Long-range Assembly Research Articles

Enhanced Free Li-Ion Mobility in Solid-State Electrolytes via Long-Range Assembly of Porous Materials.

Metal-organic frameworks (MOFs), with their tunable pore sizes and high surface areas, are gaining prominence in Li metal battery applications, including their use as nanofillers in solid composite electrolytes (SCEs) for enhanced ionic conductivity. Yet, when used in SCEs, individual dispersed MOF particles in isolation as nanofillers can impede efficient ion transport in all-solid-state batteries due to the insufficient supply of ionic transport pathways within SCEs. Here, we introduced a continuous SCE nanofiller with long-range assembly interconnected porous MOFs (IMOF_SCE) for effective ion transport pathway supply along the interface between the nanofiller and the polymer matrix. IMOF_SCE achieved Li-ion conductivity (6.72 × 10-5 S cm-1 at 20 °C) and Li-ion transference number (tLi+ = 0.855), resulting in the improved electrochemical performance of Li metal batteries. Additionally, the Li/LiFePO4 full cell integrated with IMOF_SCE achieved an outstanding stable capacity retention of 98.8% in 300 cycles. This work offers insights into the design strategy of effective nanofillers for SCEs and can be adapted for other porous materials.

Predicting Assembly Geometric Errors Based on Transformer Neural Networks

Using optimal assembly relationships, companies can enhance product quality without significantly increasing production costs. However, predicting Assembly Geometric Errors presents a challenging real-world problem in the manufacturing domain. To address this challenge, this paper introduces a highly efficient Transformer-based neural network model known as Predicting Assembly Geometric Errors based on Transformer (PAGEformer). This model accurately captures long-range assembly relationships and predicts final assembly errors. The proposed model incorporates two unique features: firstly, an enhanced self-attention mechanism to more effectively handle long-range dependencies, and secondly, the generation of positional information regarding gaps and fillings to better capture assembly relationships. This paper collected actual assembly data for folding rudder blades for unmanned aerial vehicles and established a Mechanical Assembly Relationship Dataset (MARD) for a comparative study. To further illustrate PAGEformer performance, we conducted extensive testing on a large-scale dataset and performed ablation experiments. The experimental results demonstrated a 15.3% improvement in PAGEformer accuracy compared to ARIMA on the MARD. On the ETH, Weather, and ECL open datasets, PAGEformer accuracy increased by 15.17%, 17.17%, and 9.5%, respectively, compared to the mainstream neural network models.

Non-Covalent Free-Standing Monolayer Nanoarchitectonics of Heterocoronene-Based Discotic Liquid Crystal Molecules

With excellent charge carrier mobility, tendency to form long-range assembly with self-healing ability, and remarkable chemical and mechanical stability, highly conjugated discotic molecules constitute an important class of materials for electronic applications. Here, we report formation of the stable free-standing molecular film of heterocoronene-based discotic liquid crystal (DLC) molecules, held solely by supra-molecular non-covalent interactions. The films of monolayer thickness (∼4 nm) were lifted from Langmuir trough directly onto a circular ring of diameter up to 2 mm as well as onto TEM grids. Films remain free-standing up to a macroscopic length scale, as revealed by optical and secondary electron microscopy, presumably due to the synergistic effect of intermolecular π–π interactions and the dispersion forces between the peripheral alkyl chains as well as their interdigitation. The monolayer is more than 97% transparent in the visible range. Further, resistive switching measurements carried out on the monolayer DLC film transferred on a silver substrate revealed electrochemical metallization to be the governing process. The switching time was found to decrease exponentially with voltage indicating nucleation to be a possible rate-limiting step. We anticipate that the method presented here will facilitate utilization of such non-covalent free-standing films in flexible memristor and nano-electromechanical systems.

Fluorogenic response from DNA templated micrometer range self-assembled gold nanorod.

