Controlled Vertical Transfer of Individual Au Atoms Using a Surface Supported Carbon Radical for Atomically Precise Manufacturing
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SEARCH · Engineering Papers
Results for “molecular functionalization”
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The Principal Hugoniot of Iron-Bearing Olivine to 1465 GPa
Shock compression experiments on natural compositions are imperative to accurately model planetary accretion and the interior dynamics of planets. Combining shock compression experiments from the Sandia Z Machine and the OMEGA EP laser facility with density functional theory-based molecular dynamics calculations, we report the first pressure-density-temperature (P-ρ-T) relationship of natural iron (Fe)-bearing olivine ((Mg 0.91 Fe 0.09 ) 2 SiO 4 ) on the principal Hugoniot between 166 and 1,465 GPa. Additionally, we report the first reflectivities of natural olivine liquid in this pressure range. Compared to the magnesium-endmember forsterite (Mg 2 SiO 4 ), the presence of Fe in typical mantle abundance (~9 wt% FeO) alters the U S -u P relation of olivine. Furthermore, the shock temperature and reflectivity of olivine are indistinguishable from forsterite where experimental conditions overlap. Both forsterite and olivine increase in reflectivity (and hence optical conductivity) with increasing temperature, with a maximum reflectivity of ~31% at shock velocities greater than 22 km/s (~800 GPa).
58 GEOSCIENCES↗
A silicate dynamo in the early Earth
The Earth’s magnetic field has operated for at least 3.4 billion years, yet how the ancient field was produced is still unknown. The core in the early Earth was surrounded by a molten silicate layer, a basal magma ocean that may have survived for more than one billion years. Here we use density functional theory-based molecular dynamics simulations to predict the electrical conductivity of silicate liquid at the conditions of the basal magma ocean: 100–140 GPa, and 4000–6000 K. We find that the electrical conductivity exceeds 10,000 S/m, more than 100 times that measured in silicate liquids at low pressure and temperature. The magnetic Reynolds number computed from our results exceeds the threshold for dynamo activity and the magnetic field strength is similar to that observed in the Archean paleomagnetic record. We therefore conclude that the Archean field was produced by the basal magma ocean.
54 ENVIRONMENTAL SCIENCES↗
Chemistry-mediated Ostwald ripening in carbon-rich C/O systems at extreme conditions
Abstract There is significant interest in establishing a capability for tailored synthesis of next-generation carbon-based nanomaterials due to their broad range of applications and high degree of tunability. High pressure (e.g., shockwave-driven) synthesis holds promise as an effective discovery method, but experimental challenges preclude elucidating the processes governing nanocarbon production from carbon-rich precursors that could otherwise guide efforts through the prohibitively expansive design space. Here we report findings from large scale atomistically-resolved simulations of carbon condensation from C/O mixtures subjected to extreme pressures and temperatures, made possible by machine-learned reactive interatomic potentials. We find that liquid nanocarbon formation follows classical growth kinetics driven by Ostwald ripening (i.e., growth of large clusters at the expense of shrinking small ones) and obeys dynamical scaling in a process mediated by carbon chemistry in the surrounding reactive fluid. The results provide direct insight into carbon condensation in a representative system and pave the way for its exploration in higher complexity organic materials. They also suggest that simulations using machine-learned interatomic potentials could eventually be employed as in-silico design tools for new nanomaterials.
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Observation of electron orbital signatures of single atoms within metal-phthalocyanines using atomic force microscopy
Resolving the electronic structure of a single atom within a molecule is of fundamental importance for understanding and predicting chemical and physical properties of functional molecules such as molecular catalysts. However, the observation of the orbital signature of an individual atom is challenging. We report here the direct identification of two adjacent transition-metal atoms, Fe and Co, within phthalocyanine molecules using high-resolution noncontact atomic force microscopy (HR-AFM). HR-AFM imaging reveals that the Co atom is brighter and presents four distinct lobes on the horizontal plane whereas the Fe atom displays a “square” morphology. Pico-force spectroscopy measurements show a larger repulsion force of about 5 pN on the tip exerted by Co in comparison to Fe. Our combined experimental and theoretical results demonstrate that both the distinguishable features in AFM images and the variation in the measured forces arise from Co’s higher electron orbital occupation above the molecular plane. The ability to directly observe orbital signatures using HR-AFM should provide a promising approach to characterizing the electronic structure of an individual atom in a molecular species and to understand mechanisms of certain chemical reactions.
