Low-cost, Arduino-based, portable device for measurement of methane composition in biogas
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Energy & Fuels↗
SEARCH · Engineering Papers
Results for “PROGRAMMER”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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The RNA synthesis machinery of negative-stranded RNA viruses
The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and function of the ribonucleoprotein components: Atomic structure of the RNA polymerase complex. • Commonalities and differences between segmented- and non-segmented NSVs. • Transcription versus replication programmes.
60 APPLIED LIFE SCIENCES↗
Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression
Plant growth requires the integration of internal and external cues, perceived and transduced into a developmental programme of cell division, elongation and wall thickening. Mechanical forces contribute to this regulation, and thigmomorphogenesis typically includes reducing stem height, increasing stem diameter, and a canonical transcriptomic response. We present data on a bZIP transcription factor involved in this process in grasses. Brachypodium distachyon SECONDARY WALL INTERACTING bZIP (SWIZ) protein translocated into the nucleus following mechanostimulation. Classical touch-responsive genes were upregulated in B. distachyon roots following touch, including significant induction of the glycoside hydrolase 17 family, which may be unique to grass thigmomorphogenesis. SWIZ protein binding to an E-box variant in exons and introns was associated with immediate activation followed by repression of gene expression. SWIZ overexpression resulted in plants with reduced stem and root elongation. These data further define plant touch-responsive transcriptomics and physiology, offering insights into grass mechanotranduction dynamics.
Coomey, Joshua↗
Congenital toxoplasmosis in humans: an update of worldwide rate of congenital infections
Abstract The morbidity due to congenital toxoplasmosis in humans is very high. Most of these infected children are likely to develop symptoms of clinical toxoplasmosis. Sequelae in fetus resulting from Toxoplasma gondii infections in women who become infected with this parasite during pregnancy can be devastating and enormous efforts are directed in some countries to prevent these consequences. Here, an update on congenital toxoplasmosis in humans, especially the rate of congenital infections in humans worldwide, is provided. Although several countries have surveillance programmes, most information on the rate of congenital transmission is from France and Brazil. Because of compulsory national screening programme in France to detect and treat women with recently acquired T. gondii infection with anti-toxoplasma therapy, the rate of congenital transmission and the severity of disease in children are declining. Infections by this parasite are widely prevalent in Brazil. The severity of clinical toxoplasmosis in Brazilian children is very high and may be associated with the genetic characteristics of T. gondii isolates prevailing in animals and humans in Brazil. Virtually little or no information is available on this topic from China, India and other countries in Asia.
Parasitology↗
Fundamental Processes and Practical Considerations of Lead Chalcogenide Mesocrystals Formed via Self-Assembly and Directed Attachment of Nanocrystals at a Fluid Interface
Significant advances in the synthesis and processing of colloidal nanocrystals have given scientists and engineers access to a vast library of building blocks with precisely defined size, shape, and composition. These materials have inspired exciting prospects to enable bottom-up fabrication of programmable materials with properties by design. Successfully assembling and connecting the building blocks into superstructures in which constituent nanocrystals can purposefully interact requires robust understanding of and control over a complex interplay of dynamic physicochemical processes. Fluid interfaces provide an advantageous experimental workbench to both probe and control these processes. Despite the ostensible simplicity of fabricating nanocrystal assemblies at a fluid interface, sensitivity to processing conditions and limited reproducibility have underscored the complexity of this process. In situ studies have provided mechanistic insights into the competing dynamics of key subprocesses including solvent spreading and evaporation, superlattice formation, ligand detachment kinetics, and nanocrystal attachment. Understanding how these subprocesses influence the complex choreography of self-assembly, structure transformation, and oriented attachment processes presents a rich research challenge. In this context, we present a detailed methodology for self-assembly and attachment of lead chalcogenide nanocrystals at a liquid–gas interface as a model system for the fabrication of mono- and multilayer cubic connected superlattices. We discuss key experimental parameters such as the characteristics of the building blocks and processing conditions and detailed steps from colloidal nanocrystal injection to superlattice transfer. Furthermore, we hope that this Methods/Protocols paper will provide guidance for future advances in the exciting path toward bringing the prospect of nanocrystal-based programmable materials to fruition.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Quantum Package 2.0: An Open-Source Determinant-Driven Suite of Programs