Plasmonic gold nanorod (AuNR) on a macromolecular matrix exhibits an end-to-end (ETE) long-range self-assembly (AuNR)n with n > 100. In the case of small molecules as a template, the pre-synthesized macromolecular matrix is missing and this brings a synthetic challenge in directed long-range assembly of AuNR. Self-assembly with thiol-modified small DNA and AuNR shows a much short-range ETE assembly with n < 25 via a simple evaporation technique on a solid surface. In this study, the introduction of two short amine modified probe DNAs (∼2.5 nm) and one 22-mer complementary single strand (ss)-DNA template (∼7 nm) show the long-range ETE self-assembly of (AuNR)n with n > 130. In the solution state, the zigzag arrangement within the assembled structure controls the typical change in the absorption behavior for (AuNR)n ETE assembly. The formation of this long-range ETE self-assembly in a solution state was verified from the combined effect of fluorescence resonance energy transfer (FRET) and hotspot-induced fluorescence enhancement. The probe DNAs and templated DNA concentration on fluorescence enhancement have been varied to monitor the effect of (AuNR)n with n = ∼5-130 in ETE self-assembly. Primarily quenched FRET acceptor in the presence of AuNR decisively exhibits remarkable fluorogenic response in ETE self-assembly with maximum n value. Although the FRET efficiencies among the fluorophores are comparable, the fluorogenic boost in ETE AuNR is due to the increased number of intrinsic navigated hotspots in these assemblies.

Targeted de novo phasing and long-range assembly by template mutagenesis.

Short-read sequencers provide highly accurate reads at very low cost. Unfortunately, short reads are often inadequate for important applications such as assembly in complex regions or phasing across distant heterozygous sites. In this study, we describe novel bench protocols and algorithms to obtain haplotype-phased sequence assemblies with ultra-low error for regions 10 kb and longer using short reads only. We accomplish this by imprinting each template strand from a target region with a dense and unique mutation pattern. The mutation process randomly and independently converts ∼50% of cytosines to uracils. Sequencing libraries are made from both mutated and unmutated templates. Using de Bruijn graphs and paired-end read information, we assemble each mutated template and use the unmutated library to correct the mutated bases. Templates are partitioned into two or more haplotypes, and the final haplotypes are assembled and corrected for residual template mutations and PCR errors. With sufficient template coverage, the final assemblies have per-base error rates below 10–9. We demonstrate this method on a four-member nuclear family, correctly assembling and phasing three genomic intervals, including the highly polymorphic HLA-B gene.

Application of full-genome analysis to diagnose rare monogenic disorders

Current genetic tests for rare diseases provide a diagnosis in only a modest proportion of cases. The Full-Genome Analysis method, FGA, combines long-range assembly and whole-genome sequencing to detect small variants, structural variants with breakpoint resolution, and phasing. We built a variant prioritization pipeline and tested FGA’s utility for diagnosis of rare diseases in a clinical setting. FGA identified structural variants and small variants with an overall diagnostic yield of 40% (20 of 50 cases) and 35% in exome-negative cases (8 of 23 cases), 4 of these were structural variants. FGA detected and mapped structural variants that are missed by short reads, including non-coding duplication, and phased variants across long distances of more than 180 kb. With the prioritization algorithm, longer DNA technologies could replace multiple tests for monogenic disorders and expand the range of variants detected. Our study suggests that genomes produced from technologies like FGA can improve variant detection and provide higher resolution genome maps for future application.

Gold Nanorods as an Efficient Substrate for the Detection and Degradation of Pesticides.

The rapid, ultralow detection, degradation, and complete removal of pesticides demand the design of potential substrates. Herein, we discussed gold nanorods (Au NRs) as the potential substrate for the naked eye detection and degradation of two common and broad-spectrum pesticides, chlorpyrifos (CPF) and malathion (MLT), up to 0.15 ppt concentration within 2 min. Under certain environmental conditions, both the pesticides degraded and adsorbed on the surface of Au NRs. The degraded moieties of CPF and MLT on the surface of Au NRs formed side-to-side and end-to-end interactions, respectively, leading to a long-range assembly. This shows that no external agent is required, and only CPF and MLT analytes are quite enough for the formation of assembly of Au NRs. Assembly of Au NRs is confirmed by transmission electron microscopy (TEM) analysis, and degradation is supported by Fourier transform infrared (FTIR) spectroscopy, Raman spectroscopy, and gas chromatography-mass spectrometry (GC-MS) analyses. Au NRs were recovered and reused for four consecutive cycles. The fast and ultralow detection of pesticides demonstrates that Au NRs are a potential substrate for the detection and degradation of pesticides.

Depletion-Mediated Interfacial Assembly of Semiconductor Nanorods.

