Intermolecular channels direct crystal orientation in mineralized collagen
Abstract not provided
Xu, YiFei↗
SEARCH · Engineering Papers
Results for “structural modeling”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Controlling the pandemic during the SARS-CoV-2 vaccination rollout
There is a consensus that mass vaccination against SARS-CoV-2 will ultimately end the COVID-19 pandemic. However, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. We investigate relaxation scenarios using an age-structured transmission model that has been fitted to age-specific seroprevalence data, hospital admissions, and projected vaccination coverage for Portugal. Our analyses suggest that the pressing need to restart socioeconomic activities could lead to new pandemic waves, and that substantial control efforts prove necessary throughout 2021. Using knowledge on control measures introduced in 2020, we anticipate that relaxing measures completely or to the extent as in autumn 2020 could launch a wave starting in April 2021. Additional waves could be prevented altogether if measures are relaxed as in summer 2020 or in a step-wise manner throughout 2021. We discuss at which point the control of COVID-19 would be achieved for each scenario.
60 APPLIED LIFE SCIENCES↗
Microbially mediated mechanisms underlie soil carbon accrual by conservation agriculture under decade-long warming
Increasing soil organic carbon (SOC) in croplands by switching from conventional to conservation management may be hampered by stimulated microbial decomposition under warming. Here, we test the interactive effects of agricultural management and warming on SOC persistence and underlying microbial mechanisms in a decade-long controlled experiment on a wheat-maize cropping system. Warming increased SOC content and accelerated fungal community temporal turnover under conservation agriculture (no tillage, chopped crop residue), but not under conventional agriculture (annual tillage, crop residue removed). Microbial carbon use efficiency (CUE) and growth increased linearly over time, with stronger positive warming effects after 5 years under conservation agriculture. According to structural equation models, these increases arose from greater carbon inputs from the crops, which indirectly controlled microbial CUE via changes in fungal communities. As a result, fungal necromass increased from 28 to 53%, emerging as the strongest predictor of SOC content. Collectively, our results demonstrate how management and climatic factors can interact to alter microbial community composition, physiology and functions and, in turn, SOC formation and accrual in croplands.
59 BASIC BIOLOGICAL SCIENCES↗
Drivers and implications of alternative routes to fuels decarbonization in net-zero energy systems
Energy transition scenarios are characterized by increasing electrification and improving efficiency of energy end uses, rapid decarbonization of the electric power sector, and deployment of carbon dioxide removal (CDR) technologies to offset remaining emissions. Although hydrocarbon fuels typically decline in such scenarios, significant volumes remain in many scenarios even at the time of net-zero emissions. While scenarios rely on different approaches for decarbonizing remaining fuels, the underlying drivers for these differences are unclear. Here we develop several illustrative net-zero systems in a simple structural energy model and show that, for a given set of final energy demands, assumptions about the use of biomass and CO2 sequestration drive key differences in how emissions from remaining fuels are mitigated. Limiting one resource may increase reliance on another, implying that decisions about using or restricting resources in pursuit of net-zero objectives could have significant tradeoffs that will need to be evaluated and managed.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
The glassy solid as a statistical ensemble of crystalline microstates
Not Available
36 MATERIALS SCIENCE↗
CryoDRGN-AI: neural ab initio reconstruction of challenging cryo-EM and cryo-ET datasets
Proteins and other biomolecules form dynamic macromolecular machines that are tightly orchestrated to move, bind, and perform chemistry. Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) can access the intrinsic heterogeneity of these complexes and are therefore key tools for understanding their function. However, 3D reconstruction of the collected imaging data presents a challenging computational problem, especially without any starting information, a setting termed ab initio reconstruction. Here, in this study, we introduce cryoDRGN-AI, a method leveraging an expressive neural representation and combining an exhaustive search strategy with gradient-based optimization to process challenging heterogeneous datasets. Using cryoDRGN-AI, we reveal new conformational states in large datasets, reconstruct previously unresolved motions from unfiltered datasets, and demonstrate ab initio reconstruction of biomolecular complexes from in situ data. With this expressive and scalable model for structure determination, we hope to unlock the full potential of cryo-EM and cryo-ET as a high-throughput tool for structural biology and discovery.
Levy, Axel [Stanford Univ., CA (United States); SL↗
A representation-independent electronic charge density database for crystalline materials
Abstract In addition to being the core quantity in density-functional theory, the charge density can be used in many tertiary analyses in materials sciences from bonding to assigning charge to specific atoms. The charge density is data-rich since it contains information about all the electrons in the system. With the increasing prevalence of machine-learning tools in materials sciences, a data-rich object like the charge density can be utilized in a wide range of applications. The database presented here provides a modern and user-friendly interface for a large and continuously updated collection of charge densities as part of the Materials Project. In addition to the charge density data, we provide the theory and code for changing the representation of the charge density which should enable more advanced machine-learning studies for the broader community.
