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At least 37 records · Page 2

Automated methods for scalable, parallelized enzymatic biopolymer synthesis and modification using microfluidic devices

Methods for the automated template-free synthesis of user-defined sequence controlled biopolymers using microfluidic devices are described. The methods facilitate simultaneous synthesis of up to thousands of uniquely addressed biopolymers from the controlled movement and combination of regents as fluid droplets using microfluidic and EWOD-based systems. In some forms, biopolymers including nucleic acids, peptides, carbohydrates, and lipids are synthesized from step-wise assembly of building blocks based on a user-defined sequence of droplet movements. In some forms, the methods synthesize uniquely addressed nucleic acids of up to 1,000 nucleotides in length. Methods for adding, removing and changing barcodes on biopolymers are also provided. Biopolymers synthesized according to the methods, and libraries and databases thereof are also described. Modified biopolymers, including chemically modified nucleotides and biopolymers conjugated to other molecules are described.

Banal, James↗

Engineering microbial consortia with rationally designed cellular interactions

Synthetic microbial consortia represent a frontier of synthetic biology that promises versatile engineering of cellular functions. They are primarily developed through the design and construction of cellular interactions that coordinate individual dynamics and generate collective behaviors. Here we review recent advances in the engineering of synthetic communities through cellular-interaction programming. We first examine fundamental building blocks for intercellular communication and unidirectional positive and negative interactions. Here, we then recap the assembly of the building blocks for creating bidirectional interactions in two-species ecosystems, which is followed by the discussion of engineering toward complex communities with increasing species numbers, under spatial contexts, and via model-guided design. We conclude by summarizing major challenges and future opportunities of engineered microbial ecosystems.

42 ENGINEERING↗

SOLL-E: A Module Transport and Placement Robot for Autonomous Assembly of Discrete Lattice Structures

This paper presents the design and development of a transport and placement robot that demonstrates autonomous assembly of structural building blocks. The robots are intended to serve as a critical component of automated structural assembly and maintenance systems. The Scaling Omni-directional Lattice Locomoting Explorer (SOLL-E) uses a 5-DoF bipedal inchworm locomotion architecture with locking foot and cargo grippers. The locomotion system employs large magnet gap diameter BLDC motors with moderate timing belt gearing for primary joints, and DC planetary gearmotors for turning. Foot and cargo grippers are identical, with servo-actuated locking mechanisms. Three modular controller boards are used to control these actuators in real-time, with command and telemetry data transferred between the server and each controller board via WiFi. Functionality and performance were evaluated in a ground demonstration.

robotics↗

Diversifying hierarchical ionic assembly by docking cations to anions as salt bridges

Here, we expand the diversity of building blocks available for ionic assembly by introducing tertiary (3°) ammonium cations into anion complexes. We use proton transfer between 3° amines and organo-phosphoric acids to generate H-bonding cations (R 3 NH + ) and anions (RHPO 4 – ) that co-assemble with cyanostar macrocycles into assemblies with 2:2:2 stoichiometry. At the heart is a supramolecular dimer where phosphate anions form salt bridges by H-bonding with cations. Unlike conventional 4° ammonium cations, 3,000 commercial amines provide diversity for high-throughput screening of 72 combinations (9 nitrogen bases and 8 acids), producing 13 privileged partners for quantitative assembly. Yields depend on the solvent and sterics of salt bridge formation. Ten more nitrogen bases connect to fluorophores (pyrene), photocatalysts (quinoline), drugs (Cipralex, Zytiga), and ionic liquids (imidazole). The synthesis and examination of 82 new salts exemplify how acid-base chemistry can open a pipeline to a diversity of building blocks for exploring hierarchical ionic assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Design of multi-scale protein complexes by hierarchical building block fusion

A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials.

59 BASIC BIOLOGICAL SCIENCES↗

Oxygen-responsive bacterial gene switch

The invention provided herein relates to sequence determinants that elicit certain levels of gene expression and methods for obtaining engineered ligand-responsive gene switches comprising these sequence determinants. More particularly, the invention provided herein relates to molecular building blocks (i.e., discrete nucleotide sequences), synthetic ligand-responsive gene switches comprising an assembly of these molecular building blocks, and methods of using synthetic ligand-responsive gene switches as customizable and controllable expression systems and sensors.

