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At least 1,171 records · Page 65

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↗

Dynamical phase-field model of coupled electronic and structural processes

Abstract Many functional and quantum materials derive their functionality from the responses of both their electronic and lattice subsystems to thermal, electric, and mechanical stimuli or light. Here we propose a dynamical phase-field model for predicting and modeling the dynamics of simultaneous electronic and structural processes and the accompanying mesoscale pattern evolution under static or ultrafast external stimuli. As an illustrative example of application, we study the transient dynamic response of ferroelectric domain walls excited by an ultrafast above-bandgap light pulse. We discover a two-stage relaxational electronic carrier evolution and a structural evolution containing multiple oscillational and relaxational components across picosecond to nanosecond timescales. The phase-field model offers a general theoretical framework which can be applied to a wide range of functional and quantum materials with interactive electronic and lattice orders and phase transitions to understand, predict, and manipulate their ultrafast dynamics and rich mesoscale evolution dynamics of domains, domain walls, and charges.

36 MATERIALS SCIENCE↗

eReaxFF force field development for BaZr 0.8 Y 0.2 O 3-δ solid oxide electrolysis cells applications

The use of solid-oxide materials in electrocatalysis applications, especially in hydrogen-evolution reactions, is promising. However, further improvements are warranted to overcome the fundamental bottlenecks to enhancing the performance of solid-oxide electrolysis cells (SOECs), which is directly linked to the more-refined fundamental understanding of complex physical and chemical phenomena and mass exchanges that take place at the surfaces and in the bulk of electrocatalysis materials. Here, we developed an eReaxFF force field for barium zirconate doped with 20 mol% of yttrium, BaZr 0.8 Y 0.2 O 3-δ (BZY20) to enable a systematic, large-length-scale, and longer-timescale atomistic simulation of solid-oxide electrocatalysis for hydrogen generation. All parameters for the eReaxFF were optimized to reproduce quantum-mechanical (QM) calculations on relevant condensed phase and cluster systems describing oxygen vacancies, vacancy migrations, electron localization, water adsorption, water splitting, and hydrogen generation on the surfaces of the BZY20 solid oxide. Using the developed force field, we performed both zero-voltage (excess electrons absent) and non-zero-voltage (excess electrons present) molecular dynamics simulations to observe water adsorption, water splitting, proton migration, oxygen-vacancy migrations, and eventual hydrogen-production reactions. Based on investigations offered in the present study, we conclude that the eReaxFF force field-based approach can enable computationally efficient simulations for electron conductivity, electron leakage, and other non-zero-voltage effects on the solid oxide materials using the explicit-electron concept. Moreover, we demonstrate how the eReaxFF force field-based atomistic-simulation approach can enhance our understanding of processes in SOEC applications and potentially other renewable-energy applications.

08 HYDROGEN↗

Exploring electron-beam induced modifications of materials with machine-learning assisted high temporal resolution electron microscopy

Directed atomic fabrication using an aberration-corrected scanning transmission electron microscope (STEM) opens new pathways for atomic engineering of functional materials. In this approach, the electron beam is used to actively alter the atomic structure through electron beam induced irradiation processes. One of the impediments that has limited widespread use thus far has been the ability to understand the fundamental mechanisms of atomic transformation pathways at high spatiotemporal resolution. Here, we develop a workflow for obtaining and analyzing high-speed spiral scan STEM data, up to 100 fps, to track the atomic fabrication process during nanopore milling in monolayer MoS 2 . An automated feedback-controlled electron beam positioning system combined with deep convolution neural network (DCNN) was used to decipher fast but low signal-to-noise datasets and classify time-resolved atom positions and nature of their evolving atomic defect configurations. Through this automated decoding, the initial atomic disordering and reordering processes leading to nanopore formation was able to be studied across various timescales. Using these experimental workflows a greater degree of speed and information can be extracted from small datasets without compromising spatial resolution. This approach can be adapted to other 2D materials systems to gain further insights into the defect formation necessary to inform future automated fabrication techniques utilizing the STEM electron beam.

36 MATERIALS SCIENCE↗

Applying laboratory methods for durability assessment of vitrified material to archaeological samples

Abstract Laboratory testing used to assess the long-term chemical durability of nuclear waste forms may not be applicable to disposal because the accelerated conditions may not represent disposal conditions. To address this, we examine the corrosion of vitrified archeological materials excavated from the near surface of a ~1500-year old Iron Age Swedish hillfort, Broborg, as an analog for the disposal of vitrified nuclear waste. We compare characterized site samples with corrosion characteristics generated by standard laboratory durability test methods including the product consistency test (PCT), the vapor hydration test (VHT), and the EPA Method 1313 test. Results show that the surficial layer of the Broborg samples resulting from VHT displays some similarities to the morphology of the surficial layer formed over longer timescales in the environment. This work provides improved understanding of long-term glass corrosion behavior in terms of the thickness, morphology, and chemistry of the surficial features that are formed.

