the micropores of this compound, which corresponds to 10 to 12 percent by volume.     

The molecular structure of a DNA-triostin A complex

The molecular structure of triostin A, a cyclic octadepsipeptide antibiotic, has been solved complexed to a DNA double helical fragment with the sequence CGTACG (C, cytosine; G, guanine; T, thymine; A, adenine). The two planar quinoxaline rings of triostin A bis intercalate on the minor groove of the DNA double helix surrounding the CG base pairs at either end. The alanine residues form hydrogen bonds to the guanines. Base stacking in the DNA is perturbed, and the major binding interaction involves a large number of van der Waals contacts between the peptides and the nucleic acid. The adenine residues in the center are in the syn conformation and are paired to thymine through Hoogsteen base pairing.     

Turbidity currents: monitoring their occurrence and movement with a three-dimensional sensor network

Detailed field data on the occurrence, flow pattern, and internal dynamics of both surge and continuous turbidity currents have been obtained with a three-dimensional array of optical and thermal sensors. The array, operated in a glacial lake in southeastern British Columbia, collected detailed information on the character of surge events with velocities reaching 110 centimeters per second and continuous underflows exceeding 90 centimeters per second. Thefindings (i) indicate that such currents are frequent events, occurring with density differences between the incoming stream water and the lake water as low as 0.19 kilogram per cubic meter of water; (ii) document the differences in the initiation and internal characteristics of the continuous and surge events; and (iii) support the concept of erosion by turbidity currents.     

Mesostructure design with gemini surfactants: supercage formation in a three-dimensional hexagonal array

At low temperatures, liquid crystal-like arrays made up of inorganic-cluster and organic molecular units readily undergo reversible lyotropic transformations. Gemini surfactants, with two quaternary ammonium head groups separated by a methylene chain of variable length and with each head group attached to a hydrophobic tail, can be used to control organic charge sitting relative to the bivariable hydrophobic tail configurations. This approach has led to the synthesis of a mesophase (SBA-2) that has three-dimensional hexagonal (P6(3)/mmc) symmetry, regular supercages that can be dimensionally tailored, and a large inner surface area. This mesostructure analog of a zeolite cage structure does not appear to have a lyotropic surfactant or lipid liquid crystal mesophase counterpart. Through the modification of gemini charge separation and each of the two organic tails, these syntheses can be used to optimize templating effects, including the synthesis of MCM-48 at room temperature.     

FG-rich repeats of nuclear pore proteins form a three-dimensional meshwork with hydrogel-like properties

Nuclear pore complexes permit rapid passage of cargoes bound to nuclear transport receptors, but otherwise suppress nucleocytoplasmic fluxes of inert macromolecules >/=30 kilodaltons. To explain this selectivity, a sieve structure of the permeability barrier has been proposed that is created through reversible cross-linking between Phe and Gly (FG)-rich nucleoporin repeats. According to this model, nuclear transport receptors overcome the size limit of the sieve and catalyze their own nuclear pore-passage by a competitive disruption of adjacent inter-repeat contacts, which transiently opens adjoining meshes. Here, we found that phenylalanine-mediated inter-repeat interactions indeed cross-link FG-repeat domains into elastic and reversible hydrogels. Furthermore, we obtained evidence that such hydrogel formation is required for viability in yeast.     

A cascade of structure in a drop falling from a faucet

A drop falling from a faucet is a common example of a mass fissioning into two or more pieces. The shape of the liquid in this situation has been investigated by both experiment and computer simulation. As the viscosity of the liquid is varied, the shape of the drop changes dramatically. Near the point of breakup, viscous drops develop long necks that then spawn a series of smaller necks with ever thinner diameters. Simulations indicate that this repeated formation of necks can proceed ad infinitum whenever a small but finite amount of noise is present in the experiment. In this situation, the dynamical singularity occurring when a drop fissions is characterized by a rough interface.     

The large-scale axisymmetric magnetic topology of a very-low-mass fully convective star

Understanding how cool stars produce magnetic fields within their interiors is crucial for predicting the impact of such fields, such as the activity cycle of the Sun. In this respect, studying fully convective stars enables us to investigate the role of convective zones in magnetic field generation. We produced a magnetic map of a rapidly rotating, very-low-mass, fully convective dwarf through tomographic imaging from time series of spectropolarimetric data. Our results, which demonstrate that fully convective stars are able to trigger axisymmetric large-scale poloidal fields without differential rotation, challenge existing theoretical models of field generation in cool stars.     

直驱永磁同步风电系统低电压穿越的研究

【目的】研究直驱永磁同步风电系统的控制策略,以提高其低电压穿越的能力。【方法】建立经背靠背双PWM变流器并网的直驱永磁同步风力发电系统的仿真模型,采用电流前馈控制实现两侧变换器的有功和无功功率的解耦控制。将电网电压信号引入机侧整流器参考功率的计算,提出按电网电压跌落幅度减小发电机输出功率的低电压穿越控制策略。【结果】仿真结果表明,电网电压跌落时,文章所提控制策略限制了变流器直流侧过电压和网侧逆变器过电流;辅以桨距角调节可以抑制发电机功率减小时机组机械转速的升高。【结论】保持发电机功率平衡和变流器直流侧功率平衡,可提高直驱永磁同步风电系统的低电压穿越能力,同时向系统提供无功功率支持,帮助电网电压恢复。