Physical Assemblies Research Articles

Chain trajectories, domain shapes, and terminal boundaries in block copolymers

AbstractThe packing geometry of macromolecules in complex mesophases is of key importance to self‐organization in synthetic and biological soft materials. While approximate or heuristic models rely on often‐untested assumptions about how flexible molecules “fit in” to distinct locations of complex assemblies, physical assemblies derive from ensembles of fluctuating conformations, obscuring the connection between mesophase geometry and the underlying arrangements. Here, we present an approach to extract and analyze features of molecular packing in diblock block copolymer (BCP) melts, a prototypical soft matter system, based on the statistical description of chain conformations in self‐consistent field (SCF) theory. We show how average BCP chain trajectories in ordered morphologies can be analyzed from the SCF‐derived orientational order parameter of chain segments. We use these extracted trajectories to analyze the features of local packing geometry, including chain bending and tilt, as well as the terminal boundaries that delineate distinct domains in ordered BCP morphologies. We illustrate this analysis by focusing on measurable features of packing frustration in 2D (columnar) and 3D (spherical and bicontinuous) morphologies, notably establishing an explicit link between chain conformations in complex morphologies and their medial geometry.

The Identification of Stakeholders’ Living Contexts in Stakeholder Participation Data: A Semantic, Spatial and Temporal Analysis

Stakeholders’ Participation (SP) aims to involve stakeholders in decision-making processes about significant choices affecting their organizations, cities, or communities. Stakeholders’ participation is maintained through SP processes (SPPs) that may be traditional (e.g., physical assemblies) or online (e.g., online forums). Whether traditional or online, the purpose of SPPs is to collect and analyze data in a way that it would bring a benefit to a given decision-making process. In SPPs, stakeholders try to communicate (a part of) their living contexts, i.e., to present their objectives, daily problems, intentions, and issues they are facing within their environment. A major challenge of decision-makers is then to ensure that the living contexts of stakeholders are considered in SPPs for an effective implementation of project and policies. This paper focuses on the specific issue of the “stakeholders’ living context identification” and attempts to account for how stakeholders implicitly identify their living contexts in their SP comments. Based on a qualitative analysis of SP data from four case studies in two countries, this paper identified a set of semantic, spatial, and temporal patterns allowing to capture the stakeholders’ living contexts in SPPs data. Moreover, a conceptual model emphasizing the importance for decision-makers to capture and understand semantic, spatial, and temporal dimensions in SPPs is proposed.

Cumulative geometric frustration in physical assemblies.

Geometric frustration arises whenever the constituents of a physical assembly locally favor an arrangement that cannot be realized globally. Recently, such frustrated assemblies were shown to exhibit filamentation, size limitation, large morphological variations and other exotic response properties. While these unique characteristics can be shown to be a direct outcome of the geometric frustration, some geometrically frustrated systems do not exhibit any of the above phenomena. In this work we exploit the intrinsic approach to provide a framework for directly addressing the frustration in physical assemblies. The framework highlights the role of the compatibility conditions associated with the intrinsic fields describing the physical assembly. We show that the structure of the compatibility conditions determines the behavior of small assemblies and in particular predicts their superextensive energy growth exponent. We illustrate the use of this framework to several well-known frustrated assemblies.

Large-Scale Welding Process Simulation by GPU Parallelized Computing

The computational design of industrially relevant welded structures is extremely time consuming due to coupled physics and high nonlinearity. Previously, most welding distortion and residual stress simulations have been limited to small coupons and reduced order (from three-dimensional [3D] to two-dimensional [2D]), or inherent strain approximations were used for large structures. In this current study, an explicit finite element code based on a graphics processing unit was utilized to perform 3D transient thermomechanical simulation of structural components during welding. Laser brazing of aluminum alloy panels as representative of automotive manufacturing scenarios was simulated to predict out-of-plane distortion under different clamping conditions. The predicted deformation pattern and magnitude were validated by laser scanning data of physical assemblies. In addition, the code was used to investigate residual stresses developed during multipass arc welding of a nuclear industry pressurizer surge nozzle and subsequent welding repair where a 3D simulation was necessary. Taking the experimental data as reference, the 3D model predicted better residual stress distribution than a typical 2D asymmetrical model. Stress evolution in welding repair was also presented and discussed in this study. The efficient numerical model made it feasible to use integrated computational welding engineering to simulate welding processes for large-scale structures.

