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At least 1,333 records · Page 74

Developmental assembly of multi-component polymer systems through interconnected synthetic gene networks in vitro

Abstract Living cells regulate the dynamics of developmental events through interconnected signaling systems that activate and deactivate inert precursors. This suggests that similarly, synthetic biomaterials could be designed to develop over time by using chemical reaction networks to regulate the availability of assembling components. Here we demonstrate how the sequential activation or deactivation of distinct DNA building blocks can be modularly coordinated to form distinct populations of self-assembling polymers using a transcriptional signaling cascade of synthetic genes. Our building blocks are DNA tiles that polymerize into nanotubes, and whose assembly can be controlled by RNA molecules produced by synthetic genes that target the tile interaction domains. To achieve different RNA production rates, we use a strategy based on promoter “nicking” and strand displacement. By changing the way the genes are cascaded and the RNA levels, we demonstrate that we can obtain spatially and temporally different outcomes in nanotube assembly, including random DNA polymers, block polymers, and as well as distinct autonomous formation and dissolution of distinct polymer populations. Our work demonstrates a way to construct autonomous supramolecular materials whose properties depend on the timing of molecular instructions for self-assembly, and can be immediately extended to a variety of other nucleic acid circuits and assemblies.

Science & Technology - Other Topics↗

Parametric tuning of quantum phase transitions in ultracold reactions

Advances in atomic physics have led to the possibility of a coherent transformation between ultracold atoms and molecules including between completely bosonic condensates. Such transformations are enabled by the magneto-association of atoms at a Feshbach resonance which results in a passage through a quantum critical point. In this study, we show that the presence of generic interaction between the constituent atoms and molecules can fundamentally alter the nature of the critical point, change the yield of the reaction and the order of the consequent phase transition. We find that the correlations introduced by this interaction induce nontrivial many-body physics such as coherent oscillations between atoms and molecules, and a selective formation of squeezed molecular quantum states and quantum cat states. We provide analytical and numerical descriptions of these effects, along with scaling laws for the reaction yield in non-adiabatic regimes.

36 MATERIALS SCIENCE↗

Octo-diamond crystal of nanoscale tetrahedra with interchanging chiral motifs

Despite their simplicity, tetrahedra can assemble into diverse high- and low-density structures. Here we report a low-density ‘octo-diamond’ structure formed by nanoscale solid tetrahedra with a 64-tetrahedron unit cell containing 8 cubic-diamond subcells. The formed crystal is achiral, but is composed of chiral bilayers with alternating handedness. The left- and right-handed chirality of the bilayers, combined with the plasmonic nature of the gold tetrahedra, produces chiroptical responses at the crystal surface. We uncover that the hydrophobic substrate facilitates the arrangement of tetrahedra into irregular ring-like patterns, creating a critical, uneven topography to stabilize the observed octo-diamond structure. This study reveals a potent way to affect colloidal crystallization through particle–substrate interactions, expanding the nanoparticle self-assembly toolbox.

36 MATERIALS SCIENCE↗

Modeling separation of lanthanides via heterogeneous ligand binding

Individual lanthanide elements have physical/electronic/magnetic properties that make each useful for specific applications. Several of the lanthanides cations (Ln 3+ ) naturally occur together in the same ores. They are notoriously difficult to separate from each other due to their chemical similarity. Predicting the Ln 3+ differential binding energies (ΔΔE) or free energies (ΔΔG) at different binding sites, which are key figures of merit for separation applications, will help design of materials with lanthanide selectivity. We apply ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) to calculate ΔΔG for Ln 3+ coordinated to ligands in water and embedded in metal–organic frameworks (MOFs), and ΔΔE for Ln 3+ bonded to functionalized silica surfaces, thus circumventing the need for the computational costly absolute binding (free) energies ΔG and ΔE. Perturbative AIMD simulations of water-inundated simulation cells are applied to examine the selectivity of ligands towards adjacent Ln 3+ in the periodic table. Static DFT calculations with a full Ln 3+ first coordination shell, while less rigorous, show that all ligands examined with net negative charges are more selective towards the heavier lanthanides than a charge-neutral coordination shell made up of water molecules. Amine groups are predicted to be poor ligands for lanthanide-binding. Finally, we also address cooperative ion binding, i.e., using different ligands in concert to enhance lanthanide selectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Controlling N speciation in solution synthesis of N-doped carbon materials