36 MATERIALS SCIENCE↗

Probing the interplay between lattice dynamics and short-range magnetic correlations in CuGeO 3 with femtosecond RIXS

Investigations of magnetically ordered phases on the femtosecond timescale have provided significant insights into the influence of charge and lattice degrees of freedom on the magnetic sub-system. However, short-range magnetic correlations occurring in the absence of long-range order, for example in spin-frustrated systems, are inaccessible to many ultrafast techniques. Here, we show how time-resolved resonant inelastic X-ray scattering (trRIXS) is capable of probing such short-ranged magnetic dynamics in a charge-transfer insulator through the detection of a Zhang–Rice singlet exciton. Utilizing trRIXS measurements at the O K-edge, and in combination with model calculations, we probe the short-range spin correlations in the frustrated spin chain material CuGeO 3 following photo-excitation, revealing a strong coupling between the local lattice and spin sub-systems.

36 MATERIALS SCIENCE↗

Simulating topological quantum gates in two-dimensional magnet-superconductor hybrid structures

The creation of topological quantum gates using Majorana zero modes—an outstanding problem in the field of topological quantum computing—relies on our ability to control the braiding process in time and space. Here, we propose two-dimensional magnet-superconductor hybrid structures as a new platformfor the successful implementation of topologically protected √σ z -, σ z - and σ x -quantum gates using Majorana zero modes. Employing a novel theoretical formalism to compute the full timedependent many-body wave-function and utilizing a braiding protocol motivated by recent advances in electron-spin-resonance techniques we simulate quantum gates in 2D systems up to 600 sites, on timescales from a few femto- to nanoseconds. We demonstrate that the braiding process can be visualized in time and space by computing the non-equilibrium local density of states, which is proportional to the time-dependent differential conductance measured in scanning tunneling spectroscopy experiments, allowing us to directly image Majorana world lines.

Superconducting properties and materials↗

Assessment of Wind Energy Resource Potential for Future Human Missions to Mars

Energy sustainability and redundancy for surface habitats, life support systems and scientific instrumentation represent one of the highest-priority issues for future crewed missions to Mars. However, power sources utilized for the current class of robotic missions to Mars may be potentially dangerous near human surface habitats (for example, nuclear) or lack stability on diurnal or seasonal timescales (for example, solar) that cannot be easily compensated for by power storage. Here, we evaluate the power potential for wind turbines as an alternative energy resource on the Mars surface. Using a state-of-the-art Mars global climate model, we analyse the total planetary Martian wind potential and calculate its spatial and temporal variability. We find that wind speeds at some proposed landing sites are sufficiently fast to provide a stand-alone or complementary energy source to solar or nuclear power. While several regions show promising wind energy resource potential, other regions of scientific interest can be discarded based on the natural solar and wind energy potential alone. We demonstrate that wind energy compensates for diurnal and seasonal reductions in solar power particularly in regions of scientific merit in the midlatitudes and during regional dust storms. Critically, proposed turbines stabilize power production when combined with solar arrays, increasing the percent time that power exceeds estimated mission requirements from ~40% for solar arrays alone to greater than 60-90% across a broad fraction of the Mars surface. We encourage additional study aimed at advancing wind turbine technology to operate efficiently under Mars conditions and to extract more power from Mars winds.

atmospheric dynamics↗

Diamond precipitation dynamics from hydrocarbons at icy planet interior conditions

The pressure and temperature conditions at which precipitation of diamond occurs from hydrocarbon mixtures is important for modelling the interior dynamics of icy planets. However, there is substantial disagreement from laboratory experiments, with those using dynamic compression techniques finding much more extreme conditions are required than in static compression. Here we report the time-resolved observation of diamond formation from statically compressed polystyrene, (C 8 H 8 ) n , heated using the 4.5 MHz X-ray pulse trains at the European X-ray Free Electron Laser facility. Diamond formation is observed above 2,500 K from 19 GPa to 27 GPa, conditions representative of Uranus’s and Neptune’s shallow interiors, on 30 μs to 40 μs timescales. This is much slower than may be observed during the ~10 ns duration of typical dynamic compression experiments, revealing reaction kinetics to be the reason for the discrepancy. In conclusion, reduced pressure and temperature conditions for diamond formation has implications for icy planetary interiors, where diamond subduction leads to heating and could drive convection in the conductive ice layer that has a role in their magnetic fields.

