Computational design of self-assembling protein nanomaterials with atomic level accuracy

We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.     

Nanoparticle superlattice engineering with DNA

A current limitation in nanoparticle superlattice engineering is that the identities of the particles being assembled often determine the structures that can be synthesized. Therefore, specific crystallographic symmetries or lattice parameters can only be achieved using specific nanoparticles as building blocks (and vice versa). We present six design rules that can be used to deliberately prepare nine distinct colloidal crystal structures, with control over lattice parameters on the 25- to 150-nanometer length scale. These design rules outline a strategy to independently adjust each of the relevant crystallographic parameters, including particle size (5 to 60 nanometers), periodicity, and interparticle distance. As such, this work represents an advance in synthesizing tailorable macroscale architectures comprising nanoscale materials in a predictable fashion.     

Catalytic nanoarchitectures--the importance of nothing and the unimportance of periodicity

Heterogeneous catalysis has always been an inherently nanoscopic phenomenon with important technological and societal consequences for energy conversion and the production of chemicals. New opportunities for improved performance arise when the multifunctionality inherent in catalytic processes, including molecular transport of reactants and products, is rethought in light of architectures designed and fabricated from the appropriate nanoscale building blocks, including the use of "nothing" (void space) and deliberate disorder as design components. Architectures with all of the appropriate electrochemical and catalytic requirements, including large surface areas readily accessible to molecules, may now be assembled on the benchtop. Designing catalytic nanoarchitectures that depart from the hegemony of periodicity and order offers the promise of even higher activity.     

Generating diverse skeletons of small molecules combinatorially

Lack of efficient access to collections of synthetic compounds that have skeletal diversity is a key bottleneck in the small-molecule discovery process. We report a synthesis strategy that involves transforming substrates with different appendages that pre-encode skeletal information, named sigma elements, into products that have different skeletons with the use of common reaction conditions. With this approach, split-pool synthesis can be used to pre-encode skeletal diversity combinatorially and thereby generate such small molecules very efficiently. A split-pool synthesis of more than 1000 compounds produced overlapping, combinatorial matrices of molecular skeletons and appended building blocks in both enantiomeric and diastereomeric forms.     

Directed assembly of one-dimensional nanostructures into functional networks

One-dimensional nanostructures, such as nanowires and nanotubes, represent the smallest dimension for efficient transport of electrons and excitons and thus are ideal building blocks for hierarchical assembly of functional nanoscale electronic and photonic structures. We report an approach for the hierarchical assembly of one-dimensional nanostructures into well-defined functional networks. We show that nanowires can be assembled into parallel arrays with control of the average separation and, by combining fluidic alignment with surface-patterning techniques, that it is also possible to control periodicity. In addition, complex crossed nanowire arrays can be prepared with layer-by-layer assembly with different flow directions for sequential steps. Transport studies show that the crossed nanowire arrays form electrically conducting networks, with individually addressable device function at each cross point.     

Scaling up digital circuit computation with DNA strand displacement cascades

To construct sophisticated biochemical circuits from scratch, one needs to understand how simple the building blocks can be and how robustly such circuits can scale up. Using a simple DNA reaction mechanism based on a reversible strand displacement process, we experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands. These multilayer circuits include thresholding and catalysis within every logical operation to perform digital signal restoration, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays. The design naturally incorporates other crucial elements for large-scale circuitry, such as general debugging tools, parallel circuit preparation, and an abstraction hierarchy supported by an automated circuit compiler.     

Interwoven metal-organic framework on a periodic minimal surface with extra-large pores

Interpenetration (catenation) has long been considered a major impediment in the achievement of stable and porous crystalline structures. A strategy for the design of highly porous and structurally stable networks makes use of metal-organic building blocks that can be assembled on a triply periodic P-minimal geometric surface to produce structures that are interpenetrating-more accurately considered as interwoven. We used 4,4',4"-benzene-1,3,5-triyl-tribenzoic acid (H(3)BTB), copper(II) nitrate, and N,N'-dimethylformamide (DMF) to prepare Cu(3)(BTB)(2)(H(2)O)(3).(DMF)(9)(H(2)O)(2) (MOF-14), whose structure reveals a pair of interwoven metal-organic frameworks that are mutually reinforced. The structure contains remarkably large pores, 16.4 angstroms in diameter, in which voluminous amounts of gases and organic solvents can be reversibly sorbed.     