Quantum chemistry is a discipline which relies heavily on very expensive numerical computations. The scaling of correlated wave function methods lies, in their standard implementation, between O(N-5) and O(e(N)), where N is proportional to the system size. Therefore, performing accurate calculations on chemically meaningful systems requires (i) approximations that can lower the computational scaling and (ii) efficient implementations that take advantage of modern massively parallel architectures. QUANTUM PACKAGE is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multireference second-order perturbation theory (PT2). The determinant-driven framework allows the programmer to include any arbitrary set of determinants in the reference space, hence providing greater methodological freedom. The sCI method implemented in QUANTUM PACKAGE is based on the CIPSI (Configuration Interaction using a Perturbative Selection made Iteratively) algorithm which complements the variational sCI energy with a PT2 correction. Additional external plugins have been recently added to perform calculations with multireference coupled cluster theory and range-separated density-functional theory. All the programs are developed with the IRPF90 code generator, which simplifies collaborative work and the development of new features. QUANTUM PACKAGE strives to allow easy implementation and experimentation of new methods, while making parallel computation as simple and efficient as possible on modern supercomputer architectures. Currently, the code enables, routinely, to realize runs on roughly 2 000 CPU cores, with tens of millions of determinants in the reference space. Moreover, we have been able to push up to 12 288 cores in order to test its parallel efficiency. In the present manuscript, we also introduce some key new developments: (i) a renormalized second-order perturbative correction for efficient extrapolation to the full CI limit and (ii) a stochastic version of the CIPSI selection performed simultaneously to the PT2 calculation at no extra cost.
Garniron, Yann↗
Characterizing DNA Corona Rigidity in DNA-Directed Gold Nanoparticle Crystalline Structures
DNA-linked gold nanoparticle systems have become an adaptable self-assembly tool for programming various crystalline orders. The programmability lies in the DNA corona, a highly dense outer shell of DNA linkers that binds the nanoparticles together. Various self-assembled structures can be formed by changing the properties of the DNA corona, particularly the size ratio. However, uncertainty still remains as to the actual behavior and structural rigidity of the DNA itself, impeding advances in structural diversification. Specifically, the DNA could adopt an A-form structure after crystallization, or a more flexible DNA corona could be generated if B-form DNA persists but becomes physically bent and adsorbed to the nanoparticle surface in crystal formations. To understand the rigidity of the DNA corona, we devised a method to stretch the DNA between two nanoparticles by simultaneously using short and long linkers. This linker combination flexibly acts as a single linker, rather than two separate linkers that create two ranges of interactions. By measuring the edge-to-edge distance between the two nanoparticles using both linkers in small-angle X-ray scattering (SAXS) experiments, we recorded the first per-base contribution that is consistent with the B-form DNA rise of 3.4 Å. Here, the elucidation of DNA behavior within nanoparticle crystals is essential for understanding the programmability of DNA-linked nanoparticle systems.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Selective and Scalable Control of Spin Quantum Memories in a Photonic Circuit
A central goal in many quantum information processing applications is a network of quantum memories that can be entangled with each other while being individually controlled and measured with high fidelity. This goal has motivated the development of programmable photonic integrated circuits (PICs) with integrated spin quantum memories using diamond color center spin-photon interfaces. However, this approach introduces a challenge into the microwave control of individual spins within closely packed registers. Here, we present a quantum memory-integrated photonics platform capable of (i) the integration of multiple diamond color center spins into a cryogenically compatible, high-speed programmable PIC platform, (ii) selective manipulation of individual spin qubits addressed via tunable magnetic field gradients, and (iii) simultaneous control of qubits using numerically optimized microwave pulse shaping. The combination of localized optical control, enabled by the PIC platform, together with selective spin manipulation opens the path to scalable quantum networks on intrachip and interchip platforms.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Toward Computation-Guided Design of Tunable Organic-Inorganic CdS Quantum Dot Binary Superlattices
Combining the advantages of structural programmability in sequence-defined biomimetic molecules and the controllable packing geometry in nanoparticle superlattices, we demonstrate a self-assembled organic-inorganic superlattice whose structure can be altered with the slightest change in the sequence of the organic counterpart. Here, oleate-coated CdS quantum dots (QDs) form a square-packed superlattice with a 1:1 molar equivalence of a di-block amphiphilic peptoid (Nbrpe6Dig) in chloroform. In contrast, no apparent structure is observed in the organic solvent alone. Based on theoretical evidence, we show that the assembly is a binary superlattice where both the CdS QDs and the peptoids serve as building blocks and further predict a correlation between the superlattice structure and the peptoid sequence. The computationally guided prediction is validated by experiments where superlattice transformation is observed with modified peptoids. The mechanism identified in our work inspires new ways to control and tune organic-inorganic hybrid nanomaterial self-assembly.
