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At least 1,153 records · Page 64

Binding mechanism and binding free energy of amino acids and citrate to hydroxyapatite surfaces as a function of crystallographic facet, pH, and electrolytes

Hydroxyapatite (HAP) is the major mineral phase in bone and teeth. The interaction of individual amino acids and citrate ions with different crystallographic HAP surfaces has remained uncertain for decades, creating a knowledge gap to rationally design interactions with peptides, proteins, and drugs. In this contribution, we quantify the binding mechanisms and binding free energies of the 20 end-capped natural amino acids and citrate ions on the basal (001) and prismatic (010)/(020) planes of hydroxyapatite at pH values of 7 and 5 for the first time at the molecular scale. We utilized over 1500 steered molecular dynamics simulations with highly accurate potentials that reproduce surface and hydration energies of (hkl) hydroxyapatite surfaces at different pH values. Charged residues demonstrate a much higher affinity to HAP than charge-neutral species due to the formation of superficial ion pairs and ease of penetration into layers of water molecules on the mineral surface. Binding free energies range from 0 to -60 kJ/mol and were determined with ~10% uncertainty. The highest affinity was found for citrate, followed by Asp(-) and Glu(-), and followed after a gap by Arg(+), Lys(+), as well as by His(+) at pH 5. The (hkl)-specific area density of calcium ions, the protonation state of phosphate ions, and subsurface directional order of the ions in HAP lead to surface-specific binding patterns. Amino acids without ionic side groups exhibit weak binding, between -3 and 0 kJ/mol, due to difficulties to penetrate the first layer of water molecules on the apatite surfaces. We explain recognition processes that remained elusive in experiments, in prior simulations, discuss agreement with available data, and reconcile conflicting interpretations. In conclusion, the findings can serve as useful input for the design of peptides, proteins, and drug molecules for the modification of bone and teeth-related materials, as well as control of apatite mineralization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DeepM&Mnet: Inferring the electroconvection multiphysics fields based on operator approximation by neural networks

Electroconvection is a multiphysics problem involving coupling of the flow field with the electric field as well as the cation and anion concentration fields. Here, we use electroconvection as a benchmark problem to put forward a new data assimilation framework, the DeepM&Mnet, for simulating multiphysics and multiscale problems at speeds much faster than standard numerical methods using pre-trained neural networks. We first pre-train DeepONets that can predict independently each field, given general inputs from the rest of the fields of the coupled system. DeepONets can approximate nonlinear operators and are composed of two sub-networks, a branch net for the input fields and a trunk net for the locations of the output field. DeepONets, which are extremely fast, are used as building blocks in the DeepM&Mnet and form constraints for the multiphysics solution along with some sparse available measurements of any of the fields. We demonstrate the new methodology and document the accuracy of each individual DeepONet, and subsequently we present two different DeepM&Mnet architectures that infer accurately and efficiently 2D electroconvection fields for unseen electric potentials. Furthermore, the DeepM&Mnet framework is general and can be applied for building any complex multiphysics and multiscale models based on very few measurements using pre-trained DeepONets in a “plug-and-play” mode.

97 MATHEMATICS AND COMPUTING↗

Coherent addition of high power broad-area laser diodes with a compact VBG V-shaped external Talbot cavity

In this paper, we introduced a compact V-shaped external Talbot cavity for phase locking of high power broad-area laser diodes. The length of compact cavity is ~25 mm. Near diffraction-limit coherent addition of 10 broad-area laser diodes indicated that high quality phase locking was achieved. We measured the near-field emission mode of each individual broad-area laser diode with different feedback, such as a volume Bragg grating and a high reflection mirror. Finally, we found out that the best result of phase locking broad-area laser diodes was achieved by the compact V-shaped external Talbot cavity with volume Bragg grating feedback.