36 MATERIALS SCIENCE↗
Bridging microscopy with molecular dynamics and quantum simulations: an atomAI based pipeline
Recent advances in (scanning) transmission electron microscopy have enabled a routine generation of large volumes of high-veracity structural data on 2D and 3D materials, naturally offering the challenge of using these as starting inputs for atomistic simulations. In this fashion, the theory will address experimentally emerging structures, as opposed to the full range of theoretically possible atomic configurations. However, this challenge is highly nontrivial due to the extreme disparity between intrinsic timescales accessible to modern simulations and microscopy, as well as latencies of microscopy and simulations per se. Addressing this issue requires as a first step bridging the instrumental data flow and physics-based simulation environment, to enable the selection of regions of interest and exploring them using physical simulations. Here we report the development of the machine learning workflow that directly bridges the instrument data stream into Python-based molecular dynamics and density functional theory environments using pre-trained neural networks to convert imaging data to physical descriptors. Additionally, the pathways to ensure structural stability and compensate for the observational biases universally present in the data are identified in the workflow. This approach is used for a graphene system to reconstruct optimized geometry and simulate temperature-dependent dynamics including adsorption of Cr as an ad-atom and graphene healing effects. However, it is universal and can be used for other material systems.
36 MATERIALS SCIENCE↗
De novo design of protein structure and function with RFdiffusion
Abstract There has been considerable recent progress in designing new proteins using deep-learning methods 1–9 . Despite this progress, a general deep-learning framework for protein design that enables solution of a wide range of design challenges, including de novo binder design and design of higher-order symmetric architectures, has yet to be described. Diffusion models 10,11 have had considerable success in image and language generative modelling but limited success when applied to protein modelling, probably due to the complexity of protein backbone geometry and sequence–structure relationships. Here we show that by fine-tuning the RoseTTAFold structure prediction network on protein structure denoising tasks, we obtain a generative model of protein backbones that achieves outstanding performance on unconditional and topology-constrained protein monomer design, protein binder design, symmetric oligomer design, enzyme active site scaffolding and symmetric motif scaffolding for therapeutic and metal-binding protein design. We demonstrate the power and generality of the method, called RoseTTAFold diffusion (RFdiffusion), by experimentally characterizing the structures and functions of hundreds of designed symmetric assemblies, metal-binding proteins and protein binders. The accuracy of RFdiffusion is confirmed by the cryogenic electron microscopy structure of a designed binder in complex with influenza haemagglutinin that is nearly identical to the design model. In a manner analogous to networks that produce images from user-specified inputs, RFdiffusion enables the design of diverse functional proteins from simple molecular specifications.
Science & Technology - Other Topics↗
Knockout of ABC transporter gene ABCA2 confers resistance to Bt toxin Cry2Ab in Helicoverpa zea
Evolution of pest resistance reduces the benefits of widely cultivated genetically engineered crops that produce insecticidal proteins derived from Bacillus thuringiensis (Bt). Better understanding of the genetic basis of pest resistance to Bt crops is needed to monitor, manage, and counter resistance. Previous work shows that in several lepidopterans, resistance to Bt toxin Cry2Ab is associated with mutations in the gene encoding the ATP-binding cassette protein ABCA2. The results here show that mutations introduced by CRISPR/Cas9 gene editing in the Helicoverpa zea (corn earworm or bollworm) gene encoding ABCA2 (HzABCA2) can cause resistance to Cry2Ab. Disruptive mutations in HzABCA2 facilitated the creation of two Cry2Ab-resistant strains. A multiple concentration bioassay with one of these strains revealed it had > 200-fold resistance to Cry2Ab relative to its parental susceptible strain. All Cry2Ab-resistant individuals tested had disruptive mutations in HzABCA2. We identified five disruptive mutations in HzABCA2 gDNA. The most common mutation was a 4-bp deletion in the expected Cas9 guide RNA target site. The results here indicate that HzABCA2 is a leading candidate for monitoring Cry2Ab resistance in field populations of H. zea.