36 MATERIALS SCIENCE↗
Tracking the protein conformational motions driving HIV-1 membrane fusion
HIV-1 Env (trimeric gp120/gp41) is the surface protein responsible for membrane fusion. The Env binds to the receptor proteins, which induces gp120 shedding leading to conformational changes of gp41 from the pre-fusion to post-fusion state, allowing its fusion peptide to embed in the host cell membrane and bringing the viral and host cell membranes together. The gp41 refolding is a target of several peptide inhibitors. Yet, the molecular mechanism of this dynamic process is still not well understood. In this study, we successfully simulate the conformational change of gp41 from pre-fusion to post-fusion state in atomistic resolution using all-atom structure-based models. We reveal that maintaining the directionality of protomer interactions in both pre-fusion and post-fusion states is crucial for gp41 refolding. Additionally, we find that HR1 inherently extends as a three-helical bundle toward the host-cell membrane without any bias. Importantly, we identify native contacts in the pre-fusion state that are critical for the proper refolding of gp41 towards the post-fusion state. Lastly, by incorporating the membrane-fusion inhibitors, T20 and SFT, we identify the most vulnerable stage in the fusion pathway that exhibits the greatest sensitivity to these drugs, which could aid in a better understanding of drug resistance mechanisms.
59 BASIC BIOLOGICAL SCIENCES↗
Bio-inspired strategies for next-generation perovskite solar mobile power sources
Smart electronic devices are becoming ubiquitous due to many appealing attributes including portability, long operational time, rechargeability and compatibility with the user-desired form factor. Integration of mobile power sources (MPS) based on photovoltaic technologies with smart electronics will continue to drive improved sustainability and independence. With high efficiency, low cost, flexibility and lightweight features, halide perovskite photovoltaics have become promising candidates for MPS. Realization of these photovoltaic MPS (PV-MPS) with unconventionally extraordinary attributes requires new ‘out-of-box’ designs. Natural materials have provided promising designing solutions to engineer properties under a broad range of boundary conditions, ranging from molecules, proteins, cells, tissues, apparatus to systems in animals, plants, and humans optimized through billions of years of evolution. Applying bio-inspired strategies in PV-MPS could be biomolecular modification on crystallization at the atomic/meso-scale, bio-structural duplication at the device/system level and bio-mimicking at the functional level to render efficient charge delivery, energy transport/utilization, as well as stronger resistance against environmental stimuli (e.g., self-healing and self-cleaning). In this paper, we discuss the bio-inspired/-mimetic structures, experimental models, and working principles, with the goal of revealing physics and bio-microstructures relevant for PV-MPS. Here the emphasis is on identifying the strategies and material designs towards improvement of the performance of emerging halide perovskite PVs and strategizing their bridge to future MPS.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Analysis of the classical trajectory treatment of photon dynamics for polaritonic phenomena
Simulating photon dynamics in strong light–matter coupling situations via classical trajectories is proving to be powerful and practical. Here, in this work, we analyze the performance of the approach through the lens of the exact factorization approach. Since the exact factorization enables a rigorous definition of the potentials driving the photonic motion, it allows us to identify that the underestimation of photon number and intensities observed in earlier work is primarily due to an inadequate accounting of light–matter correlation in the classical Ehrenfest force rather than errors from treating the photons quasiclassically per se. The latter becomes problematic when the number of photons per mode begins to exceed a half.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Electromagnetic pinned solitons for space debris detection
Electromagnetic “pinned” solitons in the form of stationary nonlinear waves are studied within the framework of an inertial magneto-hydrodynamic model. These structures, that can arise when a charged source moves in a magnetized plasma, have a velocity that is equal to the source velocity and, hence, appear as “pinned” structures that envelope the source. We investigate the excitation of such solitons in the Low Earth Orbit region due to the passage of charged orbital debris objects. The spatial size of these electromagnetic solitons, typically of the order of a few ion skin depths, can be very large in this region. Such solitons can be detected using a variety of ground- or orbit-based radio sounding techniques and may provide a convenient additional means of tracking small sized orbital debris objects that are difficult to spot optically.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Polyimide dynamically compressed to decomposition pressures: Two-wave structures captured by velocimetry and modeling
