Rules For Assembly Research Articles

Co-encapsulation of organic polymers and inorganic superparamagnetic iron oxide colloidal crystals requires matched diffusion time scales.

Nanoparticles (NPs) that contain both organic molecules and inorganic metal or metal oxide colloids in the same NP core are "composite nanoparticles" which are of interest in many applications, particularly in biomedicine as "theranostics" for the combined delivery of colloidal diagnostic imaging agents with therapeutic drugs. The rapid precipitation technique Flash NanoPrecipitation (FNP) enables continuous and scalable production of composite nanoparticles with hydrodynamic diameters between 40-200 nanometers (nm) that contain hydrophobic superparamagnetic iron oxide primary colloids. Composite NPs co-encapsulate these primary colloids (diameters of 6 nm, 15 nm, or 29 nm), a fluorescent dye (600 Daltons), and poly(styrene) homopolymer (1800, 50 000, or 200 000 Daltons) with NPs stabilized by a poly(styrene)-block-poly(ethylene glycol) (1600 Da-b-5000 Da) block copolymer. Nanoparticle assembly in FNP occurs by diffusion limited aggregation of the hydrophobic core components followed by adsorption of the hydrophobic block of the stabilizing polymer. The hydrodynamic diameter mismatch between the collapsed organic species and the primary colloids (0.5-5 nm versus 6-29 nm) creates a diffusion-aggregation time scale mismatch between components that can lead to nonstoichiometric co-encapsulation in the final nanoparticles; some nanoparticles are composites with primary colloids co-encapsulated alongside organics while others are devoid of the primary colloids and contain only organic species. We use a magnetic capture process to separate magnetic composite nanoparticles from organic-only nanoparticles and quantify the amount of iron oxide colloids and hydrophobic fluorescent dye (as a proxy for total hydrophobic polymer content) in the magnetic and nonmagnetic fractions of each formulation. Analysis of the microstructure in over 1100 individual nanoparticles by TEM imaging and composition measurements identifies the conditions that produce nonstoichiometric composite NP populations without co-encapsulated magnetic iron oxide colloids. Stoichiometric magnetically responsive composite NPs are produced when the ratio of characteristic diffusion-aggregation time scales between the inorganic primary colloid and the organic core component is less than 30 and all NPs in a dispersion contain organic and inorganic species in approximately the same ratio. These rules for assembly of colloids and organic components into homogeneous composite nanoparticles are broadly applicable.

Ribosome-independent peptide biosynthesis: the challenge of a unifying nomenclature.

The first machineries for non-ribosomal peptide (NRP) biosynthesis were uncovered over 50 years ago, and the dissection of these megasynthetases set the stage for the nomenclature system that has been used ever since. Although the number of exceptions to the canonical biosynthetic pathways has surged in the intervening years, the NRP synthetase (NRPS) classification system has remained relatively unchanged. This has led to the exclusion of many biosynthetic pathways whose biosynthetic machineries violate the classical rules for NRP assembly, and ultimately to a rupture in the field of NRP biosynthesis. In an attempt to unify the classification of NRP pathways and to facilitate the communication within the research field, we propose a revised framework for grouping ribosome-independent peptide biosynthetic pathways based on recognizable commonalities in their biosynthetic logic. Importantly, the framework can be further refined as needed.

Protein Materials Engineering with DNA.