42 ENGINEERING↗

Correlations between Transition Metal Chemistry, Local Structure and Global Structure in Li 2 Ru 0.5 Mn 0.5 O 3 Investigated in a Wide Voltage Window

Li 2 Ru 0.5 Mn 0.5 O 3 , a high capacity lithium rich layered cathode material for lithium-ion batteries, was subject to comprehen-sive diagnostic studies including in situ/ex situ X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), pair distribu-tion function (PDF) and high resolution scanning transmission electron microscopy (STEM) analysis, to understand the cor-relations between transition metal chemistry, structure and lithium storage electrochemical behavior. Ru-Ru dimers have been identified in the as-prepared sample and found to be preserved upon prolonged cycling. Presence of these dimers, which are likely caused by the delocalized nature of 4d electrons, is found to favor the stabilization of the structure in a lay-ered phase. The in situ XAS results confirm the participation of oxygen redox into the charge compensation at high charge voltage, and the great flexibility of the covalent bond between Ru and O may provide great reversibility of the global struc-ture despite of the significant local distortion around Ru. In contrast, the local distortion around Mn occurs at low discharge voltage and is accompanied by a “layered to 1T” phase transformation, which is found to be detrimental to the cycle per-formances. It is clear that the changes of local structure around individual transition metal cations respond separately and differently to lithium intercalation/deintercalation. Here, cations with the capability to tolerate the lattice distortion will benefit for maintaining the integrality of the crystal structure and therefore is able to enhance the long-term cycling performance of the electrode materials.

25 ENERGY STORAGE↗

Well-Defined Nanoparticle Electrocatalysts for the Refinement of Theory

The relationship between experiment and theory in electrocatalysis is one of profound importance. Until fairly recently, the principal role of theory in this field was interpreting experimental results. Over the course of the past decade (roughly the period covered by this review), however, that has begun to change, with theory now frequently leading the design of electrocatalytic materials. Though rewarding, this has not been a particularly easy union. For one thing, experimentalists and theorists have to come to grips with the fact that they rely on different models. Theorists make predictions based on individual, perfect structural models, while experimentalists work with more complex and heterogeneous ensembles of electrocatalysts. As discussed in this review, computational capabilities have improved in recent years, so that theory is better represented by the structures that experimentalists are able to prepare. Likewise, synthetic chemists are able to make ever more complex electrocatalysts with high levels of control, which provide a more extensive palette of materials for testing theory. Finally, the goal of this review is to highlight research from the last ~10 years that focuses on carefully controlled electrocatalytic experiments which, in combination with theoretical predictions, bring us closer to bridging the gap between real catalysts and computational models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unsteady- and Steady-State Relative Permeability Study with X-ray and Acoustic Monitoring for CO 2 Storage in Deep Saline Aquifers

In this study, we link the multiphase flow measurements with controls of sedimentary structures (e.g., heterogeneity and anisotropy) on relative permeability to variations in ultrasonic velocities for two deep saline aquifer formations (Entrada and Bluff Sandstones) in the San Juan Basin of the Southwestern USA. The rock specimens were extracted from outcrop sites near Durango, CO, USA. They have distinct differences in grain size, cementation composition, and individual chemical amounts, despite both formations being eolian sandstones. We performed a series of unsteady- and steady-state CO 2 -brine relative permeability experiments under capillary-controlled displacement rates. Unsteady-state experiments were conducted at 71 °C and 9.65 MPa; steady-state experiments were conducted at 85 °C and 22.8 MPa and 89 °C and 24.1 MPa for the Bluff and Entrada Sandstones, respectively. During the unsteady experiments, X-ray computed tomography was used to visualize multiphase flow in porous media and quantify saturations during brine drainage under various flow rates. Scan images and saturation profiles indicate that the CO 2 distribution in the pore volume was strongly impacted by the presence of high-angle cross-laminations, heterogeneous rock structure, and direction of bedding orientation. Those factors contribute to dramatic and quick initial breakthroughs and affect the overall saturation dynamics. Steady-state relative permeability tests were conducted at net flow rates of 1 mL/min for both brine drainage and imbibition. During the experimental steps, the CO 2 fractional flow was increased and decreased for both drainage and imbibition scenarios to mimic the front when CO 2 contacts brine and behind the front when brine enters space previously occupied by CO 2 . It was found that compressional velocity decreased, while shear waves slightly increased as brine saturation decreased. The hysteresis effects for the relative permeability and acoustic velocities were distinct. Furthermore, the CO 2 /brine front stability is quantified by applying a mobility ratio approach to spot saturations at which the boundary line between fluids becomes uneven. The results presented in this work can potentially boost the quality and precision of forecasts for the CO 2 storage projects in which the vertical and horizontal core-scale heterogeneity and anisotropy impact the plume migration within host reservoirs.