60 APPLIED LIFE SCIENCES↗
Surface softening in palladium nanoparticles: effects of a capping agent on vibrational properties
The presence of a capping agent (CTAB) on Pd nanoparticles produces a strong static disorder in the surface region. This results in a surface softening, which contributes to an overall increase in the Debye–Waller coefficient measured by X-ray powder diffraction. Here, molecular dynamics and density functional theory simulations show that the adsorption-induced surface disorder is strong enough to overcome the effects of nanoparticle size and shape.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Unexpected electrochemical behavior of an anolyte redoxmer in flow battery electrolytes: solvating cations help to fight against the thermodynamic–kinetic dilemma
Redoxmers are redox-active molecules that can store energy in electrolytes for redox flow batteries (RFBs), and their electrochemical properties are significantly affected by the choice of supporting electrolytes. Herein, we use 2,1,3-benzothiadiazole (BzNSN) as a model system to scrutinize the supporting electrolyte impact. By systemically varying the components of supporting salts, BzNSN not only shows substantial redox potential shifts but also exhibits varying electrochemical stabilities. Specifically, changing the size of cations can effectively alter the coordination between the supporting salt and BzNSN species. From Li + , Na + , K + , to NEt 4 + , the redox potential of BzNSN shifts negatively, from -1.63 V to -1.82 V vs. Ag/Ag + . Molecular dynamics and density functional theory simulations revealed that smaller cations, like Li + , are closer to the charged BzNSN when coordinated, implying stronger coordination, while larger cations, like K + and NEt 4 + , are farther away. Interestingly, the large cation electrolytes also lead to much improved electrochemical stability, evidenced by the extraordinarily enhanced kinetic lifetime from electron paramagnetic resonance measurement. This study demonstrates the first example of tuning an anolyte redoxmer toward a concurrent improvement of lowered redox potentials AND enhanced calendar lives via solvation means, which is usually constrained by the thermodynamic–kinetic relation.
2,1,3-benzothiadiazole↗
Nanoconfinement and mass transport in metal–organic frameworks
The ubiquity of metal–organic frameworks in recent scientific literature underscores their highly versatile nature. MOFs have been developed for use in a wide array of applications, including: sensors, catalysis, separations, drug delivery, and electrochemical processes. Often overlooked in the discussion of MOF-based materials is the mass transport of guest molecules within the pores and channels. Given the wide distribution of pore sizes, linker functionalization, and crystal sizes, molecular diffusion within MOFs can be highly dependent on the MOF-guest system. In this paper, we discuss the major factors that govern the mass transport of molecules through MOFs at both the intracrystalline and intercrystalline scale; provide an overview of the experimental and computational methods used to measure guest diffusivity within MOFs; and highlight the relevance of mass transfer in the applications of MOFs in electrochemical systems, separations, and heterogeneous catalysis.
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Relativistic nonorthogonal configuration interaction: application to L 2,3 -edge X-ray spectroscopy
In this article, we develop a relativistic exact-two-component nonorthogonal configuration interaction (X2C-NOCI) for computing L-edge X-ray spectra. This article to our knowledge is the first time NOCI has been used for relativistic wave functions. A set of molecular complexes, including SF 6 , SiCl 4 and [FeCl 6 ] 3– , are used to demonstrate the accuracy and computational scaling of the X2C-NOCI method. Here, our results suggest that X2C-NOCI is able to satisfactorily capture the main features of the L 2,3 -edge X-ray absorption spectra. Excitations from the core require a large amount of orbital relaxation to yield reasonable energies and X2C-NOCI allows us to treat orbital optimization explicitly. However, the cost of computing the nonorthogonal coupling is higher than in conventional CI. Here, we propose an improved integral screening using overlap-scaled density combined with a continuous measure of the generalized Slater–Condon rules that allows us to estimate if an element is zero before attempting a two-electron integral contraction.
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Ionic-content-driven restructuring of spirobisindane ionene networks: implications for mechanics, self-healing, and gas transport
Polymers of intrinsic microporosity (PIMs) offer exceptional gas permeability but remain brittle and susceptible to physical aging, limiting their durability in separation applications. Here, we introduce a reconfigurable microporous polymer network that uniquely integrates permanent PIM microporosity with autonomous, intrinsic self-healing driven by imidazolium-based ionic motifs. Spirobisindane units generate the intrinsic free-volume architecture, while an imidazolium-containing polyamide ionene supplies dynamic ionic and hydrogen-bonding interactions that reorganize under mild activation. Incorporation of imidazolium-based ionic liquids further tunes cohesion, mobility, and densification, enabling the network to relax, re-associate, and retain microporosity without structural collapse. Through a comprehensive multiscale approach combining spectroscopy, scattering, thermal and mechanical characterization with all-atom molecular dynamics and density functional theory calculations, we elucidate how ionic content, as a single control parameter that reshapes free-volume distributions, modulates local coordination environments, and governs relaxation and healing kinetics. At intermediate ionic loadings, the networks achieve rapid, repeatable self-healing while maintaining CO$_2$ selectivity, demonstrating an optimal balance between segmental mobility and structural integrity. By establishing how hierarchical ionic interactions couple structure, dynamics, and transport in microporous ionene networks, this work provides generalizable design rules for adaptive soft-matter systems that require simultaneous mechanical resilience, reconfigurability, and selective gas transport.