We performed a series of six plate impact experiments on polyimide and modeled them using new reactant and products equations of state combined with an Arrhenius rate model. The first experiment was diagnosed with embedded electromagnetic velocity gauges through which we directly observed attenuation of the lead shock to an approximately constant state over a propagation distance of roughly 4 mm. Simulated gauge profiles were in excellent qualitative agreement with experiment and suggested a sluggish chemical reaction that did not proceed to completion. The remaining five experiments were conducted in a transmission geometry and diagnosed velocimetrically at the sample/window interface. All five of these yielded profiles with a sharp shock followed by a more gradual approach to maximum interface velocity that was “rounded” to varying degree. These profiles proved difficult to interpret unambiguously due to the convolution of the reactive wave upon first shock with reflection of the lead wave and reshock or release by the window. Comparison with thermochemical calculations strongly suggests that the point of maximum interface velocity corresponds to the equilibrium reshock or release locus. We discuss the implications of this point for the practice of impedance matching based on the reflected Hugoniot of reactive materials such as polymers. The reactant and thermochemical products equations of state are developmental SESAME tables 97710 and 97720, respectively.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Static and shock compression studies of eutectic high-entropy alloy AlCoCrFeNi 2.1 to ultrahigh pressures
The high-entropy alloy with composition AlCoCrFeNi 2.1 , additively manufactured with the laser powder-bed fusion technique, has a far-from-equilibrium BCC/FCC eutectic nanolamellar structure. We studied the high-pressure response of this alloy under both static compression and high-strain rate shock compression. The response to static compression using a diamond anvil cell was studied at pressures up to 302 GPa with synchrotron x-ray diffraction at the advanced photon source. The high-pressure FCC-only phase of the EHEA previously observed by Pope et al. [AIP Adv. 13, 035124 (2023)] is found to be stable up to the highest pressure achieved in this study with a volume compression of V/V 0 = 0.587 at ambient temperature. The shock experiments were performed by using GEKKO XII lasers at the Institute of Laser Engineering, Osaka University. The principal Hugoniot equation-of-state of the EHEA was measured up to a pressure of 515 GPa and a compression of V/V 0 = 0.613. Additionally, the thermal equation of state of the EHEA was measured up to 6.2 GPa and 1623 K using a large-volume Paris–Edinburgh cell to obtain the temperature dependence of bulk modulus and thermal expansion coefficients. The melting temperature for EHEA AlCoCrFeNi 2.1 at a pressure of 5.6 GPa was measured to be 1648 ± 25 K. These results can be used to refine stochastic (or special) quasi-random structure (SQS) models for high-pressure high-temperature behavior of high-entropy alloys.
36 MATERIALS SCIENCE↗
The C2 domain augments Ras GTPase-activating protein catalytic activity
Regulation of Ras GTPases by GTPase-activating proteins (GAPs) is essential for their normal signaling. Nine of the ten GAPs for Ras contain a C2 domain immediately proximal to their canonical GAP domain, and in RasGAP (p120GAP, p120RasGAP;RASA1) mutation of this domain is associated with vascular malformations in humans. Here, we show that the C2 domain of RasGAP is required for full catalytic activity toward Ras. Analyses of the RasGAP C2-GAP crystal structure, AlphaFold models, and sequence conservation reveal direct C2 domain interaction with the Ras allosteric lobe. This is achieved by an evolutionarily conserved surface centered around RasGAP residue R707, point mutation of which impairs the catalytic advantage conferred by the C2 domain in vitro. In mice,R707Cmutation phenocopies the vascular and signaling defects resulting from constitutive disruption of theRASA1gene. In SynGAP, mutation of the equivalent conserved C2 domain surface impairs catalytic activity. Our results indicate that the C2 domain is required to achieve full catalytic activity of GAPs for Ras.
Science & Technology - Other Topics↗
Cross-sectoral synergies for household energy savings: the role of electric vehicles, solar photovoltaics, and remote work
Over the past two decades, new technologies and behavioral shifts – such as electric vehicles, solar photovoltaics, and increased work-from-home practices – have reshaped residential electricity consumption and cost. However, their combined or synergistic impact on a household’s electricity cost remains unexplored. Leveraging data from the 2020 Residential Energy Consumption Survey, this study uses a structural equation model to unravel the extent to which the bundled adoption of EV-PV and stay-at-home decisions impact the total electricity cost of households. Results indicate that adopting both EVs and PV reduces electricity costs by 31% despite a 16% rise in consumption. When combined with stay-at-home practices, households still experience a 13% cost reduction, even with a 25% increase in electricity consumption. In conclusion, these findings suggest that financial savings are not merely a byproduct of adopting new technologies or behavioral changes but could serve as a key consideration for household contemplating engagement with multiple modern energy solutions simultaneously.