Qi, Xin↗
Nanotubes Growth by Self-Assembly of DNA Strands at Room Temperature
Artificial biomolecular nanotubes are a promising approach to building materials mimicking the capacity of the cellular cytoskeleton to grow and self-organize dynamically. Nucleic acid nanotechnology has demonstrated a variety of self-assembling nanotubes with programmable, robust features and morphological similarities to actual cytoskeleton components. However, their production typically requires thermal annealing, which not only poses a general constraint on their potential applications but is also incompatible with physiological conditions. Here, we demonstrate that DNA nanotubes can self-assemble from a simple mixture of five short DNA strands at constant room temperature, growing for extended periods of time in bulk conditions as well as under confinement. Assembly is achieved using a monovalent salt buffer, which ensures a faithful nanoscale arrangement and avoids nanotube aggregation. We observe the formation of individual nanotubes up to 20 days with a diameter of 22 ± 4 nm and length of several tens of micrometers. We finally encapsulate the strands in microsized compartments, such as water-in-oil microdroplets and giant unilamellar vesicles serving as simple cell models. Notably, nanotubes not only isothermally self-assemble directly inside the microcompartments but also self-organize into dynamic higher-order structures resembling rings and dynamic networks. Our study provides an advantageous method for in situ assembly of programmable biomolecular scaffolds and materials using synthetic DNA strands without requirements of thermal treatment.
Chemistry↗
Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals
The foundational goal of structural DNA nanotechnology—the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems—was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest–DNA conjugates with a specified crystalline hand.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Controllable 0–π Josephson junctions containing a ferromagnetic spin valve
Superconductivity and ferromagnetism are antagonistic forms of order, and rarely coexist. Many interesting new phenomena occur, however, in hybrid superconducting/ferromagnetic systems. For example, a Josephson junction containing a ferromagnetic material can exhibit an intrinsic phase shift of π in its ground state for certain thicknesses of the material. Such ‘π-junctions’ were first realized experimentally in 2001, and have been proposed as circuit elements for both high-speed classical superconducting computing and for quantum computing. Here we demonstrate experimentally that the phase state of a Josephson junction containing two ferromagnetic layers can be toggled between 0 and pi by changing the relative orientation of the two magnetizations. These controllable 0–π junctions have immediate applications in cryogenic memory, where they serve as a necessary component to an ultralow power superconducting computer. Such a fully superconducting computer is estimated to be orders of magnitude more energy-efficient than current semiconductor-based supercomputers. Here, phase-controllable junctions also open up new possibilities for superconducting circuit elements such as superconducting ‘programmable logic’, where they could function in superconducting analogues to field-programmable gate arrays.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Dynamic self-assembly of compartmentalized DNA nanotubes
Abstract Bottom-up synthetic biology aims to engineer artificial cells capable of responsive behaviors by using a minimal set of molecular components. An important challenge toward this goal is the development of programmable biomaterials that can provide active spatial organization in cell-sized compartments. Here, we demonstrate the dynamic self-assembly of nucleic acid (NA) nanotubes inside water-in-oil droplets. We develop methods to encapsulate and assemble different types of DNA nanotubes from programmable DNA monomers, and demonstrate temporal control of assembly via designed pathways of RNA production and degradation. We examine the dynamic response of encapsulated nanotube assembly and disassembly with the support of statistical analysis of droplet images. Our study provides a toolkit of methods and components to build increasingly complex and functional NA materials to mimic life-like functions in synthetic cells.