Carbon-based materials, such as graphite and its functionalized/doped derivatives, are promising lightweight layered materials for hydrogen activation and storage. Their propensity to control the thermodynamics of hydrogen binding and the kinetics of hydrogen mobility strongly depends on the speciation and the arrangement of dopants. In this study, we demonstrate precise control over dopant speciation and clustering in nitrogen-containing layered carbon materials during hydrothermal synthesis. Through extensive spectroscopic characterization and first principles simulations, we demonstrate that the formation of N-motifs can be controlled by the choice of precursor and synthesis temperature. The distinct three-dimensional architecture and porosity in graphene oxide and carbon nitride-derived materials furnish a synthetic pathway for precise control over the local and global structure of nitrogen-doped carbon materials and their activity toward the activation of molecular hydrogen.

Byun, Mi Yeon [Pacific Northwest National Laborato↗

Effects of elevated-temperature deposition on the atomic structure of amorphous Ta 2 O 5 films

Brownian thermal noise as a result of mechanical loss in optical coatings will become the dominant source of noise at the most sensitive frequencies of ground-based gravitational-wave detectors. Experiments found, however, that a candidate material, amorphous Ta 2 O 5 , is unable to form an ultrastable glass and, consequently, to yield a film with significantly reduced mechanical loss through elevated-temperature deposition alone. X-ray scattering PDF measurements are carried out on films deposited and subsequently annealed at various temperatures. Inverse atomic modeling is used to analyze the short and medium range features in the atomic structure of these films. Furthermore, in silico deposition simulations of Ta 2 O 5 are carried out at various substrate temperatures and an atomic level analysis of the growth at high temperatures is presented. It is observed that upon elevated-temperature deposition, short range features remain identical, whereas medium range order increases. After annealing, however, both the short and medium range orders of films deposited at different substrate temperatures are nearly identical. A discussion on the surface diffusion and glass transition temperatures indicates that future pursuits of ultrastable low-mechanical-loss films through elevated temperature deposition should focus on materials with a high surface mobility, and/or lower glass transition temperatures in the range of achievable deposition temperatures.

36 MATERIALS SCIENCE↗

Atomic cluster expansion potential for large scale simulations of hydrocarbons under shock compression

We present an Atomic Cluster Expansion (ACE) machine learned potential developed for high-fidelity atomistic simulations of hydrocarbons, targeting pressures and temperatures near and above supercritical fluid regimes for molecular fluids. A diverse set of stoichiometries were covered in training, including 1:0 (pure carbon), 1:4 (methane), and 1:1 (benzene), and rich bonding environments sampled at supercritical temperatures, hydrogen rich, reactive mixtures where metastable stoichiometries arise, including 1:2 (ethylene) and 1:3 (ethane). A high-fidelity training database was constructed by performing large-scale quantum molecular dynamic simulations [density functional theory (DFT) MD] of diamond, graphite, methane, and benzene. A novel approach to selecting structures from DFT MD is also presented, which allows for the rapid selection of unique DFT MD frames from complex trajectories. Comparisons to DFT and experimental data demonstrate that the presented ACE potential accurately reproduces isotherms, carbon melting curves, radial distribution functions, and shock Hugoniots for carbon and hydrocarbon systems for pressures up to 100 GPa and temperatures up to 6000 K for hydrocarbon systems and up to 9000 K for pure carbon systems. This work delivers a potential that can be used for accurate, large-scale simulations of shocked hydrocarbons and demonstrates a methodology for fitting and validating machine learning interatomic potentials to complex molecular environments, which can be applied to energetic materials in future works.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Free-electron Auger quenching of the Fe{sup 2+} excited state in ZnSe

The influence of free electrons in Fe{sup 2+}: ZnSe crystals on the nonlinear transmission of high-power laser radiation with a wavelength of 2940 nm at room and low temperatures is experimentally found. Fe{sup 2+} : ZnSe samples additionally doped with Al are used. The transmission of an Al : Fe : ZnSe sample with electron conduction in a strong (peak intensity about 4.6 MW cm{sup −2}) field is almost the same as in a weak field both at low and room temperatures. The absence of an increase in the transmission of this sample under the action of high-power radiation is explained by increasing absorption saturation intensity of Fe{sup 2+} at this wavelength due a decrease in the lifetime of the excited state of Fe{sup 2+}. The decrease in the lifetime is related to the well-known Auger quenching of impurity luminescence in semiconductors by free electrons. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Closing the loop between microstructure and charge transport in conjugated polymers by combining microscopy and simulation