Kiley, Patricia J.↗

Directing the adsorption and assembly of laponite nano-discs at oil–water interfaces

Achieving tunable controls on the adsorption and self-assembly of nanoscale building blocks at immiscible fluid interfaces is essential for synthesizing advanced materials, stabilizing emulsions, and the sustainable storage and recovery of fluids. Although extensive efforts have been directed toward resolving the assembly of spherical nanoparticles at water–hydrocarbon interfaces, 2D nanoparticles have received far less attention. In this study, we developed novel controls to direct the adsorption and assembly of 2D laponite nano-discs (diameter = ∼30 nm and thickness = ∼1 nm) at water–heptane interfaces using traces of sodium dodecyl sulfate (SDS) surfactant, demonstrated by advanced in situ small-angle X-ray scattering, atomic force microscopy, spinning drop tensiometer measurements and molecular dynamics simulations. The results show that SDS surfactant displaces the adsorbed laponite nano-discs from the interface toward the aqueous phase. The extent of this displacement increases with SDS concentration such that high SDS concentrations convert laponite-rich interfaces to SDS-rich interfaces free of laponite nano-discs. This transformation is associated with significant alterations in the rheological and nanomechanical properties of the host interface. In this context, reduction in interfacial tension and interfacial stiffness and an increase in the interfacial deformation is observed on increasing the SDS concentration from 0 to 0.1 wt%. The displacement of laponite nano-discs from the interface is driven by strong electrostatic interactions between the hydrophilic SDS group and interfacial water molecules. These studies unlock new insights into the adsorption and assembly of 2D nanoscale particles at water–hydrocarbons interfaces that are relevant for various applications related to energy and environmental science and engineering.

interfacial tension↗

Development of a Cryogenic Thermal Distortion Measurement Facility for Testing the James Webb Space Telescope Instrument Support Integration Module 2-D Test Assemblies

The James Webb Space Telescope Instrument Support Integration Module (ISIM) is being designed and developed at the Goddard Space Flight Center. The ISM Thermal Distortion Testing (ITDT) program was started with the primary objective to validate the ISM mechanical design process. The ITDT effort seeks to establish confidence and demonstrate the ability to predict thermal distortion in composite structures at cryogenic temperatures using solid element models. This-program's goal is to better ensure that ISIM meets all the mechanical and structural requirements by using test results to verify or improve structural modeling techniques. The first step to accomplish the ITDT objectives was to design, and then construct solid element models of a series 2-D test assemblies that represent critical building blocks of the ISIM structure. Second, the actual test assemblies consisting of composite tubes and invar end fittings were fabricated and tested for thermal distortion. This paper presents the development of the GSFC Cryo Distortion Measurement Facility (CDMF) to meet the requirements of the ISIM 2-D test. assemblies, and other future ISIM testing needs. The CDMF provides efficient cooling with both a single, and two-stage cryo-cooler. Temperature uniformity of the test assemblies during thermal transients and at steady state is accomplished by using sapphire windows for all of the optical ports on the radiation shields and by using .thermal straps to cool the test assemblies. Numerical thermal models of the test assemblies were used to predict the temperature uniformity of the parts during cooldown and at steady state. Results of these models are compared to actual temperature data from the tests. Temperature sensors with a 0.25K precision were used to insure that test assembly gradients did not exceed 2K lateral, and 4K axially. The thermal distortions of two assemblies were measured during six thermal cycles from 320K to 35K using laser interferometers. The standard deviation for all of the distortion measurements is less than 0.5 microns, which falls within the ISIM requirement of 3 microns.

Miller, Franklin↗

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly

The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed “fatal,” and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context.

59 BASIC BIOLOGICAL SCIENCES↗

Shaping Peptide Assemblies Using Multifaceted Cyclic Tectons

Constructing distinct biomacromolecular assemblies typically necessitates target-specific selection and engineering of building blocks alongside optimization of assembly conditions. The challenge lies in achieving diverse morphological outcomes using simple, shared modules under identical conditions, a hallmark of natural systems that remains elusive in synthetic approaches. Here, in this work, we present a molecular scaffold-based strategy to instruct the coassembly of the same set of peptides into a variety of nanostructures across multiple dimensions. We create trifaceted cyclic scaffolds to manipulate two pairs of dimeric coiled-coil peptides prior to coassembly. These scaffolds, with addressable and orthogonal modules, allow controlled exposure of their cohesive faces, directing the formation of nanotriangles and fibrillar and lamellar assemblies. By tuning interpeptide arrangements that dictate scaffold geometry, we construct nonstraight fibrils with tunable curvature, which are rarely observed before. Notably, these scaffolds exhibit plasticity in adapting the sizes and orientations of cohesive faces to different assembly morphologies. The resultant nanostructures are consistent with the design and simulation results, demonstrating the reliability and predictability of this approach. Multifaceted cyclic scaffolds bridge the intellectual and physical gaps between building peptides and assemblies, holding promise for endowing various existing assembly systems with high tunability and versatility.

assembly morphology↗

Discrete Assemblers Utilizing Conventional Motion Systems

An alternative to additive manufacturing is disclosed, introducing an end-to-end workflow in which discrete building blocks are reversibly joined to produce assemblies called digital materials. Described is the design of the bulk-material building blocks and the devices that are assembled from them. Detailed is the design and implementation of an automated assembler, which takes advantage of the digital material structure to avoid positioning errors within a large tolerance. To generate assembly sequences, a novel CAD/CAM workflow is described for designing, simulating, and assembling digital materials. The structures assembled using this process have been evaluated, showing that the joints perform well under varying conditions and that the assembled structures are functionally precise.