Thermo- and pH-Responsive Gelatin/Polyphenolic Tannin/Graphene Oxide Hydrogels for Efficient Methylene Blue Delivery.

Gelatin (GE), amino-functionalized polyphenolic tannin derivative (TN), and graphene oxide (GO) were associated to yield thermo- and pH-responsive hydrogels for the first time. Durable hydrogel assemblies for drug delivery purposes were developed using the photosensitizer methylene blue (MB) as a drug model. The cooling GE/TN blends provide brittle physical assemblies. To overcome this disadvantage, different GO contents (between 0.31% and 1.02% wt/wt) were added to the GE/TN blend at 89.7/10.3 wt/wt. FTIR and RAMAN spectroscopy analyses characterized the materials, indicating GO presence in the hydrogels. Incorporation studies revealed a total MB (0.50 mg/mL) incorporation into the GE/TN-GO hydrogel matrices. Additionally, the proposed systems present a mechanical behavior similar to gel. The GO presence in the hydrogel matrices increased the elastic modulus from 516 to 1650 Pa. SEM revealed that hydrogels containing MB present higher porosity with interconnected pores. Dissolution and swelling degree studies revealed less stability of the GE/TN-GO-MB hydrogels in SGF medium (pH 1.2) than SIF (pH 6.8). The degradation increased in SIF with the GO content, making the polymeric matrices more hydrophilic. MB release studies revealed a process controlled by Fickian diffusion. Our results point out the pH-responsible behavior of mechanically reinforced GE/TN-GO-MB hydrogels for drug delivery systems purposes.

Hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies.

A general principle of biology is the self‐assembly of proteins into functional complexes. Characterizing their composition is, therefore, required for our understanding of cellular functions. Unfortunately, we lack knowledge of the comprehensive set of identities of protein complexes in human cells. To address this gap, we developed a machine learning framework to identify protein complexes in over 15,000 mass spectrometry experiments which resulted in the identification of nearly 7,000 physical assemblies. We show our resource, hu.MAP 2.0, is more accurate and comprehensive than previous state of the art high‐throughput protein complex resources and gives rise to many new hypotheses, including for 274 completely uncharacterized proteins. Further, we identify 253 promiscuous proteins that participate in multiple complexes pointing to possible moonlighting roles. We have made hu.MAP 2.0 easily searchable in a web interface (http://humap2.proteincomplexes.org/), which will be a valuable resource for researchers across a broad range of interests including systems biology, structural biology, and molecular explanations of disease.

RoboGrammar

We present RoboGrammar , a fully automated approach for generating optimized robot structures to traverse given terrains. In this framework, we represent each robot design as a graph, and use a graph grammar to express possible arrangements of physical robot assemblies. Each robot design can then be expressed as a sequence of grammar rules. Using only a small set of rules our grammar can describe hundreds of thousands of possible robot designs. The construction of the grammar limits the design space to designs that can be fabricated. For a given input terrain, the design space is searched to find the top performing robots and their corresponding controllers. We introduce Graph Heuristic Search - a novel method for efficient search of combinatorial design spaces. In Graph Heuristic Search, we explore the design space while simultaneously learning a function that maps incomplete designs (e.g., nodes in the combinatorial search tree) to the best performance values that can be achieved by expanding these incomplete designs. Graph Heuristic Search prioritizes exploration of the most promising branches of the design space. To test our method we optimize robots for a number of challenging and varied terrains. We demonstrate that RoboGrammar can successfully generate nontrivial robots that are optimized for a single terrain or a combination of terrains.