A grand challenge in materials science is to identify the impact of molecular composition and structure across a range of length scales on macroscopic properties. We demonstrate a unified experimental–theoretical framework that coordinates experimental measurements of mesoscale structure with molecular-level physical modeling to bridge multiple scales of physical behavior. Here we apply this framework to understand charge transport in a semiconducting polymer. Spatially-resolved nanodiffraction in a transmission electron microscope is combined with a self-consistent framework of the polymer chain statistics to yield a detailed picture of the polymer microstructure ranging from the molecular to device relevant scale. Using these data as inputs for charge transport calculations, the combined multiscale approach highlights the underrepresented role of defects in existing transport models. Short-range transport is shown to be more chaotic than is often pictured, with the drift velocity accounting for a small portion of overall charge motion. Local transport is sensitive to the alignment and geometry of polymer chains. At longer length scales, large domains and gradual grain boundaries funnel charges preferentially to certain regions, creating inhomogeneous charge distributions. While alignment generally improves mobility, these funneling effects negatively impact mobility. The microstructure is modified in silico to explore possible design rules, showing chain stiffness and alignment to be beneficial while local homogeneity has no positive effect. This combined approach creates a flexible and extensible pipeline for analyzing multiscale functional properties and a general strategy for extending the accesible length scales of experimental and theoretical probes by harnessing their combined strengths.

42 ENGINEERING↗

Sonic horizons and causality in phase transition dynamics

A system gradually driven through a symmetry-breaking phase transition is subject to the Kibble-Zurek mechanism (KZM). As a consequence of the critical slowing down, its state cannot follow local equilibrium, and its evolution becomes nonadiabatic near the critical point. In the simplest approximation, that stage can be regarded as an “impulse” where the state of the system remains unchanged. It leads to the correct KZM scaling laws. However, such a “freeze-out” might suggest that the coherence length of the nascent order parameter remains unchanged as the critical region is traversed. By contrast, the original causality-based discussion emphasized the role of the sonic horizon: Domains of the broken symmetry phase can expand with a velocity limited by the speed of the relevant sound. This effect was demonstrated in the quantum Ising chain where the dynamical exponent z = 1 and quasiparticles excited by the transition have a fixed speed of sound. To elucidate the role of the sonic horizon, in this paper we study two systems with z > 1 where the speed of sound is no longer fixed, and the fastest excited quasiparticles set the size of the sonic horizon. Their effective speed decays with increasing transition time. In the extreme case, the dynamical exponent z can diverge such as in the Griffiths region of the random Ising chain where the localization of excited quasiparticles freezes the growth of the correlation range when the critical region is traversed. Of particular interest is an example with z < 1 , the long-range extended Ising chain, where there is no upper limit to the velocity of excited quasiparticles with small momenta. Initially, the power-law tail of the correlation function grows adiabatically, but in the nonadiabatic stage it lags behind the adiabatic evolution.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quantum many-body simulations of the two-dimensional Fermi-Hubbard model in ultracold optical lattices

Understanding quantum many-body states of correlated electrons is one main theme in modern condensed-matter physics. Given that the Fermi-Hubbard model, the prototype of correlated electrons, was recently realized in ultracold optical lattices, it is highly desirable to have controlled numerical methodology to provide precise finite-temperature results upon doping to directly compare with experiments. Here, we demonstrate the exponential tensor renormalization group (XTRG) algorithm [Chen et al., Phys. Rev. X 8, 031082 (2018)], complemented by independent determinant quantum Monte Carlo, offers a powerful combination of tools for this purpose. XTRG provides full and accurate access to the density matrix and thus various spin and charge correlations, down to an unprecedented low temperature of a few percent of the tunneling energy. Finally, we observe excellent agreement with ultracold fermion measurements at both half filling and finite doping, including the sign-reversal behavior in spin correlations due to formation of magnetic polarons, and the attractive hole-doublon and repulsive hole-hole pairs that are responsible for the peculiar bunching and antibunching behaviors of the antimoments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Efficient time-dependent orbital-free density functional theory: Semilocal adiabatic response

Orbital-free density functional theory and its time-dependent extension are efficient ab initio methods for calculating the electronic structure and dynamics of large systems. Through the calculation of the optical spectra of selected clusters, we reach three important conclusions: (1) The quality of the spectra is strongly affected by the quality of the corresponding ground-state electron density; (2) the adiabatic part of the electronic response to external perturbations can be safely evaluated at the semilocal level; and (3) the nonadiabatic, current-dependent part of the time-dependent Pauli potential is key to recover correct spectral envelopes.