DNA-templated carbon nanotube field-effect transistor

The combination of their electronic properties and dimensions makes carbon nanotubes ideal building blocks for molecular electronics. However, the advancement of carbon nanotube-based electronics requires assembly strategies that allow their precise localization and interconnection. Using a scheme based on recognition between molecular building blocks, we report the realization of a self-assembled carbon nanotube field-effect transistor operating at room temperature. A DNA scaffold molecule provides the address for precise localization of a semiconducting single-wall carbon nanotube as well as the template for the extended metallic wires contacting it.     

Computer-aided molecular design

Theoretical chemistry, as implemented on fast computers, is beginning to yield accurate predictions of the thermodynamic and kinetic properties of large molecular assemblies. In addition to providing detailed insights into the origins of molecular activity, theoretical calculations can be used to design new molecules with specific properties. This article describes two types of calculations that show special promise as design tools, the thermodynamic cycle-perturbation method and the Brownian reactive dynamics method. These methods can be applied to calculate equilibrium and rate constants that describe many aspects of molecular recognition, stability, and reactivity.     

混凝土小型空心砌块砌体房屋墙体裂缝的防治

近年来，新型墙体材料混凝土小型空心砌块在住宅工程中得到了越来越多的应用．然而，混凝土小型空心砌块建筑墙体的裂缝问题制约着混凝土小型空心砌块建筑的发展．分析了混凝土小型空心砌块墙体裂缝的特征及产生的原因，从材料本身、设计及施工方面提出了防治裂缝的有效措施．     

Functional nanoscale electronic devices assembled using silicon nanowire building blocks

Because semiconductor nanowires can transport electrons and holes, they could function as building blocks for nanoscale electronics assembled without the need for complex and costly fabrication facilities. Boron- and phosphorous-doped silicon nanowires were used as building blocks to assemble three types of semiconductor nanodevices. Passive diode structures consisting of crossed p- and n-type nanowires exhibit rectifying transport similar to planar p-n junctions. Active bipolar transistors, consisting of heavily and lightly n-doped nanowires crossing a common p-type wire base, exhibit common base and emitter current gains as large as 0.94 and 16, respectively. In addition, p- and n-type nanowires have been used to assemble complementary inverter-like structures. The facile assembly of key electronic device elements from well-defined nanoscale building blocks may represent a step toward a "bottom-up" paradigm for electronics manufacturing.     

Divalent metal nanoparticles

Nanoparticles can be used as the building blocks for materials such as supracrystals or ionic liquids. However, they lack the ability to bond along specific directions as atoms and molecules do. We report a simple method to place target molecules specifically at two diametrically opposed positions in the molecular coating of metal nanoparticles. The approach is based on the functionalization of the polar singularities that must form when a curved surface is coated with ordered monolayers, such as a phase-separated mixture of ligands. The molecules placed at these polar defects have been used as chemical handles to form nanoparticle chains that in turn can generate self-standing films.     

防火林带营造技术的研究

本文通过山区山脚田边果木防火林带营造技术的研究,结果表明:建立主、副防火林带和山脚田边果木防火林带,把森林分割切块,形成闭合的防火网络,是一种易推广、多效益的防火生物工程。能把山火造成损失降到最低限度。     

Process modelling in demand-driven supply chains: A reference model for the fruit industry

The growing importance of health in consumption is expected to result in a significant increase of European fruit demand. However, the current fruit supply does not yet sufficiently meet demand requirements. This urges fruit supply chains to become more demand-driven, that is, able to continuously match supply capabilities to changing demand requirements. Realisation of such dynamic supply chains requires the design of customised supply chain configurations and subsequently the engineering of enabling information systems. Reference process models can be valuable means to support this. Based on a case study in four European countries, this paper presents a reference model for designing business processes in demand-driven fruit supply chains. The model consists of a reference modelling framework and an application of the framework to fruit supply chains. The framework defines process models at different levels of abstraction and includes a method of how they can be composed from a repository of building blocks. The applied model comprises a definition of the model building blocks in fruit supply chains and a set of pre-configure models (templates). Together, they combine fruit-specific knowledge with the reuse of generic knowledge as captured in cross-industry standards. The developed reference model bridges the gap between supply chain design and information systems engineering by providing a consistent set of process models that are on the one hand understandable for business managers and on the other hand serve as a basis for information system implementation.     