The cooling of blends in water supports durable, thermo-responsive, and porous gelatin-polyphenolic tannin assemblies with antimicrobial activities

We applied an amino-functionalized polyphenolic tannin derivative (TN), commercially called Tanfloc, to stabilize gelatin (GE) chains and provide physical assemblies. Zeta potential measurements showed that the TN presents an isoelectric point of 4.45. Hydrolyzed tannins comprise the TN structure, supporting negative Zeta potentials at pHs higher than 4.45. Aqueous GE (1.0, 2.0, 3.0, and 4.0 % wt/vol) and polyphenolic tannin derivative (TN, 4.6 g⋅L―1) mixtures in distilled water (pH 5.5, at 50 °C) provided physical assemblies after cooling at 4 °C. The thermosensitive hydrogels often showed gelation temperatures between 41 and 45 °C. A durable, porous, and organized structure with solid-liquid phase transition (gelation) higher than 60 °C was obtained at 4.0 % wt/vol GE and 50/50 GE/TN volume ratio at GE + TN equal to 134.0 mg. Viscoelastic materials were created by blending GE (4.0 % wt/vol) and TN (4.6 g⋅L―1) aliquots at GE/TN volume ratios equal to 90/10 vol/vol (assembly 4-90/10 at GE + TN equal to 212.3 mg) and 50/50 vol/vol (assembly 4/50/50 at GE + TN = 134.0 mg). A pure GE material showed the highest porosity (89 %). The TN presence reduced the material porosity to 65 % (assembly 4-90/10) and 63 % (assembly 4-50/50). The assembly 4-90/10 showed aqueous instability because the polymer blend had no enough TN to stabilize the GE chains. However, the assembly 4-90/10 had antimicrobial activities against Escherichia coli (E. coli) with minimal inhibitory and minimum bactericidal concentrations of 500 μg⋅ mL―1. The disk diffusion method showed that the assembly 4-90/10 provided an inhibition halo of 11 mm toward E. coli after 24 h of exposure at pH 6.0. GE/TN assemblies can provide physical hydrogels for biomedical applications (wound dressings).

Strength and Dimension Accuracy in Fused Deposition Modeling : A Comparative Study on Parts Making Using ABS and PLA Polymers

Rapid prototyping is a group of techniques used to quickly scale physical parts or assemblies using three-dimensional computer-aided design (CAD) data. The process of 3D printing constructs three-dimensional objects from CAD models, usually by adding layers by a layer of material in a row. Therefore it is also called making addictive manufacturing. Along with the development of rapid prototyping, there are many choices of materials on the market to make parts of 3D printing. The material can be in the solid filament, liquid resin, or powder. Solid filament FDM technology material is the most commonly used by industry — these materials such as ABS, PLA, PETG, HIPS, and others. In 3D printing products, several variables can be observed to produces specific responses desirable. Some of the responses are the efficiency of materials, dimensional accuracy of mechanical, and others. This research was conducted to compare ABS and PLA materials in the fused deposition modeling process. The strength and dimensional accuracy are the response that used in this study. The study reports that ABS has more significant tensile strength than PLA. The tensile strength of ABS is 7.66 MPa and 1.79 for PLA. PLA found has a more accurate dimension compare to ABS. Both on length and thickness, deviation of PLA lower than ABS. On a length, deviation of PLA was 0.06 mm and 0.86 for ABS. On thickness, deviation of PLA was 0.04 and 0.05 for ABS.

High-density NGS-based map construction and genetic dissection of fruit shape and rind netting in Cucumis melo.