Electronic devices comprised of nanocrystal (NC) thin film are projected to demonstrate enhanced figure of merit if NC building blocks self-assemble into highly uniform, 2-dimensional (2-D) superstructures with long-range order. Despite intensive research efforts and remarkable progress, long-range assembly of colloidal anisotropic NCs into thin films with orientational and positional order has remained to be addressed. One of the most promising approaches is to dissolve excess free molecules into NC solution, which has enabled the formation of NC monolayers with exceptional quality at air/solution interface. Nevertheless, the assembly mechanism and the role of free molecules have not been comprehensively elucidated, restricting the use of the approach. Here, we find that the interfacial assembly of CdSe/CdS core/shell nanorods (NRs) results in various ordered structures in the presence of free oleic acid molecules. The structures include a bundle of standing NRs, a belt of multilayered lying NRs, and a monolayer smectic phase, obtained by simple change in density of surface ligands on the NRs. Experimental observation and theoretical calculation reveal that the assembly is initiated at the air/solution interface due to the preferential depletion attraction of NRs to the interface. However, subsequent growth is significantly altered depending on the ligand density that determines the relative magnitude of interface-NR depletion attraction to inter-NR attraction. Highly ordered structures of NRs, especially for the monolayer smectic phase, are promising as a polarized light-emitting layer for thin-film optical devices. In addition, our findings on the depletion-mediated NR assembly provide important and universal design criteria for 2-D structuring of NCs with diverse geometries and compositions.

Long-Range Hierarchical Nanocrystal Assembly Driven by Molecular Structural Transformation.

The hierarchical control in biogenic minerals, from precise nanomorphology control to subsequent macroscopic assembly, remains a formidable challenge in artificial synthesis. Studies in biomineralization, however, are largely limited to atomicandmolecular scale crystallization, devoting little attention to biomolecular higher-order structures (HOSs) which critically impact long-range assembly of biominerals. Here we demonstrate a biomimetic route and quantitative simulationsthat explore peptide HOSs on guiding nanocrystal formation and anisotropic assembly into hierarchical structures. It is found that thePt{100}-specific peptide T7 (Ac-TLTTLTN-CONH2) adopts ST-turnsecondary structure, promoting cubic Pt nanocrystal formation at low concentration, and spontaneously transforms into a β-sheet with increased concentration. The β-sheet T7-Pt{100} specificity drives cubic Pt nanocrystals to self-assemble into large-area, long-range, [100] linear assemblies. This study provides a robust demonstration for bio/nonbiogenic material specificity, nanoscale synthesis, and long-range self-organization with biomolecular HOSs and opens vast opportunities for multiscale programmable structures.

Sustaining global agriculture through rapid detection and deployment of genetic resistance to deadly crop diseases.

Contents Summary 45 I. Introduction 45 II. Targeted chromosome-based cloning via long-range assembly (TACCA) 46 III. Resistance gene cloning through mutational mapping (MutMap) 47 IV. Cloning through mutant chromosome sequencing (MutChromSeq) 47 V. Rapid cloning through resistance gene enrichment and sequencing (RenSeq) 49 VI. Cloning resistance genes through transcriptome profiling (RNAseq) 49 VII. Resistance gene deployment strategies 49 VIII. Conclusions 50 Acknowledgements 50 References 50 SUMMARY: Genetically encoded resistance is a major component of crop disease management. Historically, gene loci conferring resistance to pathogens have been identified through classical genetic methods. In recent years, accelerated gene cloning strategies have become available through advances in sequencing, gene capture and strategies for reducing genome complexity. Here, I describe these approaches with key emphasis on the isolation of resistance genes to the cereal crop diseases that are an ongoing threat to global food security. Rapid gene isolation enables their efficient deployment through marker-assisted selection and transgenic technology. Together with innovations in genome editing and progress in pathogen virulence studies, this creates further opportunities to engineer long-lasting resistance. These approaches will speed progress towards a future of farming using fewer pesticides.

Partial bisulfite conversion for unique template sequencing.

We introduce a new protocol, mutational sequencing or muSeq, which uses sodium bisulfite to randomly deaminate unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling 135 000 restriction fragments in a PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone.

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly.

Cereal crops such as wheat and maize have large repeat-rich genomes that make cloning of individual genes challenging. Moreover, gene order and gene sequences often differ substantially between cultivars of the same crop species. A major bottleneck for gene cloning in cereals is the generation of high-quality sequence information from a cultivar of interest. In order to accelerate gene cloning from any cropping line, we report 'targeted chromosome-based cloning via long-range assembly' (TACCA). TACCA combines lossless genome-complexity reduction via chromosome flow sorting with Chicago long-range linkage to assemble complex genomes. We applied TACCA to produce a high-quality (N50 of 9.76 Mb) de novo chromosome assembly of the wheat line CH Campala Lr22a in only 4 months. Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene, using molecular marker information and ethyl methanesulfonate (EMS) mutants, and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis thaliana RPM1 protein.