carbon dioxide (CO2)↗

Combining Iteration-Free Polarization with Large Time Step Stochastic-Isokinetic Integration

In order to accelerate molecular dynamics simulations using polarizable force fields, we combine a new extended Lagrangian approach that eliminates the self-consistent field step (iEL/0-SCF) with a stochastic integration scheme that allows for a long time step using a multiple time scale algorithm (SIN(R)). We consider different algorithms for the combined scheme that places different components of the nonbonded forces into different time scales, as well as splitting individual nonbonded forces across time scales, to demonstrate that the combined method works well for bulk water as well as for a concentrated salt solution, aqueous peptide, and solvated protein. Depending on system and desired accuracy, the iEL/0-SCF and SIN(R) combination yields lower bound computational speed-ups of ~6–8 relative to a molecular dynamics Verlet integration using a standard SCF solver implemented in the reference program TINKER 8.1. Finally, the combined approach embodies a significant advance for equilibrium simulations in the canonical ensemble of many-body potential energy surfaces for condensed phase systems with speed-ups that exceed what is possible by either method alone.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantifying the Importance of Rapid Adjustments for Global Precipitation Changes

Different climate drivers influence precipitation in different ways. Here we use radiative kernels to understand the influence of rapid adjustment processes on precipitation in climate models. Rapid adjustments are generally triggered by the initial heating or cooling of the atmosphere from an external climate driver. For precipitation changes, rapid adjustments due to changes in temperature, water vapor, and clouds are most important. In this study we have investigated five climate drivers (CO 2 , CH 4 , solar irradiance, black carbon, and sulfate aerosols). The fast precipitation responses to a doubling of CO 2 and a 10-fold increase in black carbon are found to be similar, despite very different instantaneous changes in the radiative cooling, individual rapid adjustments, and sensible heating. The model diversity in rapid adjustments is smaller for the experiment involving an increase in the solar irradiance compared to the other climate driver perturbations, and this is also seen in the precipitation changes.

58 GEOSCIENCES↗

Mixed metal zero-mode guides (ZMWs) for tunable fluorescence enhancement

Zero-mode waveguides (ZMWs) are capable of modifying fluorescence emission through interactions with surface plasmon modes leading to either plasmon-enhanced fluorescence or quenching. Enhancement requires spectral overlap of the plasmon modes with the absorption or emission of the fluorophore. Thus, enhancement is limited to fluorophores in resonance with metals (e.g. Al, Au, Ag) used for ZMWs. The ability to tune interactions to match a wider range of fluorophores across the visible spectra would significantly extend the utility of ZMWs. We fabricated ZMWs composed of aluminum and gold individually and also in mixtures of three different ratios, (Al : Au; 75 : 25, 50 : 50, 25 : 75). We characterized the effect of mixed-metal ZMWs on single-molecule emission for a range fluorophores across the visible spectrum. Mixed metal ZMWs exhibited a shift in the spectral range where they exhibited the maximum fluorescence enhancement allowing us to match the emission of fluorophores that were nonresonant with single metal ZMWs. We also compared the effect of mixed-metal ZMWs on the photophysical properties of fluorescent molecules due to metal–molecule interactions. We quantified changes in fluorescence lifetimes and photostability that were dependent on the ratio of Au and Al. Tuning the enhancement properties of ZMWs by changing the ratio of Au and Al allowed us to match the fluorescence of fluorophores that emit in different regions of the visible spectrum.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Off-axis electron holography of ferromagnetic multilayer nanowires