36 MATERIALS SCIENCE↗
Analysis of defects in In 2 O 3 :H synthesized in presence of water vapor and hydrogen gas mixture
Using hybrid functional-based density functional theory calculations, we analyze the structure and kinetics of defects formed in two competing synthesis routes to prepare hydrogen-doped In 2 O 3 films, using a hydrogen and oxygen gas mixture vs synthesis in the presence of water vapor. For both of these synthesis routes, we find that H + is the dominant defect species: when the Fermi level is close to the conduction band, H + has a lower formation energy than other intrinsic or extrinsic defects. Our results also suggest that water molecules spontaneously split into H + (which occupies octahedral voids) and OH – interstitials (which occupies vacant oxygen lattice sites or oxygen vacancies). From the analysis of the binding energies between these different defects, we conclude that these defects do not cluster and are most likely to stay spatially distributed throughout the films. In addition, the sum of formation energies of an oxygen (i.e., O$^{2–}_i$) and a H + interstitial is close to the formation energy of a OH – interstitial, meaning that water molecules are completely split into 2H + and O$^{2–}_i$ at the synthesis conditions. Further, in the presence of H 2 + O 2 gas mixture, oxygen interstitials occupy oxygen vacancies while hydrogen interstitials occupy vacant oxygen lattice sites and form bonds with lattice oxygens. Our analysis of the defect equilibria suggests that the hydrogen content in films synthesized in the presence of water vapor is higher than films synthesized in the presence of a hydrogen gas mixture. At high dopant concentrations, a hydrogen bond network is formed in the system and this leads to large distortions in the lattice.
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Techniques for studying materials under extreme states of high energy density compression
The properties of materials under extreme conditions of pressure and density are of key interest to a number of fields, including planetary geophysics, materials science, and inertial confinement fusion. In geophysics, the equations of state of planetary materials, such as hydrogen and iron, under ultrahigh pressure and density provide a better understanding of their formation and interior structure [Celliers et al., “Insulator-metal transition in dense fluid deuterium,” Science 361, 677–682 (2018) and Smith et al., “Equation of state of iron under core conditions of large rocky exoplanets,” Nat. Astron. 2, 591–682 (2018)]. The processes of interest in these fields occur under conditions of high pressure (100 GPa–100 TPa), high temperature (>3000 K), and sometimes at high strain rates (>103 s−1) depending on the process. With the advent of high energy density (HED) facilities, such as the National Ignition Facility (NIF), Linear Coherent Light Source, Omega Laser Facility, and Z, these conditions are reachable and numerous experimental platforms have been developed. To measure compression under ultrahigh pressure, stepped targets are ramp-compressed and the sound velocity, measured by the velocity interferometer system for any reflector diagnostic technique, from which the stress-density of relevant materials is deduced at pulsed power [M. D. Knudson and M. P. Desjarlais, “High-precision shock wave measurements of deuterium: Evaluation of exchange-correlation functionals at the molecular-to-atomic transition,” Phys. Rev. Lett. 118, 035501 (2017)] and laser [Smith et al., “Equation of state of iron under core conditions of large rocky exoplanets,” Nat. Astron. 2, 591–682 (2018)] facilities. To measure strength under high pressure and strain rates, experimenters measure the growth of Rayleigh–Taylor instabilities using face-on radiography [Park et al., “Grain-size-independent plastic flow at ultrahigh pressures and strain rates,” Phys. Rev. Lett. 114, 065502 (2015)]. The crystal structure of materials under high compression is measured by dynamic x-ray diffraction [Rygg et al., “X-ray diffraction at the national ignition facility,” Rev. Sci. Instrum. 91, 043902 (2020) and McBride et al., “Phase transition lowering in dynamically compressed silicon,” Nat. Phys. 15, 89–94 (2019)]. Medium range material temperatures (a few thousand degrees) can be measured by extended x-ray absorption fine structure techniques, Yaakobi et al., “Extended x-ray absorption fine structure measurements of laser-shocked V and Ti and crystal phase transformation in Ti,” Phys. Rev. Lett. 92, 095504 (2004) and Ping et al., “Solid iron compressed up to 560 GPa,” Phys. Rev. Lett. 111, 065501 (2013), whereas more extreme temperatures are measured using x-ray Thomson scattering or pyrometry. This manuscript will review the scientific motivations, experimental techniques, and the regimes that can be probed for the study of materials under extreme HED conditions.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Effect of surface properties and polymer chain length on polymer adsorption in solution
In polymer nanoparticle composites (PNCs) with attractive interactions between nanoparticles (NPs) and polymers, a bound layer of the polymer forms on the NP surface, with significant effects on the macroscopic properties of the PNCs. The adsorption and wetting behaviors of polymer solutions in the presence of a solid surface are critical to the fabrication process of PNCs. In this study, we use both classical density functional theory (cDFT) and molecular dynamics (MD) simulations to study dilute and semi-dilute solutions of short polymer chains near a solid surface. Using cDFT, we calculate the equilibrium properties of polymer solutions near a flat surface while varying the solvent quality, surface–fluid interactions, and the polymer chain lengths to investigate their effects on the polymer adsorption and wetting transitions. Using MD simulations, we simulate polymer solutions near solid surfaces with three different curvatures (a flat surface and NPs with two radii) to study the static conformation of the polymer bound layer near the surface and the dynamic chain adsorption process. Additionally, we find that the bulk polymer concentration at which the wetting transition in the poor solvent system occurs is not affected by the difference in surface–fluid interactions; however, a threshold value of surface–fluid interaction is needed to observe the wetting transition. We also find that with good solvent, increasing the chain length or the difference in the surface–polymer interaction relative to the surface–solvent interaction increases the surface coverage of polymer segments and independent chains for all surface curvatures. Finally, we demonstrate that the polymer segmental adsorption times are heavily influenced only by the surface–fluid interactions, although polymers desorb more quickly from highly curved surfaces.