79 ASTRONOMY AND ASTROPHYSICS↗

Tracking the ultraviolet-induced photochemistry of thiophenone during and after ultrafast ring opening

Photoinduced isomerization reactions lie at the heart of many chemical processes in nature. The mechanisms of such reactions are determined by a delicate interplay of coupled electronic and nuclear dynamics occurring on the femtosecond scale, followed by the slower redistribution of energy into different vibrational degrees of freedom. In this study, we apply time-resolved photoelectron spectroscopy with a seeded extreme ultraviolet free-electron laser to trace the ultrafast ring opening of gas-phase thiophenone molecules following ultraviolet photoexcitation. When combined with ab initio electronic structure and molecular dynamics calculations of the excited- and ground-state molecules, the results provide insights into both the electronic and nuclear dynamics of this fundamental class of reactions. The initial ring opening and non-adiabatic coupling to the electronic ground state are shown to be driven by ballistic S–C bond extension and to be complete within 350 fs. Theory and experiment also enable visualization of the rich ground-state dynamics that involve the formation of, and interconversion between, ring-opened isomers and the cyclic structure, as well as fragmentation over much longer timescales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optical control of ultrafast structural dynamics in a fluorescent protein

The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump–probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ultrafast electronic relaxation pathways of the molecular photoswitch quadricyclane

Abstract The light-induced ultrafast switching between molecular isomers norbornadiene and quadricyclane can reversibly store and release a substantial amount of chemical energy. Prior work observed signatures of ultrafast molecular dynamics in both isomers upon ultraviolet excitation but could not follow the electronic relaxation all the way back to the ground state experimentally. Here we study the electronic relaxation of quadricyclane after exciting in the ultraviolet (201 nanometres) using time-resolved gas-phase extreme ultraviolet photoelectron spectroscopy combined with non-adiabatic molecular dynamics simulations. We identify two competing pathways by which electronically excited quadricyclane molecules relax to the electronic ground state. The fast pathway (<100 femtoseconds) is distinguished by effective coupling to valence electronic states, while the slow pathway involves initial motions across Rydberg states and takes several hundred femtoseconds. Both pathways facilitate interconversion between the two isomers, albeit on different timescales, and we predict that the branching ratio of norbornadiene/quadricyclane products immediately after returning to the electronic ground state is approximately 3:2.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Shape-persistent ladder molecules exhibit nanogap-independent conductance in single-molecule junctions

Molecular electronic devices require precise control over the flow of current in single molecules. However, the electron transport properties of single molecules critically depend on dynamic molecular conformations in nanoscale junctions. Here, in this work, we report a unique strategy for controlling molecular conductance using shape-persistent molecules. Chemically diverse, charged ladder molecules, synthesized via a one-pot multicomponent ladderization strategy, show a molecular conductance (d[log( G/G 0 )]/d x ≈ -0.1 nm -1 ) that is nearly independent of junction displacement, in stark contrast to the nanogap-dependent conductance (d[log( G/G 0 )]/d x ≈ -7 nm -1 ) observed for non-ladder analogues. Ladder molecules show an unusually narrow distribution of molecular conductance during dynamic junction displacement, which is attributed to the shape-persistent backbone and restricted rotation of terminal anchor groups. These principles are further extended to a butterfly-like molecule, thereby demonstrating the strategy's generality for achieving gap-independent conductance. Overall, our work provides important avenues for controlling molecular conductance using shape-persistent molecules. Achieving robust and controllable conductance in single-molecule junctions is challenging due to the dynamic nature of molecular conformations that fluctuate over operational timescales. A strategy using shape-persistent molecules has now been developed that demonstrates nearly junction-displacement-independent conductance, providing a stable solution for single-molecule electronic properties.

molecular electronics↗

Flash droughts present a new challenge for subseasonal-to-seasonal prediction

Flash droughts are a recently recognized type of extreme event distinguished by sudden onset and rapid intensification of drought conditions with severe impacts. They unfold on subseasonal-to-seasonal timescales (weeks to months), presenting a new challenge for the surge of interest in improving subseasonal-to-seasonal prediction. In this perspective we discuss existing prediction capability for flash droughts and what is needed to establish their predictability. We place them in the context of synoptic to centennial phenomena, consider how they could be incorporated into early warning systems and risk management, and propose two definitions. The growing awareness that flash droughts involve particular processes and severe impacts, and probably a climate change dimension, makes them a compelling frontier for research, monitoring and prediction.