Melon is an important crop that exhibits broad variation for fruit morphology traits that are the substrate for genetic mapping efforts. In the post-genomic era, the link between genetic maps and physical genome assemblies is key for leveraging QTL mapping results for gene cloning and breeding purposes. Here, using a population of 164 melon recombinant inbred lines (RILs) that were subjected to genotyping-by-sequencing, we constructed and compared high-density sequence- and linkage-based recombination maps that were aligned to the reference melon genome. These analyses reveal the genome-wide variation in recombination frequency and highlight regions of disrupted collinearity between our population and the reference genome. The population was phenotyped over 3years for fruit size and shape as well as rind netting. Four QTLs were detected for fruit size, and they act in an additive manner, while significant epistatic interaction was found between two neutral loci for this trait. Fruit shape displayed transgressive segregation that was explained by the action of four QTLs, contributed by alleles from both parents. The complexity of rind netting was demonstrated on a collection of 177 diverse accessions. Further dissection of netting in our RILs population, which is derived from a cross of smooth and densely netted parents, confirmed the intricacy of this trait and the involvement of major locus and several other interacting QTLs. A major netting QTL on chromosome 2 co-localized with results from two additional populations, paving the way for future study toward identification of a causative gene for this trait.

РАСЧЕТ ПАРАМЕТРОВ СТОХАСТИЧЕСКОЙ КИНЕТИКИ НЕЙТРОНОВ В ЯДЕРНОМ РЕАКТОРЕ НУЛЕВОЙ МОЩНОСТИ

The majority of neutron-physical problems of nuclear power plants design can be solved on the basis of various approximations to the Boltzmann transport equation in terms of the averaged characteristics of the reactor: the effective multiplication factor, neutron flux, average neutron lifetime, etc. However, the neutron chain reaction itself is always stochastic. There are situations in which the stochastic nature of the chain reaction cannot be ignored. This is the so-called “blind” start-up problem with a weak external neutron source, the work of physical assemblies of “zero” power, the analysis of the reactivity noise of such assemblies, etc. Despite the well-developed theoretical basis for the stochastic description of the behavior of neutrons in a nuclear reactor, there are still not enough calculation algorithms and programs for stochastic kinetics analysis. The paper presents two computational algorithms for point reactor model, which are developed on the basis of the theory of Markov branching random processes. The first one is based on the balance equation for the probabilities of death and birth of prompt and delayed neutrons in a reactor, the second one is based on calculating the first and second moments of neutron number distributions and using the assumption that these distributions can be approximated by gamma distributions with sufficient accuracy. On the basis of these algorithms, programs have been created that allow one to calculate various scenarios for introducing reactivity and an external source into the system. The calculation of pulsed experiments on prompt and delayed neutrons to determine the waiting time of the threshold neutron pulse at the Godiva II installation showed a qualitative agreement of the results for both the two computational algorithms and the experimental data.

Encapsulating phosphorus inside carbon nanotubes via a solution approach for advanced lithium ion host

Conventional phosphorus anode materials in lithium/sodium-ion batteries are mainly based on the physical mixing and evaporation/condensation, in which external phosphorus on conductive matrix is unavoidable and hard to be removed due to the formation of crystalline phase. It has been found to break off from conductive matrix easily and deteriorate capacity rapidly. In this communication, we first report a solution processed encapsulation method which facilitates phosphorus anchored inside multi-walled carbon nanotubes (MWCNTs). Any possible external phosphorus adsorbents are hard to transform into crystalline and enable an easy removal by polar solvents. Eventually, the phosphorus rings and chains are successfully encapsulated only inside MWCNTs, exhibiting high cycling stability in lithium-ion battery because of the efficient physical confinement and unique discrete phosphorus segment assemblies inside MWCNTs which ensured enough vacant space for volume expansion.