Proteins are a class of nanoscale building block with remarkable chemical complexity and sophistication: their diverse functions, shapes, and symmetry as well as atomically monodisperse structures far surpass the range of conventional nanoparticles that can be accessed synthetically. The chemical topologies of proteins that drive their assembly into materials are central to their functions in nature. However, despite the importance of protein materials in biology, efforts to harness these building blocks synthetically to engineer new materials have been impeded by the chemical complexity of protein surfaces, making it difficult to reliably design protein building blocks that can be robustly transformed into targeted materials. Here we describe our work aimed at exploiting a simple but important concept: if one could exchange complex protein-protein interactions with well-defined and programmable DNA-DNA interactions, one could control the assembly of proteins into structurally well-defined oligomeric and polymeric materials and three-dimensional crystals. As a class of nanoscale building block, proteins with surface DNA modifications have a vast design space that exceeds what is practically and conceptually possible with their inorganic counterparts: the sequences of the DNA and protein and the chemical nature and position of DNA attachment all play roles in dictating the assembly behavior of protein-DNA conjugates. We summarize how each of these design parameters can influence structural outcome, beginning with proteins with a single surface DNA modification, where energy barriers between protein monomers can be tuned through the sequence and secondary structure of the oligonucleotide. We then explore challenges and progress in designing directional interactions and valency on protein surfaces. The directional binding properties of protein-DNA conjugates are ultimately imposed by the amino acid sequence of the protein, which defines the spatial distribution of DNA modification sites on the protein. Through careful design and mutagenesis, bivalent building blocks that bind directionally to form one-dimensional assemblies can be realized. Finally, we discuss the assembly of proteins densely modified with DNA into crystalline superlattices. At first glance, these protein building blocks display crystallization behavior remarkably similar to that of their DNA-functionalized inorganic nanoparticle counterparts, which allows design principles elucidated for DNA-guided nanoparticle crystallization to be used as predictive tools in determining structural outcomes in protein systems. Proteins additionally offer design handles that nanoparticles do not: unlike nanoparticles, the number and spatial distribution of DNA can be controlled through the protein sequence and DNA modification chemistry. Changing the spatial distributions of DNA can drive otherwise identical proteins down distinct crystallization pathways and yield building blocks with exotic distributions of DNA that crystallize into structures that are not yet attainable using isotropically functionalized particles. We highlight challenges in accessing other classes of architectures and establishing general design rules for DNA-mediated protein assembly. Harnessing surface DNA modifications to build protein materials creates many opportunities to realize new architectures and answer fundamental questions about DNA-modified nanostructures in both materials and biological contexts. Proteins with surface DNA modifications are a powerful class of nanomaterial building blocks for which the DNA and protein sequences and the nature of their conjugation dictate the material structure.

A performance analysis of dispatch rules for semiconductor assembly & test operations

The purpose of this paper is to statistically compare six dispatch rules for semiconductor assembly & test operations with respect to two hierarchical objectives: minimise the weighted sum of key device (chip) shortages and maximise the weighted throughput of lots processed. Three factors affecting system performances are studied: the different rules, whether the machines are set up at time zero, and whether the maximum number of changeovers is restricted over the planning horizon. System performance is determined with both a discrete event AutoSched AP simulation model and a greedy randomised adaptive search procedure (GRASP) for 30 real and randomly generated data sets. A full factorial design with common random numbers was conducted to concurrently investigate the interaction among the three factors. The statistical analysis showed that the two rules designed to process as many hot lots (i.e., key device lots) as possible performed the best in minimising the weighted shortage. We also found that initial setups and limiting the number of setups over a 2- to 3-day planning horizon can significantly weaken the rules’ performance but in some cases the interaction of these factors mitigated their negative impacts. Due to the general nature of the models, the results should be applicable to most reentrant flow shops. The GRASP is now being used by the sponsoring company and the most promising dispatch rules are being studied in an experimental environment.

Triblock peptide-oligonucleotide chimeras (POCs): programmable biomolecules for the assembly of morphologically tunable and responsive hybrid materials.

Triblock peptide-oligonucleotide chimeras (POCs) consisting of peptides and oligonucleotides interlinked by an organic core are presented and their assembly behaviour is investigated. Several factors influence POC assembly, resulting in the formation of either vesicles or fibres. Design rules are introduced and used to predict and alter POC assembly morphology.

Interactions and design rules for assembly of porous colloidal mesophases.