We have used electron holography to investigate the local magnetic behavior of isolated ferromagnetic nanowires (NWs) in their remanent states. The NWs consisted of periodic magnetic layers of soft, high-saturation magnetization CoFeB alloys, and non-magnetic layers of Cu. All NWs were fabricated by pulsed-potential electrodeposition in nanoporous alumina membranes. The NW composition and layer thicknesses were measured using scanning transmission electron microscopy and energy dispersive spectroscopy. The magnetization of individual NWs depended upon the thicknesses of the layers and the direction of an external magnetic field, which had been applied in situ. When the CoFeB was thicker than the diameter (50 nm), magnetization was axial for all external field directions, while thinner layers could be randomized via a perpendicular field. In some cases, magnetization inside the wire was detected at an angle with respect to the axis of the wires. In thinner Cu/CoFeB (<10 nm each) multilayer, magnetic field vortices were detected, associated with opposing magnetization in neighbouring layers. The measured crystallinity, compositions, and layer thicknesses of individual NWs were found to be significantly different from those predicted from calibration growths based on uniform composition NWs. In particular, a significant fraction of Cu (up to 50 at. %) was present in the CoFeB layers such that the measured magnetic induction was lower than expected. These results will be used to better understand previously measured effective anisotropy fields of similar NW arrays.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

The confinement of phonon propagation in TiAlN/Ag multilayer coatings with anomalously low heat conductivity

TiAlN/Ag multilayer coatings with a different number of bilayers and thicknesses of individual layers were fabricated by DC magnetron co-sputtering. Thermal conductivity was measured in dependence of Ag layer thickness. It was found anomalous low thermal conductivity of silver comparing to TiAlN and Ag bulk standards and TiAlN/TiN multilayers. The physical nature of such thermal barrier properties of the multilayer coatings was explained on the basis of reflection electron energy loss spectroscopy. The analysis shows that nanostructuring of the coating decreases the density of states and velocity of acoustic phonons propagation. At the same time, multiphonon channels of heat propagation degenerate. These results demonstrate that metal-dielectric interfaces in TiAlN/Ag coatings are insurmountable obstacles for acoustic phonons propagation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quantum optimal control of multiple weakly interacting molecular rotors in the time-dependent Hartree approximation

In this work we perform quantum optimal control simulations, based on the Time-Dependent Hartree (TDH) approximation, for systems of three to five dipole-dipole coupled OCS rotors. A control electric field is used to steer all of the individual rotors, arranged in chains and regular polygons in a plane, toward either identical or unique objectives. The goal is to explore the utility of the TDH approximation to model the field-induced dynamics of multiple interacting rotors in the weak dipole-dipole coupling regime. A stochastic hill climbing approach is employed to seek an optimal control field that achieves the desired objectives at a specified target time. We first show that multiple rotors in chain and polygon geometries can be identically oriented in the same direction; these cases do not significantly depend on the presence of the dipole-dipole interaction. Additionally, in particular geometrical arrangements, we demonstrate that individual rotors can be uniquely manipulated toward different objectives with the same field. Specifically, it is shown that for a three rotor chain, the two end rotors can be identically oriented in a specific direction while keeping the middle rotor in its ground state, and for an equilateral triangle, two rotors can be identically oriented in a specific direction while the third rotor is oriented in the opposite direction. These multirotor unique objective cases exploit the shape of the field in coordination with dipole-dipole coupling between the rotors. Comparisons to numerically exact calculations, utilizing the TDH-determined fields, are given for all optimal control studies involving systems of three rotors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterization of low-mass, wide-separation substellar companions to stars in upper SCORPIUS: Near-infrared photometry and spectroscopy