14 SOLAR ENERGY↗
Magnetic state switching in FeGa microstructures
This work demonstrates that magnetoelectric composite heterostructures can be designed at the length scale of 10µms that can be switched from a magnetized state to a vortex state, effectively switching the magnetization off, using electric field induced strain. This was accomplished using thin film magnetoelectric heterostructures of Fe 81.4 Ga 18.6 on a single crystal (011) [Pb(Mg 1/3 Nb 2/3 )O 3 ] 0.68 -[PbTiO 3 ] 0.32 (PMN-32PT) ferroelectric substrate. Here, the heterostructures were tripped from a multi-domain magnetized state to a flux closure vortex state using voltage induced strain in a piezoelectric substrate. FeGa heterostructures were deposited on a Si-substrate for superconducting quantum interference device magnetometry characterization of the magnetic properties. The magnetoelectric coupling of a FeGa continuous film on PMN-32PT was characterized using a magneto optical Kerr effect magnetometer with bi-axial strain gauges, and magnetic multi-domain heterostructures were imaged using x-ray magnetic circular dichroism—photoemission electron microscopy during the transition to the vortex state. The domain structures were modelled using MuMax 3 , a micromagnetics code, and compared with observations. The results provide considerable insight into designing magnetoelectric heterostructures that can be switched from an ‘on’ state to an ‘off’ state using electric field induced strain.
36 MATERIALS SCIENCE↗
Theoretical evidence that root penetration ability interacts with soil compaction regimes to affect nitrate capture
Abstract Background and Aims Although root penetration of strong soils has been intensively studied at the scale of individual root axes, interactions between soil physical properties and soil foraging by whole plants are less clear. Here we investigate how variation in the penetration ability of distinct root classes and bulk density profiles common to real-world soils interact to affect soil foraging strategies. Methods We utilize the functional–structural plant model ‘OpenSimRoot’ to simulate the growth of maize (Zea mays) root systems with variable penetration ability of axial and lateral roots in soils with (1) uniform bulk density, (2) plow pans and (3) increasing bulk density with depth. We also modify the availability and leaching of nitrate to uncover reciprocal interactions between these factors and the capture of mobile resources. Key Results Soils with plow pans and bulk density gradients affected overall size, distribution and carbon costs of the root system. Soils with high bulk density at depth impeded rooting depth and reduced leaching of nitrate, thereby improving the coincidence of nitrogen and root length. While increasing penetration ability of either axial or lateral root classes produced root systems of comparable net length, improved penetration of axial roots increased allocation of root length in deeper soil, thereby amplifying N acquisition and shoot biomass. Although enhanced penetration ability of both root classes was associated with greater root system carbon costs, the benefit to plant fitness from improved soil exploration and resource capture offset these. Conclusions While lateral roots comprise the bulk of root length, axial roots function as a scaffold determining the distribution of these laterals. In soils with high soil strength and leaching, root systems with enhanced penetration ability of axial roots have greater distribution of root length at depth, thereby improving capture of mobile resources.
59 BASIC BIOLOGICAL SCIENCES↗
A framework to measure the properties of intergalactic metal systems with two-point flux statistics
ABSTRACT The abundance, temperature, and clustering of metals in the intergalactic medium are important parameters for understanding their cosmic evolution and quantifying their impact on cosmological analysis with the Ly α forest. The properties of these systems are typically measured from individual quasar spectra redward of the quasar’s Ly α emission line, yet that approach may provide biased results due to selection effects. We present an alternative approach to measure these properties in an unbiased manner with the two-point statistics commonly employed to quantify large-scale structure. Our model treats the observed flux of a large sample of quasar spectra as a continuous field and describes the one-dimensional, two-point statistics of this field with three parameters per ion: the abundance (column density distribution), temperature (Doppler parameter), and clustering (cloud–cloud correlation function). We demonstrate this approach on multiple ions (e.g. ${\rm C\, \small {\rm IV}}$ , ${\rm Si\, \small {\rm IV}}$ , and ${\rm Mg\, \small {\rm II}}$ ) with early data from the Dark Energy Spectroscopic Instrument (DESI) and high-resolution spectra from the literature. Our initial results show some evidence that the ${\rm C\, \small {\rm IV}}$ abundance is higher than previous measurements and evidence for abundance evolution over time. The first full year of DESI observations will have over an order of magnitude more quasar spectra than this study. In a future paper, we will use those data to measure the growth of clustering and its impact on the Ly α forest, as well as test other DESI analysis infrastructure such as the pipeline noise estimates and the resolution matrix.
79 ASTRONOMY AND ASTROPHYSICS↗