54 ENVIRONMENTAL SCIENCES↗

Reduced CO 2 uptake and growing nutrient sequestration from slowing overturning circulation

Current Earth system models (ESMs) project dramatic slowing (28–42% by 2100) of Atlantic Meridional Overturning Circulation and Southern Meridional Overturning Circulation (SMOC) across a range of climate scenarios, with a complete shutdown of SMOC possible by year 2300. Slowing meridional overturning circulation (MOC) differentially impacts the ocean biological and solubility carbon pumps, leaving the net impact on ocean carbon uptake uncertain. Here using a suite of ESMs, we show that slowing MOC reduces anthropogenic carbon uptake by the solubility pump but increases deep-ocean storage of carbon and nutrients by the biological pump. The net effect reduces ocean uptake of anthropogenic CO 2 . The deep-ocean nutrient sequestration will increasingly depress global-scale, marine net primary production over time. As a result, MOC slowdown represents a positive feedback that could extend or intensify peak-warmth climate conditions on multi-century timescales.

58 GEOSCIENCES↗

Global evidence for the acclimation of ecosystem photosynthesis to light

Photosynthesis responds quickly to changes in light, increasing with incoming photosynthetic photon flux density (PPFD) until the leaves become light saturated. This instantaneous response to PPFD, which is widely studied and incorporated into models of photosynthesis, is overlaid on non-instantaneous photosynthetic changes resulting from the acclimation of plants to average PPFD over intermediate timescales of a week to months ($\overline{PPFD}$). Such photosynthetic light acclimation is not typically incorporated into models, due to the lack of observational constraints. In this work, we use eddy covariance observations from globally distributed and automated sensor networks, along with photosynthesis estimates from nine terrestrial biosphere models (TBMs), to quantify and assess photosynthetic acclimation to light in natural environments. We also use recent theoretical developments to incorporate light acclimation in a TBM. Our results show widespread light acclimation of ecosystem photosynthesis. On average, a 1 μmol m -2 s -1 increase in $\overline{PPFD}_{10}$ (ten-day average PPFD) leads to a 0.031 ± 0.013 μmol C m -2 s -1 increase in the maximum photosynthetic assimilation rate (A max ), with croplands having stronger acclimation rates than grasslands and forests. Our analysis shows that the TBMs examined either neglect or substantially underestimate light acclimation. By updating a TBM to include photosynthetic acclimation, successfully reproducing the $\overline{PPFD}_{10}$-A max relationship, we provide a robust method for the incorporation of photosynthetic light acclimation in future models.

59 BASIC BIOLOGICAL SCIENCES↗

Exacerbated drought impacts on global ecosystems due to structural overshoot

Vegetation dynamics are affected not only by the concurrent climate but also by memory-induced lagged responses. For example, favourable climate in the past could stimulate vegetation growth to surpass the ecosystem carrying capacity, leaving an ecosystem vulnerable to climate stresses. This phenomenon, known as structural overshoot, could potentially contribute to worldwide drought stress and forest mortality but the magnitude of the impact is poorly known due to the dynamic nature of overshoot and complex influencing timescales. Here, we use a dynamic statistical learning approach to identify and characterize ecosystem structural overshoot globally and quantify the associated drought impacts. We find that structural overshoot contributed to around 11% of drought events during 1981-2015 and is often associated with compound extreme drought and heat, causing faster vegetation declines and greater drought impacts compared to non-overshoot related droughts. The fraction of droughts related to overshoot is strongly related to mean annual temperature, with biodiversity, aridity and land cover as secondary factors. These results highlight the large role vegetation dynamics play in drought development and suggest that soil water depletion due to warming-induced future increases in vegetation could cause more frequent and stronger overshoot droughts.

54 ENVIRONMENTAL SCIENCES↗

Detecting macroevolutionary genotype–phenotype associations using error-corrected rates of protein convergence

On macroevolutionary timescales, extensive mutations and phylogenetic uncertainty mask the signals of genotype–phenotype associations underlying convergent evolution. To overcome this problem, we extended the widely used framework of non-synonymous to synonymous substitution rate ratios and developed the novel metric ω C , which measures the error-corrected convergence rate of protein evolution. While ω C distinguishes natural selection from genetic noise and phylogenetic errors in simulation and real examples, its accuracy allows an exploratory genome-wide search of adaptive molecular convergence without phenotypic hypothesis or candidate genes. Using gene expression data, we explored over 20 million branch combinations in vertebrate genes and identified the joint convergence of expression patterns and protein sequences with amino acid substitutions in functionally important sites, providing hypotheses on undiscovered phenotypes. We further extended our method with a heuristic algorithm to detect highly repetitive convergence among computationally non-trivial higher-order phylogenetic combinations. Our approach allows bidirectional searches for genotype–phenotype associations, even in lineages that diverged for hundreds of millions of years.

59 BASIC BIOLOGICAL SCIENCES↗