Rapid Identification of Rust Resistance Genes Through Cultivar-Specific De Novo Chromosome Assemblies.

"Map-based cloning" is a frequently used approach to isolate rust resistance genes. A critical step during map-based cloning is the transition from genetic information, i.e., a genetic map, to physical sequence information. Bacterial artificial chromosome clones are often used to establish sequence information spanning a genetic interval. However, a major limitation of BAC clones consists in their small insert size of 100-200kb. Targeted chromosome-based cloning via long-range assembly (TACCA) is a method that can replace BAC library screening. This approach involves chromosome flow-sorting and the establishment of a long-range de novo assembly. This chapter provides an overview of TACCA as well as a detailed description of sequence analyses, molecular marker development, and candidate gene identification.

Influence of the shell thickness and charge distribution on the effective interaction between two like-charged hollow spheres.

The mean-force and the potential of the mean force between two like-charged spherical shells were investigated in the salt-free limit using the primitive model and Monte Carlo simulations. Apart from an angular homogeneous distribution, a discrete charge distribution where point charges localized on the shell outer surface followed an icosahedral arrangement was considered. The electrostatic coupling of the model system was altered by the presence of mono-, trivalent counterions or small dendrimers, each one bearing a net charge of 9 e. We analyzed in detail how the shell thickness and the radial and angular distribution of the shell charges influenced the effective interaction between the shells. We found a sequence of the potential of the mean force similar to the like-charged filled spheres, ranging from long-range purely repulsive to short-range purely attractive as the electrostatic coupling increased. Both types of potentials were attenuated and an attractive-to-repulsive transition occurred in the presence of trivalent counterions as a result of (i) thinning the shell or (ii) shifting the shell charge from the outer towards the inner surface. The potential of the mean force became more attractive with the icosahedrally symmetric charge model, and additionally, at least one shell tended to line up with 5-fold symmetry axis along the longest axis of the simulation box at the maximum attraction. The results provided a basic framework of understanding the non-specific electrostatic origin of the agglomeration and long-range assembly of the viral nanoparticles.

Long‐range assembly of DNA into nanofibers and highly ordered networks

Long-range assembly of DNA currently comprises both top-down and bottom-up methods. The top-down techniques consist of physical alignment of DNA and lithographic patterning to organize DNA on surfaces. The bottom-up approaches include lipid-and polymer-DNA co-assembly, the self-assembly of DNA amphiphiles, and the remarkably specific and versatile methods of DNA nanotechnology. DNA-based materials possess unprecedented molecular control and may offer innovative solutions in the fields of nanotechnology, sensing, nanomedicine, as well as optical and electronic devices. To realize the potential of these materials, a number of hurdles must be addressed. Bridging the gap between top-down fabrication and bottom-up assembly is of critical importance to the successful development of functional DNA-based technology. A profound understanding of both regimes is necessary to achieve this goal.

Modeling particle scattering structure factor for branched bio-inspired polymers in solution: A small angle X-ray scattering study

We present a study which illustrates the modeling of the Particle Scattering Structure Factor of an hyperbranched biopolymer in water solution using the Small Angle X-ray Scattering (SAXS) data. The studied sample was a sodium carboxilate terminated poly(amidoamine) dendrimer (generation 2.5) dispersed in water medium. The experimental inter-dendrimer structure factor S(q) has been analyzed in the framework of liquid integral equation theory for charged systems in solution. From that, we derive an effective interparticle interaction composed of a screened Coulombic plus hard-sphere repulsion potential, which allows the estimation of the dendrimer effective charge Zeff. The present analysis strongly supports the finding that structures and interaction of dendrimer are strongly influenced by charge effects. As a result, this quantity can be considered as a crucial parameter for the modulation of the degree of structural organization in solution, suitable for a number of potential applications. We conclude our form factor analysis with the investigation of the long-range assembly conditions during the growth of the intermediate nanoaggregates generated by the inclusion of aluminosilicate components of zeolite 13X on the surface of dendrimers.