New material architectures through graphene nanosheet assembly

Over the last decade, graphene research has developed into a large and multi-faceted field concerned with the synthesis, structure, properties, and applications of various ultrathin sheet-like carbon forms. This article presents a historical perspective on ultrathin carbons, and on the traditional role of the “graphene layer” as a conceptual model for describing crystalline polymorphs in sp < sup > 2 -based carbon materials. Bulk carbons can often be usefully modelled as physical assemblies of distinct graphene layers whose length, curvature, packing, and orientation determine carbon properties and their observed anisotropy. The article then gives a brief perspective on the emerging subfield of graphene research that uses nanosheets as physical building blocks to assemble new material architectures. In analogy with macroscopic sheets of paper or fabric, graphene nanosheets can be manipulated by stacking, wrapping, folding, wrinkling, or crumpling, to make novel carbons not accessible through traditional routes based on molecular or solid-state precursors. These include aerogels, crumpled particles, encapsulation sacks, and a variety of engineered films structures that can be planar or microtextured. While much work has been done in this graphene subfield, important research opportunities remain. Among these are the creation of hybrid structures involving graphene nanosheets systematically combined with other substances to form graphene-molecular hybrids, graphene-nanoparticle hybrids (2D-0D), graphene-nanofiber hybrids (2D-1D), and nanosheet heterostructures (2D-2D).

Thermal Cracking Analysis of Microbial Cemented Sand under Various Strains Based on the DEM

Microbial‐induced calcite precipitation (MICP) is a novel ground improvement method to increase the strength and stiffness of sand. However, the influences of temperature load on the internal microstructure of microbial cemented sand (MCS) material under the experimented strain have always been a key concern for the extensive application. Three kinds of experiments, X‐ray diffraction (XRD), X‐ray computed tomography (XCT), and scanning electron microscopy (SEM), were conducted to explore the composition, shape, and bonding characteristics of physical assemblies in this paper. A precision DEM modelling of MCS, mainly composed of irregular particle modelling and a mesoparameter calibration algorithm, has been proposed for the thermal cracking analysis under various strains (i.e., 1.0‰–3.0‰). Research results indicate that three kinds of bonding (that is sand‐calcite, calcite‐calcite, and sand‐sand) are present in the MCS material. The application of temperature has a superposition effect on the damage of MCS material with increasing strain. Moreover, as the heating duration gradually increases, the effect of thermal rupture produces a distinct quiet period. The length of thermal cracks in the transverse direction increases throughout the heating process.

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

SummaryThe assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC‐by‐BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high‐resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high‐resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome‐scale analysis of repetitive sequences and revealed a ~800‐kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone‐by‐clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC‐contig physical map and validate sequence assembly on a chromosome‐arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome‐by‐chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.

Genetic Linkage Map and Comparative Genome Analysis for the Atlantic Killifish (&amp;lt;i&amp;gt;Fundulus heteroclitus&amp;lt;/i&amp;gt;)

Genetic linkage maps are valuable tools in evolutionary biology; however, their availability for wild populations is extremely limited. Fundulus heteroclitus (Atlantic killifish) is a non-migratory estuarine fish that exhibits high allelic and phenotypic diversity partitioned among subpopulations that reside in disparate environmental conditions. An ideal candidate model organism for studying gene-environment interactions, the molecular toolbox for F. heteroclitus is limited. We identified hundreds of novel microsatellites which, when combined with existing microsatellites and single nucleotide polymorphisms (SNPs), were used to construct the first genetic linkage map for this species. By integrating independent linkage maps from three genetic crosses, we developed a consensus map containing 24 linkage groups, consistent with the number of chromosomes reported for this species. These linkage groups span 2300 centimorgans (cM) of recombinant genomic space, intermediate in size relative to the current linkage maps for the teleosts, medaka and zebrafish. Comparisons between fish genomes support a high degree of synteny between the consensus F. heteroclitus linkage map and the medaka and (to a lesser extent) zebrafish physical genome assemblies.

A Collaborative Assembly Strategy for Tumor-Targeted siRNA Delivery.