36 MATERIALS SCIENCE↗

Medium-range atomic correlation in simple liquids. I. Distinction from short-range order

Physical properties of liquids and glasses are controlled not only by the short-range order (SRO) in the nearest-neighbor atoms but also by the medium-range order (MRO) observed for atoms beyond the nearest neighbors. In this article the nature of the MRO as the descriptor of point-to-set atomic correlation is discussed focusing on simple liquids, such as metallic liquids. Through the results of x-ray diffraction and simulation with classical potentials we show that the third peak of the pair-distribution function, which describes the MRO, shows a distinct change in temperature dependence at the glass transition, whereas the first peak, which represents the SRO, changes smoothly through the glass transition. Finally, the result suggests that the glass transition is induced by the freezing of the MRO rather than that of the SRO, implying a major role of the MRO on the viscosity of supercooled liquid.

74 ATOMIC AND MOLECULAR PHYSICS↗

Emergent Ergodicity at the Transition between Many-Body Localized Phases

Strongly disordered systems in the many-body localized (MBL) phase can exhibit ground state order in highly excited eigenstates. The interplay between localization, symmetry, and topology has led to the characterization of a broad landscape of MBL phases ranging from spin glasses and time crystals to symmetry protected topological phases. Understanding the nature of phase transitions between these different forms of eigenstate order remains an essential open question. In this work, we conjecture that no direct transition between distinct MBL orders can occur in one dimension; rather, an ergodic phase always intervenes. Motivated by recent advances in Rydberg-atom-based quantum simulation, we propose an experimental protocol where the intervening ergodic phase can be diagnosed via the dynamics of local observables.

1-dimensional spin chains↗

Temperature-Dependent Spin-Lattice Relaxation of the Nitrogen-Vacancy Spin Triplet in Diamond

Spin-lattice relaxation within the nitrogen-vacancy (NV) center’s electronic ground-state spin triplet limits its coherence times, and thereby impacts its performance in quantum applications. We report measurements of the relaxation rates on the NV center’s $|m_s = 0 \rangle ↔ |m_s = ± 1 \rangle$ and $|m_s = -1 \rangle ↔ |m_s = + 1\rangle$ transitions as a function of temperature from 9 to 474 K in high-purity samples. We show that the temperature dependencies of the rates are reproduced by an ab initio theory of Raman scattering due to second-order spin-phonon interactions, and we discuss the applicability of the theory to other spin systems. Using a novel analytical model based on these results, we suggest that the high-temperature behavior of NV spin-lattice relaxation is dominated by interactions with two groups of quasilocalized phonons centered at 68.2(17) and 167(12) meV.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Interstitial solute segregation at triple junctions: Implications for nanomaterials and a case study of hydrogen in palladium

At very fine grain sizes, grain boundary segregation can deviate from conventional behavior due to triple junction effects. While this issue has been addressed in prior work for substitutional alloys, here we develop a framework that accounts for interstitial sites in the grains, grain boundaries, and triple junctions of model Pd(H) polycrystals. This approach allows computation of interstitial segregation spectra separately at both defect types, which permits an understanding of segregation at all grain sizes via a size-scaling spectral isotherm. Here, the size dependencies of dilute Pd(H) are found to be influenced not only by the triple junction content, but also by grain size–dependent lattice strains; the latter effect is evidenced by size dependencies of individual grain boundary and junction subspectra. The framework proposed here is applicable to interstitial alloys in general and may serve as a basis for interfacial engineering in interstitial nanocrystalline alloys. As an example, we show that using the dilute limit isotherm, hydrogen density can triple in nanocrystalline vis-à-vis microcrystalline Pd due to hydrogen adsorption at intergranular defect sites.

Alloys↗