Porous mesophases, where well-defined particle-depleted 'void' spaces are present within a particle-rich background fluid, can be self-assembled from colloidal particles interacting via isotropic pair interactions with competing attractions and repulsions. While such structures could be of wide interest for technological applications (e.g., filtration, catalysis, absorption, etc.), relatively few studies have investigated the interactions that lead to these morphologies and how they compare to those that produce other micro-phase-separated structures, such as clusters. In this work, we use inverse methods of statistical mechanics to design model isotropic pair potentials that form porous mesophases. We characterize the resulting porous structures, correlating features of the pair potential with the targeted pore size and the particle packing fraction. The former is primarily encoded by the amplitude and range of the repulsive barrier of the designed pair potential and the latter by the attractive well depth. We observe a trade-off with respect to the packing fraction of the targeted morphology: greater values support more spherical and monodisperse pores that themselves organize into periodic structures, while lower values yield more mobile pores that do not assemble into ordered structures but remain stable over a larger range of packing fraction. We conclude by commenting on the limitations of targeting a specific pore diameter within the present inverse design approach as well as by describing future directions to overcome these limitations.

Finite element design of a temperature field for high-pressure diamond synthesis

The temperature field in a high-pressure synthetic cavity for diamond production is optimized by adjusting the cavity assembly. This paper aims to propose design rules for high-pressure cavity assembly and apply finite element simulation for analysis. Three assemblies, namely, conventional, D1, and D2, are presented and compared. The temperature field of each assembly is visualized via the finite element method. High-pressure experiments are then performed in a diamond synthesis factory. Compared with conventional assembly, D1 and D2 assemblies established on the basis of the proposed design rules can improve the conditions for diamond synthesis.

Entropy-Driven Crystallization Behavior in DNA-Mediated Nanoparticle Assembly.

Herein, we report an example of entropy-driven crystallization behavior in DNA-nanoparticle superlattice assembly, marking a divergence from the well-established enthalpic driving force of maximizing nearest-neighbor hybridization connections. Such behavior is manifested in the observation of a non-close-packed, body-centered cubic (bcc) superlattice when using a system with self-complementary DNA linkers that would be predicted to form a close-packed, face-centered cubic (fcc) structure based solely on enthalpic considerations and previous design rules for DNA-linked particle assembly. Notably, this unexpected phase behavior is only observed when employing long DNA linkers with unpaired "flexor" bases positioned along the length of the DNA linker that increase the number of microstates available to the DNA ligands. A range of design conditions are tested showing sudden onsets of this behavior, and these experiments are coupled with coarse-grained molecular dynamics simulations to show that this entropy-driven crystallization behavior is due to the accessibility of additional microstates afforded by using long and flexible linkers.

Establishing the Structural Rules for Ligand Recognition, Signaling and Assembly in Innate Immune Receptors

Type-I transmembrane Toll-like receptors (TLRs) are central to host defense against pathogens. Of the ten human TLRs, TLR4 is of particular interest given the complex mechanism required to recognize lipopolysaccharide (LPS) from the outer membranes of Gram-negative bacteria, culminating in transfer of LPS by membrane-bound CD14 to TLR4 in complex with the MD-2 coreceptor. Atomically detailed and enhanced sampling molecular simulations have recently enabled us to identify the allosteric switch in TLR4 activation; key to the switching mechanism is the remarkable conformational plasticity of the coreceptor, which we show is functionally conserved across an entire family of lipid recognition domains. As well as unravelling the experimentally-established structure-activity relationships of natural and synthetic LPS derivatives, we have combined simulations with biochemical data for TLR4 interaction with dietary fatty acids, challenging the long-accepted notion that the link between obesity, chronic inflammation, and insulin resistance occurs via this receptor. Related approaches have uncovered the mechanisms by which LPS derivatives are transferred from bacterial LPS aggregates to the CD14 coreceptor, and identified both the dynamic gating mechanism and final bound state of a hypothesized amino-terminal pocket, consistent with available NMR data. Finally, we have constructed multiscale models of truncated and full-length receptor libraries spanning the human TLR family, enabling observation of their transmembrane oligomerization. We correlate this with in vitro association and acceptor photobleaching FRET data for dimerization within live cells, helping to identify key stabilizing motifs and rationalize disruptive mutations. Our results reveal the structural basis for the tight coupling between extracellular, transmembrane, and intracellular domains required for higher order assembly, conformational change and adaptor recruitment. Collectively, these studies extend our mechanistic understanding of membrane receptor function, and pave the way for novel immunomodulatory therapeutic approaches.