59 BASIC BIOLOGICAL SCIENCES↗
Quantum fluctuations drive nonmonotonic correlations in a qubit lattice
Abstract Fluctuations may induce the degradation of order by overcoming ordering interactions, consequently leading to an increase of entropy. This is particularly evident in magnetic systems characterized by nontrivial, constrained disorder, where thermal or quantum fluctuations can yield counterintuitive forms of ordering. Using the proven efficiency of quantum annealers as programmable spin system simulators, we present a study based on entropy postulates and experiments on a platform of programmable superconducting qubits to show that a low level of uncertainty can promote ordering in a system impacted by both thermal and quantum fluctuations. A set of experiments is proposed on a lattice of interacting qubits arranged in a triangular geometry with precisely controlled disorder, effective temperature, and quantum fluctuations. Our results demonstrate the creation of ordered ferrimagnetic and layered anisotropic disordered phases, displaying characteristics akin to the elegant order-by-disorder phenomenon. Extensive experimental evidence is provided for the role of quantum fluctuations in lowering the total energy of the system by increasing entropy and defect clustering. Our thorough and comprehensive application of an intentionally introduced noise on a quantum platform provides insight into the dynamics of defects and fluctuations in quantum devices, which may help to reduce the cost associated with quantum processing.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Tunable quantum emitters on large-scale foundry silicon photonics
Abstract Controlling large-scale many-body quantum systems at the level of single photons and single atomic systems is a central goal in quantum information science and technology. Intensive research and development has propelled foundry-based silicon-on-insulator photonic integrated circuits to a leading platform for large-scale optical control with individual mode programmability. However, integrating atomic quantum systems with single-emitter tunability remains an open challenge. Here, we overcome this barrier through the hybrid integration of multiple InAs/InP microchiplets containing high-brightness infrared semiconductor quantum dot single photon emitters into advanced silicon-on-insulator photonic integrated circuits fabricated in a 300 mm foundry process. With this platform, we achieve single-photon emission via resonance fluorescence and scalable emission wavelength tunability. The combined control of photonic and quantum systems opens the door to programmable quantum information processors manufactured in leading semiconductor foundries.
Larocque, Hugo (ORCID:000900095849780X)↗
Colloidal quasicrystals engineered with DNA
In principle, designing and synthesizing almost any class of colloidal crystal is possible. Nonetheless, the deliberate and rational formation of colloidal quasicrystals has been difficult to achieve. Here we describe the assembly of colloidal quasicrystals by exploiting the geometry of nanoscale decahedra and the programmable bonding characteristics of DNA immobilized on their facets. Further, this process is enthalpy-driven, works over a range of particle sizes and DNA lengths, and is made possible by the energetic preference of the system to maximize DNA duplex formation and favour facet alignment, generating local five- and six-coordinated motifs. This class of axial structures is defined by a square–triangle tiling with rhombus defects and successive on-average quasiperiodic layers exhibiting stacking disorder which provides the entropy necessary for thermodynamic stability. Taken together, these results establish an engineering milestone in the deliberate design of programmable matter.
36 MATERIALS SCIENCE↗
Particle physics at accelerators in the United States and Asia
Particle physics experiments in the United States and Asia have greatly contributed to the understanding of elementary particles and their interactions. With the recent discovery of the Higgs boson at CERN, interest in the development of next-generation colliders has been rekindled. A linear electron–positron collider in Japan and a circular collider in China have been proposed for precision studies of the Higgs boson. In addition to the Higgs programme, new accelerator-based long-baseline neutrino mega-facilities are being built in the United States and Japan. Here, we outline the present status of key particle physics programmes at accelerators, and future plans in the United States and Asia that largely complement approaches being explored in the European Strategy for Particle Physics Update. Furthermore, we encourage the pursuit of this global approach, reaching beyond regional boundaries for optimized development and operations of major accelerator facilities worldwide, to ensure an active and productive future of the field.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Crystal engineering with DNA
This Review chronicles over two decades of research into creating a genetic code for crystal engineering. Rather than directing biological processes, this code uses synthetic forms of DNA to programme the assembly of nanoparticles and microparticles into 1D, 2D and 3D crystalline architectures, in which almost every aspect of the resultant structures can be systematically controlled. Within this conceptual framework, the structural and functional advances are described in an effort to define the present level of sophistication and to predict future directions of the platform. These advances include exotic structures with programmable lattice symmetries and well-defined crystal habits, responsive materials that leverage the intrinsic properties of nucleic acids to manipulate structures on demand, nanoparticle superlattices grown epitaxially from surfaces and colloidal crystals that offer insights into light–matter interactions. Looking forward, we challenge the community to leverage the extraordinary structural control afforded by crystal engineering with DNA to synthesize classes of functional materials that push beyond what has been possible with naturally occurring crystalline materials or those made by more conventional strategies.
catalysis (homogeneous), solar (photovoltaic), bio↗