Langford, William Kai↗

ATRP Enhances Structural Correlations In Polymerization–Induced Phase Separation**

Synthetic methods to control the structure of materials at sub–micron scales are typically based on the self–assembly of structural building blocks with precise size and morphology. On the other hand, many living systems can generate structure across a broad range of length scales in one step directly from macromolecules, using phase separation. Here, we introduce and control structure at the nano– and microscales through polymerization in the solid state, which has the unusual capability of both triggering and arresting phase separation. In particular, we show that atom transfer radical polymerization (ATRP) enables control of nucleation, growth, and stabilization of phase–separated poly–methylmethacrylate (PMMA) domains in a solid polystyrene (PS) matrix. ATRP yields durable nanostructures with low size dispersity and high degrees of structural correlations. Furthermore, we demonstrate that the length scale of these materials is controlled by the synthesis parameters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Inkjet printing of epitaxially connected nanocrystal superlattices

Access to a blossoming library of colloidal nanomaterials provides building blocks for complex assembled materials. The journey to bring these prospects to fruition stands to benefit from the application of advanced processing methods. Epitaxially connected nanocrystal (or quantum dot) superlattices present a captivating model system for mesocrystals with intriguing emergent properties. The conventional processing approach to creating these materials involves assembling and attaching the constituent nanocrystals at the interface between two immiscible fluids. Processing small liquid volumes of the colloidal nanocrystal solution involves several complexities arising from the concurrent spreading, evaporation, assembly, and attachment. The ability of inkjet printers to deliver small (typically picoliter) liquid volumes with precise positioning is attractive to advance fundamental insights into the processing science, and thereby potentially enable new routes to incorporate the epitaxially connected superlattices into technology platforms. In this study, we identified the processing window of opportunity, including nanocrystal ink formulation and printing approach to enable delivery of colloidal nanocrystals from an inkjet nozzle onto the surface of a sessile droplet of the immiscible subphase. We demonstrate how inkjet printing can be scaled-down to enable the fabrication of epitaxially connected superlattices on patterned sub-millimeter droplets. Furthermore, we anticipate that insights from this work will spur on future advances to enable more mechanistic insights into the assembly processes and new avenues to create high-fidelity superlattices.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Superatomic chemistry

Superatoms are atomic clusters with tailored size and composition that mimic the chemistry of atoms in the periodic table. However, unlike the atoms whose chemistry is governed by their valence electron orbitals, the chemistry of superatoms is governed by their highest occupied molecular orbitals. In addition, due to their large size and non-spherical geometry, superatoms can promote unusual reactions and serve as the building blocks of cluster assembled materials with properties very different from conventional materials. This perspective highlights the unique role of superatoms in chemical and material sciences by focusing on superhalogens, which not only possess electron affinities larger than those of halogens but also can be stable when multiply charged. We discuss how these unique features of superhalogens enable noble gas atoms like argon to form chemical bonds at room temperature and zinc to exhibit an oxidation state of +3. Here, the advantages of using superhalogens in the synthesis of water-resistant materials for solar cells, halogen-free electrolytes for solid-state batteries, and multiferroic materials are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Driving forces for particle-based crystallization: From experiments to theory and simulations

The multi-step crystallization processes involving the formation of stable building blocks that subsequently assemble into a crystal are ubiquitous in mineral formation and biomineralization and are particularly attractive in materials synthesis. Utilizing these pathways offers the approach to overcoming the restrictions on the expression of various crystal faces imposed by the interfacial energy during monomer-by-monomer growth to unlock the breadth of architectures with unique properties. Further, controlling particle-based crystallization proved challenging despite its promise due to the complex interdependence of interfacial forces and their non-linear dependence on synthesis parameters. Here, the status of the development of state-of-the-art approaches to measuring interparticle forces and predictive theoretical models of particle-based crystallization are reviewed.

36 MATERIALS SCIENCE↗

VLSI architecture for a Reed-Solomon decoder

A basic single-chip building block for a Reed-Solomon (RS) decoder system is partitioned into a plurality of sections, the first of which consists of a plurality of syndrome subcells each of which contains identical standard-basis finite-field multipliers that are programmable between 10 and 8 bit operation. A desired number of basic building blocks may be assembled to provide a RS decoder of any syndrome subcell size that is programmable between 10 and 8 bit operation.

Hsu, In-Shek↗

Fast truncated SVD of sparse and dense matrices on graphics processors

We investigate the solution of low-rank matrix approximation problems using the truncated singular value decomposition (SVD). For this purpose, we develop and optimize graphics processing unit (GPU) implementations for the randomized SVD and a blocked variant of the Lanczos approach. Our work takes advantage of the fact that the two methods are composed of very similar linear algebra building blocks, which can be assembled using numerical kernels from existing high-performance linear algebra libraries. Furthermore, the experiments with several sparse matrices arising in representative real-world applications and synthetic dense test matrices reveal a performance advantage of the block Lanczos algorithm when targeting the same approximation accuracy.

Computer Science↗