PERANCANGAN PENJADWALAN FLOWSHOP MENGGUNAKAN PARTICLE SWARM OPTIMIZATION UNTUK MEMINIMASI NUMBER OF TARDY JOBS

This paper propose an algorithm for general flowshop scheduling problems using Particle Swarm Optimization that can minimize number of tardy jobs. The algorithm is illustrated in a case study from the heavy equipment manufacturing industry. The proposed algorithm based on Particle Swarm Optimization algorithm developed by Tasgetiren using routing symbols, combined with the characteristic of its production. The jobs would be process in first work station using Particle Swarm Optimization approaches, for 2nd until 11th works stasion using first come first served rules and earliest due date rules for assembly’s works station.

Simple Rules for Efficient Assembly Predict the Layout of a Packaged Viral RNA

Single-stranded RNA (ssRNA) viruses, which include major human pathogens, package their genomes as they assemble their capsids. We show here that the organization of the viral genomes within the capsids provides intriguing insights into the highly cooperative nature of the assembly process. A recent cryo-electron microscopy structure of bacteriophage MS2, determined with only 5-fold symmetry averaging, has revealed the asymmetric distribution of its encapsidated genome. Here we show that this RNA distribution is consistent with an assembly mechanism that follows two simple rules derived from experiment: (1) the binding of the MS2 maturation protein to the RNA constrains its conformation into a loop, and (2) the capsid must be built in an energetically favorable way. These results provide a new level of insight into the factors that drive efficient assembly of ssRNA viruses in vivo.

Establishing the Design Rules for DNA‐Mediated Programmable Colloidal Crystallization

DNA-programmable colloidal crystals are assembled with 5–80 nm nanoparticles, and the lattice parameters of the resulting crystals vary from 25 to 225 nm. A predictable and mathematically definable relationship between particle size and DNA length dictates the assembly and crystallization processes, creating a set of design rules for DNA-based nanoscale assembly.

A Rule Based Assembly Sequence Generation Method for Product Design

In concurrent engineering, the integration of the designers' knowledge and experience, and computer technology into the design process is very important to improve design quality and production efficiency. A feasible design alternative that follows the design rules for assembly will make product manufacturing and assembly more successful. However, designers seldom consider assembly problems in their product development processes. This drawback often occurs due to conflicts in communication between the design and production departments and will cause severe assembly and manufacturing problems. To assist designers with the assembly issue in the design process this research presents a contact relation matrix (CRM) approach to generate assembly sequences for product design. The procedure developed for the CRM approach is based on the four rules identified from the part contact relations and a matrix representation to match the recommended design alternative with the four rules. A procedure is then employed to identify the assembly priority for the recommended design alternative. The part assembly sequence is generated with a sorting procedure. A hand-held hairdryer and an Italian style coffee maker are used as cases to help explain the feasibility of the CRM approach. The results from this study should help designers to examine the possible part combinations and make the necessary modifications for the recommended design alternative. The CRM approach can also be linked with an existing matrix approach in generating and evaluating design alternatives. By integrating the CRM and matrix approaches, the design quality and efficiency will be greatly improved.