Ge(001) As a Template for Long-Range Assembly of π-Stacked Coronene Rows

The adsorption of coronene molecules (C(24)H(12)) on the Ge(001) surface has been studied by means of scanning tunnelling microscopy (STM). Upon room temperature deposition, the coronene molecules adsorb in an upright geometry forming compact layers patterned in rows for coverages of one monolayer and less, being the only example investigated so far in which a pure aromatic hydrocarbon forms a well-ordered monolayer on a non-passivated semiconductor surface. At half monolayer, the molecular rows consist of long chains of π-stacked molecules and the distance between molecular planes is 8 Å. This configuration is maintained upon cooling the system below the transition temperature of Ge(001) (~220 K), but the molecular layer experiences also a transition from rows perpendicular to rows parallel to the Ge dimer rows. We interpret our observations in terms of a weak bonging between molecules and substrate, which facilitates the formation of large ordered domains of molecules, revealing Ge(001) as an ideal template for the growth of this and other aromatic hydrocarbons.

Stimuli-responsive organization of block copolymers on DNA nanotubes

DNA nanotubes are an attractive class of materials that can be assembled with precise control over their size, shape, length and porosity, and can encapsulate and release materials in response to specific added molecules. In parallel, block copolymer assemblies can provide biocompatibility, stability, nuclease resistance, the ability to encapsulate small molecules, long-range assembly and numerous additional functionalities that can be tuned with subtle chemical modifications. Herein, we describe a new class of hybrid materials in which block copolymer assemblies are sequence-specifically and longitudinally positioned on robust DNA nanotubes constructed using rolling circle amplification. These materials are dynamic, allowing the polymer structures to be cleanly removed from the DNA nanotubes only when a specific DNA sequence is added, and creating a single-stranded form of these nanotubes. Specifically, we first describe the use of rolling circle amplification to create a long DNA strand containing a repeat sequence. This is used as a guide strand in a new method to construct robust nanotubes with a non-nicked backbone. We then synthesize polymer–DNA conjugates through on-column functionalization of a DNA strand with a polymer. These conjugates self-assemble into spherical aggregates, which then position themselves onto the DNA nanotubes using sequence-specific hybridization, creating a ‘striped' structure. The polymer aggregates can be cleanly lifted off the nanotubes using a strand displacement strategy, thus uncapping these DNA nanotubes. We also show that this longitudinal alignment of polymer aggregates on DNA nanotubes is general for a variety of DNA–block copolymers.

Towards Reconfigurable Optical Metamaterials: Colloidal Nanoparticle Self-Assembly and Self-Alignment in Liquid Crystals

We explore the nanoscale colloidal self-assembly and self-alignment in liquid crystals. We use model particles with controlled shapes and sizes, including quantum dots and rods and metal nanoparticles in the form of spheres, rods, and polygonal platelets. To study these composites on the scales ranging from nanometers to millimeters and to motivate their use in metamaterial fabrication, we utilize optical microscopies, freeze-fracture transmission electron microscopy, and cryogenic transmission electron microscopy. We discuss the long-range alignment and assembly of anisotropic nanoparticles imposed by the orientational elasticity of liquid crystals, showing that these composites provide a powerful platform for self-assembly of metamaterials.

Long-Range Assembly of DNA into Nanofibers and Highly Ordered Networks Using a Block Copolymer Approach

A simple method to introduce the long-range order achieved by block copolymers into DNA structures is described. This results in the hierarchical assembly of short DNA strands into a new one-dimensional material, with high aspect ratio and the ability to further align into highly ordered surfaces over tens of micrometers. Fibers derived from biological materials have a wide range of potential applications, such as scaffolds for nanowires and one-dimensional (1D) materials, templates for tissue growth, and ligand display tools for multivalent biological interactions. Fibers derived from short DNA strands are an attractive class of materials, as they combine long-range 1D ordering with the programmability of DNA, and its ability to undergo structure switching with specifically added DNA strands. Here, we present the first examples of long fibers self-assembled from short (10-20 base-pairs), blunt-ended DNA strands. This was accomplished by covalently attaching a dendritic oligoethylene glycol (OEG) unit to a DNA strand to form a dendritic DNA molecule (D-DNA). Hybridization of this unit with complementary DNA creates a block copolymer/double-stranded DNA architecture, which readily undergoes self-assembly into long fibers upon the addition of a selective solvent. These fibers can further align into parallel rows, to yield highly ordered micrometer-sized surfaces. We demonstrate that a DNA nanotechnology motif, a three-helix DNA bundle, can also be readily induced to form long fibers upon incorporation of D-DNA. Thus, this provides a straightforward method to introduce hierarchical long-range ordering into DNA motifs, simply through hybridization with short D-DNA strands.