A novel "collaborative assembly" approach was reported for the synthesis of an siRNA delivery system via a combination of an electrostatically driven physical assembly and a facile click reaction-mediated chemical assembly, which showed various advantages of more safety, efficiency, and flexibility over the conventional approach that is only based on the physical assembly. This strategy remained a high cationic property of lipid-based complex for high siRNA loading capacity. The direct chemical modification of a model polyanion, hyaluronic acid (HA) on the cationic complex via click chemistry shielded the positive charge of complex without affecting the siRNA binding, which reduced the toxicity and enhanced the blood stability of the complex. In addition, the incorporated polyanion might be prefunctionalized, which endued the carrier with better biological characteristics such as long circulating or tumor targeting. We demonstrated that the obtained lipid-polymer hybrid nanoparticle (RSC-HA) using collaborative assembly presented greater in vivo stability in the blood for efficient tumor targeting than the physically assembled RSC/HA in which HA was physically adsorbed on the complex. After endocytosis into the cells, the protection of RSC-HA on siRNA turned off, while the release of siRNA induced by the intracellular signals for enhanced gene-silencing capacity. This combination of physical and chemical assemblies provides an efficient strategy for the exploitation of safe, stable, and functionalized siRNA delivery systems.

Computational capacity and energy consumption of complex resistive switch networks

Resistive switches are a class of emerging nanoelectronics devices that exhibit a wide variety of switching characteristics closely resembling behaviors of biological synapses. Assembled into random networks, such resistive switches produce emerging behaviors far more complex than that of individual devices. This was previously demonstrated in simulations that exploit information processing within these random networks to solve tasks that require nonlinear computation as well as memory. Physical assemblies of such networks manifest complex spatial structures and basic processing capabilities often related to biologically-inspired computing. We model and simulate random resistive switch networks and analyze their computational capacities. We provide a detailed discussion of the relevant design parameters and establish the link to the physical assemblies by relating the modeling parameters to physical parameters. More globally connected networks and an increased network switching activity are means to increase the computational capacity linearly at the expense of exponentially growing energy consumption. We discuss a new modular approach that exhibits higher computational capacities, and energy consumption growing linearly with the number of networks used. The results show how to optimize the trade-o between computational capacity and energy e ciency and are relevant for the design and fabrication of novel computing architectures that harness random assemblies of emerging nanodevices.

Integrating Physical and Digital Assemblies

Computer-based tools have changed the focus and modes of design thinking in architecture. While often criticized for its overemphasis on formal expressions and its pursuit of the spectacular, digital creativity has begun to take into account a multiplicity of design factors that define architecture. These factors relate to performance simulation and analysis, constructability, and building information modeling (BIM). This paper discusses the use of physical and digital mock-ups in the context of building technology courses. It uses these mock-ups as an important vehicle that provides students with a feedback mechanism regarding often digitally idealized creative thinking.

Evidence for Complex Molecular Architectures for Solvent-Extracted Lignins.

Lignin, an abundant, naturally occurring biopolymer, is often considered "waste" and used as a simple fuel source in the paper-making process. However, lignin has emerged as a promising renewable resource for engineering materials, such as carbon fibers. Unfortunately, the molecular architecture of lignin (in vivo and extracted) is still elusive, with numerous conflicting reports in the literature, and knowledge of this structure is extremely important, not only for materials technologies, but also for production of biofuels such as cellulosic ethanol due to biomass recalcitrance. As such, the molecular structures of solvent-extracted (sulfur-free) lignins, which have been modified using various acyl chlorides, have been probed using small-angle X-ray (SAXS) and neutron (SANS) scattering in tetrahydrofuran (THF) solution along with hydrodynamic characterization using dilute solution viscometry and gel permeation chromatography (GPC) in THF. Mass spectrometry shows an absolute molecular weight ≈18-30 kDa (≈80-140 monomers), while GPC shows a relative molecular weight ∼3 kDa. A linear styrene oligomer (2.5 kDa) was also analyzed in THF using SANS. Results clearly show that lignin molecular architectures are somewhat rigid and complex, ranging from nanogels to hyperbranched macromolecules, not linear oligomers or physical assemblies of oligomers, which is consistent with previously proposed delignification (extraction) mechanisms. Future characterization using the methods discussed here can be used to guide extraction processes as well as genetic engineering technologies to convert lignin into value added materials with the potential for high positive impact on global sustainability.