Role of Hydrophobic Clusters in the Stability of α-Helical Coiled Coils and Their Conversion to Amyloid-like β-Sheets

We designed a library of short peptides using standard rules for coiled-coil assembly. Depending on the composition of amino acids in the non-interacting region of the coiled coil (positions b, c, and f) these peptides are able to convert from alpha-helical to beta-sheet secondary structure. This type of transition is observed in amyloid-like proteins and is a key feature associated with many types of neurodegenerative diseases. Studies on peptides that are 14 amino acids in length indicated that positioning hydrophobic amino acids at an f position within a heptad repeat accelerated the rate of conformational conversion as compared to that at a c position. We believe that this occurs because of the formation of a hydrophobic pocket that preferentially stabilizes beta-sheets over alpha-helices. This effect was also observed in longer 21 amino acid peptides. Our study shows that the relative rates of structural conversion correlate with the formation of a continuous three-amino-acid hydrophobic patch consisting of amino acids in the d, f, and a positions and not on the secondary structure propensities of the individual amino acids. The sequence-structure relationship observed in this study will be used to help understand the mechanism of amyloid fiber formation and design future coiled-coil and beta-sheet-forming peptide systems.

Exploring the Conceptual Space of LEGO: Teaching and Learning the Psychology of Creativity

This paper reports on the use of the construction toy LEGO as an effective learning resource for undergraduate classes in the psychology of creativity. Students first attended a short series of lectures on aspects of creativity, including learner characteristics such as motivation and metacognition, and theoretical approaches to problem-finding and problem-solving including the Geneplore model and the metaphor of learning as navigation in a multidimensional conceptual space. This was followed by three sessions in which students explored the conceptual space of LEGO under each of three conditions: freeplay in session 1, constraints on process in session 2 (rules for assembly), and constraints on product in session 3 (set goals). Throughout this time, students were required to keep a ‘metacognitive diary’ of their experiences, and to reflect on their own learning processes within and across sessions. Evaluation was carried out by means of a post-activity questionnaire. The paper reports on the kinds of structures produced under each set of constraints, patterns of student learning experiences, motivational changes, and student evaluations of the activity as a whole. It is suggested that, used in this way, LEGO provides a simple, highly enjoyable, yet effective medium for teaching, learning and research in the psychology of creativity.

The essential role of RI alpha in the maintenance of regulated PKA activity.

Cloning of the individual regulatory (R) and catalytic (C) subunits of the cAMP-dependent protein kinase (PKA) and expression of these subunits in cell culture have provided mechanistic answers about the rules for PKA holoenzyme assembly. One of the central findings of these studies is the essential role of the RI alpha regulatory subunit in maintaining the catalytic subunit under cAMP control. The role of RI alpha as the key compensatory regulatory subunit in this enzyme family was confirmed by gene knockouts of the three other regulatory subunits in mice. In each case, RI alpha has demonstrated the capacity for significant compensatory regulation of PKA activity in tissues where the other regulatory subunits are expressed, including brain, brown and white adipose tissue, skeletal muscle, and sperm. The essential requirement of the RI alpha regulatory subunit in maintaining cAMP control of PKA activity was further corroborated by the knockout of RI alpha in mice, which results in early embryonic lethality due to failed cardiac morphogenesis. Closer examination of RI alpha knockout embryos at even earlier stages of development revealed profound deficits in the morphogenesis of the mesodermal embryonic germ layer, which gives rise to essential structures including the embryonic heart tube. Failure of the mesodermal germ layer in RI alpha knockout embryos can be rescued by crossing RI alpha knockout mice to C alpha knockout mice, supporting the conclusion that inappropriately regulated PKA catalytic subunit activity is responsible for the phenotype. Isolation of primary embryonic fibroblasts from RI alpha knockout embryos reveals profound alterations in the actin-based cytoskeleton, which may account for the failure in mesoderm morphogenesis at gastrulation.

Subunit association and conformational flexibility in the head subdomain of human CD81 large extracellular loop.

The large extracellular loop of human CD81, a tetraspanin mediating hepatitis C virus envelope protein E2 binding to human cells, has been crystallized in a hexagonal form. The three-dimensional structure, solved and refined at 2.6 A resolution (R-factor = 22.8%), shows that the protein adopts a dimeric assembly, based on an association interface built up by tetraspanin-conserved residues. Structural comparisons with the tertiary structure of human CD81 large extracellular loop, previously determined in a different crystal form, show marked conformational fluctuations in the molecular regions thought to be involved in binding to the viral protein, suggesting rules for recognition and assembly within the tetraspan web.