We present new 0.9–2.45 μm spectroscopy (R∼1000 ), and Y, J, H, K{sub s}, L{sup ′} photometry, obtained at Gemini North, of three low-mass brown dwarf companions on wide orbits around young stars of the Upper Scorpius OB association: HIP 78530 B, [PGZ 2001] J161031.9-191305 B, and GSC 06214-00210 B. We use these data to assess the companions’ spectral type, temperature, surface gravity, and mass, as well as the ability of the BT-SETTL and Drift-Phoenix atmosphere models to reproduce the spectral features of young substellar objects. For completeness, we also analyze the archival spectroscopy and photometry of the Upper Scorpius planetary mass companion 1RXS J160929.1-210524 b. Based on a comparison with model spectra we find that the companions, in the above order, have effective temperatures of 2700 ± 100, 2500 ± 200, 2300 ± 100, and 1700 ± 100 K. These temperatures are consistent with our inferred spectral types, respectively M7 β, M9 γ, M9 γ, and L4 γ, obtained from spectral indices and comparisons with templates. From bolometric luminosities estimated from atmosphere model spectra adjusted to our photometry, and using evolution models at 5–10 Myr, we estimate masses of 21–25, 28–70, 14–17, and 7–12 M{sub Jup}, respectively. [PGZ 2001] J161031.9-191305 B appears significantly overluminous for its inferred temperature, which explains its higher mass estimate. Synthetic spectra based on the BT-Settl and Drift-Phoenix atmosphere models generally offer a good fit to our observed spectra, although our analysis has highlighted a few problems. For example, the best fits in the individual near-infrared bands occur at different model temperatures. Also, temperature estimates based on a comparison of the broadband magnitudes and colors of the companions to synthetic magnitudes from the models are systematically lower than the temperature estimates based on a comparison with synthetic spectra.

79 ASTRONOMY AND ASTROPHYSICS↗

In situ ambient pressure XPS study of Pt/Cu(111) single-atom alloy in catalytically relevant reaction conditions

The presence of multiple reactant gases as well as reaction intermediates in a heterogeneous catalytic reaction results in a complex interaction between different components of the catalyst with each gas, which can alter the surface and chemical state of the catalyst differently than in the presence of an individual gas alone. In this study, we used in situ ambient pressure x-ray photoelectron spectroscopy to study the surface state of Pt/Cu(111) single-atom alloy model system in two catalytically relevant reaction conditions: CO 2 hydrogenation and CO oxidation. We found that the activation of CO 2 results in the formation of CO, which adsorbs on Pt sites at up to 400 K. In the presence of CO 2 and H 2 , Pt catalyzes the reverse water–gas shift reaction, which produces more CO and further stabilizes surface Pt atoms at 450 K. On the other hand, in CO oxidation condition, the presence of O 2 results in the formation of a thick Cu 2 O layer at higher temperatures, and Pt atoms are no longer detected in the surface and subsurface layers. When O 2 is introduced to the sample before CO, the formation of a complete Cu 2 O layer that covers all Pt atoms occurs immediately at room temperature. Finally, however, when CO is introduced at room temperature before O 2 , the presence of adsorbed CO on Pt sites stabilizes the surface Pt atoms and prevents the formation of a complete Cu 2 O layer, thus exposing the Pt atoms in 'holes' in the Cu 2 O layer.

36 MATERIALS SCIENCE↗

Biokinetics of 238 Pu oxides: Inferences from bioassay data

The bioassay data collected from several workers involved in 238 Pu inhalation incidents have been analyzed using the most recent biokinetic models described in Occupational Intakes of Radionuclides (OIR) series of publications. Although all exposures were thought to be to 238 Pu oxides, the observed urinary excretion patterns differed in different inhalation incidents. The urinary excretion from individuals involved in one of the incidents increased steadily with time peaking around 2-3 years before decreasing. This pattern is described in Part 4 of the OIR series using the ‘ 238 PuO 2 , ceramic’ model. This non-monotonic behavior, explained as being due to fragmentation and dissolution, was not specific to the incident, but was also observed in other incidents. The urinary excretion data collected from individuals involved in another incident showed dissolution behavior between Type M and Type S. Finally, the bioassay data from yet another incident showed a pattern that appears to represent behavior more insoluble than Type S, which is possibly a result of self-heating due to the decay heat from 238 Pu. The urinary excretion patterns and the corresponding dose coefficients have been calculated and compared.