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Local structure of zinc–indium–tin oxide films via grazing-incidence x-ray pair-distribution functions and theoretical methods
A detailed experimental and theoretical study on the local (r ≤ 4.5 Å) atomic structure of amorphous and crystalline zinc–indium–tin oxide (ZITO) thin films using grazing-incidence x-ray Pair-Distribution Functions (PDFs), ab initio Molecular Dynamics (MD), and Empirical Potential Structure Refinement (EPSR) Monte Carlo simulations is presented. High-energy synchrotron x rays, a two-dimensional detector, and different incident angles were used to probe the depth uniformity of five (ZnO) 0.15 (In 2 O 3 ) 0.70 (SnO 2 ) 0.15 films that were deposited via pulsed-laser deposition at growth temperatures (T G ) ranging from 25 to 300 °C. Films deposited at T G ≤ 150 °C were amorphous. The partially crystalline (T G = 200 °C) and fully crystalline (T G = 300 °C) films were highly textured. Both crystalline and amorphous structures were investigated using ab initio MD and EPSR Monte Carlo simulations. The density of the amorphous films determined from the experimental data agreed with MD calculations. Coordination numbers, bond lengths, and distortion for metal–oxygen and for both the edge- and corner-shared In–metal shells up to 4.5 Å obtained from PDF analysis closely agreed with MD and EPSR simulations. There is a pronounced decrease in the edge- and corner-shared In–Zn distances arising from the shorter Zn–O bond length, Zn–O tetrahedral coordination, and In–O–Zn angle in amorphous ZITO compared to its crystalline counterpart. A maximum in electrical mobility was observed for the amorphous film just before crystallization occurred. While the peak is broad, consistent with nearly unchanged overall cation–oxygen coordination in the amorphous films, ESPR results indicate that the tetrahedral coordination follows the conductivity trend.
Grazing Incidence X-ray↗
Disentangling the chemistry of Australian plant exudates from a unique historical collection
For thousands of years, the unique physicochemical properties of plant exudates have defined uses in material culture and practical applications. Native Australian plant exudates, including resins, kinos, and gums, have been used and continue to be used by Aboriginal Australians for numerous technical and cultural purposes. A historic collection of well-preserved native Australian plant exudates, assembled a century ago by plant naturalists, gives a rare window into the history and chemical composition of these materials. Here we report the full hierarchical characterization of four genera from this collection, Xanthorrhoea, Callitris, Eucalyptus, and Acacia, from the local elemental speciation, to functional groups and main molecular markers. We use high-resolution X-ray Raman spectroscopy (XRS) to achieve bulk-sensitive chemical speciation of these plant exudates, including insoluble, amorphous, and cross-linked fractions, without the limitation of invasive and/or surface specific methods. Combinatorial testing of the XRS data allows direct classification of these complex natural species as terpenoid, aromatic, phenolic, and polysaccharide materials. Differences in intragenera chemistry was evidenced by detailed interpretation of the XRS spectral features. We complement XRS with Fourier-transform infrared (FT-IR) spectroscopy, gas chromatography–mass spectrometry (GC-MS), and pyrolysis–GC-MS (Py-GC-MS). This multimodal approach provides a fundamental understanding of the chemistry of these natural materials long used by Aboriginal Australian peoples.
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