A Note on the Electoral Rules for the Welsh Assembly

A recent article in this journal highlights,using simulated data, potential paradoxes inherent in thesystem of election to the Welsh assembly. This paper examinesthe data for the assembly elections held in 1999 to illustratethe occurrence of yet another paradoxical outcome, theelection of the first ever First Minister due to a fall insupport for his own party.

THE ECOLOGICAL CONSEQUENCES OF CHANGES IN BIODIVERSITY: A SEARCH FOR GENERAL PRINCIPLES101

This paper uses theory and experiments to explore the effects of diversity on stability, productivity, and susceptibility to invasion. A model of resource competition predicts that increases in diversity cause community stability to increase, but population stability to decrease. These opposite effects are, to a great extent, explained by how temporal variances in species abundances scale with mean abundance, and by the differential impact of this scaling on population vs. community stability. Community stability also depends on a negative covariance effect (competitive compensation) and on overyielding (ecosystem productivity increasing with diversity). A long-term study in Minnesota grasslands supports these predictions. Models of competition predict, and field experiments confirm, that greater plant diversity leads to greater primary productivity. This diversity–productivity relationship results both from the greater chance that a more productive species would be present at higher diversity (the sampling effect) and from the better “coverage” of habitat heterogeneity caused by the broader range of species traits in a more diverse community (the niche differentiation effect). Both effects cause more complete utilization of limiting resources at higher diversity, which increases resource retention, further increasing productivity. Finally, lower levels of available limiting resources at higher diversity are predicted to decrease the susceptibility of an ecosystem to invasion, supporting the diversity–invasibility hypothesis. This mechanism provides rules for community assembly and invasion resistance. In total, biodiversity should be added to species composition, disturbance, nutrient supply, and climate as a major controller of population and ecosystem dynamics and structure. By their increasingly great directional impacts on all of these controllers, humans are likely to cause major long-term changes in the functioning of ecosystems worldwide. A better understanding of these ecosystem changes is needed if ecologists are to provide society with the knowledge essential for wise management of the earth and its biological resources.

Genomic DNA sequencing by SPEL-6 primer walking using hexamer ligation1Published in conjunction with A Wisconsin Gathering Honoring Waclaw Szybalski on the occasion of his 75th year and 20years of Editorship-in-Chief of Gene, 10–11 August 1997, University of Wisconsin, Madison, WI, USA.1

DNA sequencing by SPEL-6 (Sequential Primer Elongation by Ligation of 6-mers) primer walking is based on the rapid assembly of true primers by ligation of several (three to 10) contiguous hexamers complementary to a DNA template saturated with Escherichia coli single-stranded DNA-binding protein. To prove the usefulness and to check the reliability of this method, a 3-kb DNA fragment carrying the genes encoding the EcoVIII restriction-modification (RM) system was sequenced with low redundancy (2.8). The use of both single-stranded (ss) and double-stranded (ds) DNA templates was compared. For this project, 27 primers were assembled by hexamer ligation to form 18-30-nt strings of three to five hexamers. Each primer was designed based on nucleotide sequence determined in a previous run, and was produced in a matter of minutes. The overall length of the easily readable sequencing ladders was about 300-450nt. We found that strong secondary structures in the ss DNA tend to interfere with its template function for the primer assembly by hexamer ligation, especially when they overlap the 3'-end of such a primer. This was easily overcome either by avoiding such hairpin regions or by using longer strings of hexamers, since we show that their ligation is highly cooperative, and ligation efficiency increases with the length of the string (). Some general rules for successful primer assembly and prospects for using the SPEL-6 method for large-scale, fully automated fluorescent sequencing of large genomes are discussed.