Crystallography of the hexagonal ferrites

The hexagonal ferrites form an unusual group of complex, ferrimagnetic oxides embodying some 60 known crystal structures. These include phases for which the structural unit cell is larger than that in any known inorganic materials. The various hexagonal ferrite modifications fall into two distinct structural series, each formed by the ordered interlayering (stacking) of two discrete building blocks; these blocks stack along the c crystallographic axis in varying ratios and varying permutations to form strictly coherent, reproducible crystal structures. This mixed-layering aspect of the hexagonal ferrites permits direct, visual observation of the sequence of their subunit-cell stacking elements, after etching, by means of electron microscopy. The sequence of stacked blocks in such structures constitutes the only information lacking for a complete, three-dimensional structure determination. Direct access to this information provides an immediate, unique solution of the crystal structure problem in each case and thereby avoids the dilemmas of a classical diffraction approach to such large unit cells. Ferrite structures with hexagonal c dimensions of 1455 and 1577 angstroms have been uniquely solved by direct electron microscopic readout of surface etch features. One must exercise caution, however, in generalizing these findings to other materials. The method is successful in the case of the hexagonal ferrites because these are mixed-layer structures, wherein the building blocks react at different rates to a specific etchant. Mixed-layer systems are not uncommon in crystallography, and it is likely that similar techniques can be developed for other such materials. Regardless of the validity of this prognosis, however, it is quite evident that high-resolution replica electron microscopy is a most promising tool for the direct observation of surface structure on an ultramicro scale. During the studies reported here replica resolution capability was improved to about 10 angstroms; final resolution is limited by the particle size of the platinum shadowing material. Careful control of experimental conditions during replica preparation or an alternate choice of shadowing material, or both, might reasonably improve the resolution by a factor of 2. This resolution is within the range of most unit cell dimensions and approaches interatomic distances in solid-state materials. The potential of such an experimental capability needs no elaboration.     

Self-assembly of mesoscopic metal-polymer amphiphiles

The assembly properties of two- and three-component rod-like building blocks consisting of gold and polymer block domains have been investigated. These structures behave like mesoscopic amphiphiles and form a series of single-layer superstructures consisting of bundles, tubes, and sheets depending upon the compositional periodicity. Unlike molecular systems, the template used to initially synthesize them plays a critical role in the assembly process by prealigning them in a manner that facilitates their assembly by optimizing the correct collisional orientation upon dissolution of the template. Tubular structures with tailorable diameters can be assembled in a predictable manner on the basis of an estimate of the hybrid rod packing parameters.     

Predictive self-assembly of polyhedra into complex structures

Predicting structure from the attributes of a material's building blocks remains a challenge and central goal for materials science. Isolating the role of building block shape for self-assembly provides insight into the ordering of molecules and the crystallization of colloids, nanoparticles, proteins, and viruses. We investigated 145 convex polyhedra whose assembly arises solely from their anisotropic shape. Our results demonstrate a remarkably high propensity for thermodynamic self-assembly and structural diversity. We show that from simple measures of particle shape and local order in the fluid, the assembly of a given shape into a liquid crystal, plastic crystal, or crystal can be predicted.     

Single-molecule torsional pendulum

We have built a torsional pendulum based on an individual single-walled carbon nanotube, which is used as a torsional spring and mechanical support for the moving part. The moving part can be rotated by an electric field, resulting in large but fully elastic torsional deformations of the nanotube. As a result of the extremely small restoring force associated with the torsional deformation of a single molecule, unusually large oscillations are excited by the thermal energy of the pendulum. By diffraction analysis, we are able to determine the handedness of the molecule in our device. Mechanical devices with molecular-scale components are potential building blocks for nanoelectromechanical systems and may also serve as sensors or actuators.     

油气集输系统规划方案优化计算

在系统分析的基础上，采用分级优化策略将油气集输系统规划方案优化问题分解为拓扑优化和参数优化两个子问题，并通过中间站的位置变量将这两个子问题进行有机结合，从而为该系统的优化设计开辟了一条新思路。实例计算表明，给出的油气集输系统规划方案优化计算方法是可行的，可以用于工程实际设计。     

大豆分子育种研究进展

 大豆分子育种代表了大豆育种的发展方向，主要包括分子标记育种、转基因育种和品种分子设计育种三个方面。通过综合利用基因组学、生物信息学、计算机模拟与遗传育种学等多个学科的理论和方法，大豆分子育种可对大豆从表型到分子等多个层次进行遗传操作，有助于大幅度提高育种效率，最终实现大豆品种的定向遗传改良。本文介绍了中国大豆分子标记育种、转基因育种和品种分子设计育种三个方面的开创者，将国内的主要研究进展与国外相关的最新研究成果进行了综述和比较，由于知识所限对未提及的做出重要贡献的科学家在此致歉。通过比较发现，中国大豆分子育种与国外相关研究的差距普遍存在，然而，有些分子育种相关研究如基因克隆及功能研究等方面则与国外的差距正在逐渐缩小。笔者认为，大豆分子育种正朝着遗传图谱信息多元化、基因发掘规模化、分子育种技术高效化、分子育种理论系统化的方向发展。