238Pu↗

Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.)

Abstract Background and Aims Increasing energy demands and the necessity to reduce greenhouse gas emissions are key motivating factors driving the development of lignocellulosic crops as an alternative to non-renewable energy sources. The effects of global climate change will require a better understanding of the genetic basis of complex adaptive traits to breed more resilient bioenergy feedstocks, like willow (Salix spp.). Shrub willow is a sustainable and dedicated bioenergy crop, bred to be fast-growing and high-yielding on marginal land without competing with food crops. In a rapidly changing climate, genomic advances will be vital for the sustained improvement of willow and other non-model bioenergy crops. Here, joint genetic mapping was used to exploit genetic variation garnered from both recent and historical recombination events in S. purpurea. Methods A panel of North American naturalized S. purpurea accessions and full-sib F2S. purpurea population were genotyped and phenotyped for a suite of morphological, physiological, pest and disease resistance, and wood chemical composition traits, collected from multi-environment and multi-year replicated field trials. Controlling for population stratification and kinship in the association panel and spatial variation in the F2, a comprehensive mixed model analysis was used to dissect the complex genetic architecture and plasticity of these important traits. Key Results Individually, genome-wide association (GWAS) models differed in terms of power, but the combined approach, which corrects for yearly and environmental co-factors across datasets, improved the overall detection and resolution of associated loci. Although there were few significant GWAS hits located within support intervals of QTL for corresponding traits in the F2, many large-effect QTL were identified, as well as QTL hotspots. Conclusions This study provides the first comparison of linkage analysis and linkage disequilibrium mapping approaches in Salix, and highlights the complementarity and limits of these two methods for elucidating the genetic architecture of complex bioenergy-related traits of a woody perennial breeding programme.

Plant Sciences↗

Effects of lattice geometry on the dynamic properties of dipolar-coupled magnetic nanodisk arrays

Here, we have studied the impact of lattice geometry on the dynamic properties of close-spaced arrays of circular nanomagnets, also known as magnonic crystals. To this end, we prepared 2D nanomagnet arrays with both square and hexagonal lattice symmetries (300-nm disk diameter, 400-nm center-to-center distance) and performed broadband ferromagnetic resonance (FMR) measurements. Micromagnetic simulations were used to interpret distinct features of the measured resonance spectra. The FMR bias field was applied along two distinct principal directions for each lattice, and a sample with well-separated, decoupled disks was measured for reference. We found that the interdisk dipolar coupling has a strong impact on the FMR for these 2D magnonic crystals. Distinctly different oscillation modes were found for the individual nanomagnets, dependent on lattice symmetry and direction of the bias field. Moreover, we find that spectral peak splitting from excitation of edge and center modes, as well as the damping, depends on the lattice symmetry and the orientation of the bias field. These findings demonstrate that lattice geometry has a strong influence on the excited spin-wave spectrum and is a relevant design parameter for spintronic devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

On Social Optima of Non-Cooperative Mean Field Games

This paper studies the social optima in noncooperative mean-field games for a large population of agents with heterogeneous stochastic dynamic systems. Each agent seeks to maximize an individual utility functional, and utility functionals of different agents are coupled through a mean field term that depends on the mean of the population states/controls. The paper has the following contributions. First, we derive a set of control strategies for the agents that possess *-Nash equilibrium property, and converge to the mean-field Nash equilibrium as the population size goes to infinity. Second, we study the social optimal in the mean field game. We derive the conditions, termed the socially optimal conditions, under which the *-Nash equilibrium of the mean field game maximizes the social welfare. Third, a primal-dual algorithm is proposed to compute the *-Nash equilibrium of the mean field game. Since the *-Nash equilibrium of the mean field game is socially optimal, we can compute the equilibrium by solving the social welfare maximization problem, which can be addressed by a decentralized primal-dual algorithm. Numerical simulations are presented to demonstrate the effectiveness of the proposed approach.

Li, Sen↗