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At least 235 records · Page 13

Accelerating crystal structure determination with iterative AlphaFold prediction

Experimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold . Here, an automatic procedure requiring only sequence information and crystallographic data is presented that uses AlphaFold predictions to produce an electron-density map and a structural model. Iterating through cycles of structure prediction is a key element of this procedure: a predicted model rebuilt in one cycle is used as a template for prediction in the next cycle. This procedure was applied to X-ray data for 215 structures released by the Protein Data Bank in a recent six-month period. In 87% of cases our procedure yielded a model with at least 50% of C α atoms matching those in the deposited models within 2 Å. Predictions from the iterative template-guided prediction procedure were more accurate than those obtained without templates. It is concluded that AlphaFold predictions obtained based on sequence information alone are usually accurate enough to solve the crystallographic phase problem with molecular replacement, and a general strategy for macromolecular structure determination that includes AI-based prediction both as a starting point and as a method of model optimization is suggested.

59 BASIC BIOLOGICAL SCIENCES↗

A surprising proliferation of detwinning in β -tin at extreme loading rates

Integrating data from dynamic compression experiments of condensed matter across three national laboratories has led to insight and quantitative calibration of materials strength over decades of loading rate. For many materials, a single strength model (such as PTW) is sufficient to capture the flow-stress strain rate relationship which is monotonic. Here, we show here that β -tin, a tetragonal metal, exhibits dramatic deviations from this behavior. Naive fitting to a single PTW model is insufficient to capture the behavior; indeed, such resulting inferred flow stress versus strain exhibits a non-monotonic behavior. We suggest a resolution to this by proposing that in β -tin there are important Bauschinger effects arising from favorable conditions for twinning and detwinning. A simple yield surface model when paired with PTW hardening captures the experimental data.

36 MATERIALS SCIENCE↗

A new-old approach to composite scalars with chiral fermion constituents

We develop a dynamical, Lorentz invariant theory of composite scalars in configuration space consisting of chiral fermions, interacting by the perturbative exchange of a massive “gluon” of coupling g 0 and mass M 0 2 (the coloron model). The formalism is inspired by, but goes beyond, old ideas of Yukawa and the Nambu-Jona-Lasinio (NJL) model. It yields a non-pointlike internal wave-function of the bound state, ϕ ( r ) , which satisfies a Schrödinger-Klein-Gordon (SKG) equation with eigenvalue μ 2 . For super-critical coupling, g 0 2 > g 0 c 2 , we have μ 2 < 0 leading to spontaneous symmetry breaking. The binding of chiral fermions is semiclassical, not loop-level as in NJL. The mass scale is determined by the interaction as in NJL. We mainly focus on the short-distance, large M 0 2 limit, yielding an NJL pointlike interaction, but the bound state internal wave-function, ϕ ( r → ) , remains spatially extended and dilutes ϕ ( 0 ) . This leads to power-law suppression of the induced Yukawa and quartic couplings and requires radically less fine-tuning of a hierarchy than does the NJL model. We include a discussion of loop corrections of the theory. A realistic top condensation model appears possible.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Yield strength prediction of high-entropy alloys using machine learning

Yield strength at high temperature is an important parameter in the design and application of high entropy alloys (HEAs). However, the experimental measurement of yield strength at high temperature is quite costly, complicated, and time-consuming. Therefore, it is essential to identify and apply a robust method for the accurate prediction of yield strength at high temperature from the available experimental and simulation data. In this study, for the first time, a machine learning (ML) method based on the regression technique of random forest (RF) regressor is used to predict the yield strength of HEAs at the desired temperature. Further, the yield strengths of MoNbTaTiW and HfMoNbTaTiZr at 800 °C and 1200 °C, are predicted using the RF regressor model. We find that the results are consistent with the experimental reports, showing that the RF regressor model predicts the yield strength of HEAs at the desired temperatures with high accuracy.

36 MATERIALS SCIENCE↗

Nuclear Data for Spallation Neutron Radioisotope Production (Final Technical Report)

Over 50 million nuclear medicine procedures are performed annually, leading to a multi-billion dollar market for radioisotope production. The demand for new medical and research isotopes is growing, and radioisotope supply is insufficient. Most radioisotope production today utilizes charged particle or low-energy neutron irradiation of a target. Isotope production with tens to hundred MeV incident energies is a relatively unexplored option. There is a tremendous opportunity associated with a growing number of suitable domestic and international facilities buttressed by hundred million dollar global investments (e.g., the Los Alamos and Brookhaven Isotope Production Facilities, the European Spallation Source in Lund, and the Korean Multi-purpose Accelerator Complex in Gyeongbuk). In part due to a lack of supporting nuclear data that would make modeling radioisotope yields and purities possible, these facilities do not utilize their high-energy neutron fluxes for isotope production. This project attempted to measure neutron reaction excitation functions relevant to the large-scale production of critical radioisotopes, enabling development of cost-efficient isotope production methods, contributing to the improvement of theoretical models, and enhancing the value of national isotope production facilities. Reactions which form 67 Cu, 32 Si, and alpha-emitting isotopes like 225 Ac were chosen for their consistent prioritization by expert panels, representation of diverse reaction mechanisms, and relative lack of supporting nuclear data. Accurate measurement of these data is presently made only using quasi-monoenergetic neutron beams, which are produced by bombarding thin lithium targets with protons at only a few laboratories in the world. Ultimately, the projects efforts were incompletely accomplished due to a combination of multi-year technical issues at the only laboratory in the world which can make the proposed measurements, iThemba Labs in South Africa, and the onset of a global pandemic, which precluded the significant effort and time required to develop an independent measurement capability in the United States.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Competing conduction mechanisms in high performance carbon nanotube fibers

The performance of carbon nanotube (CNT) cables, a contender for copper-wire replacement, is tied to its metallic and semi-conducting-like conductivity responses with temperature; the origin of the semi-conducting-like response however is an underappreciated incongruity in literature. With controlled aspect-ratio and doping-degree, over 61 unique cryogenic experiments including anisotropy and Hall measurements, CNT cable performance is explored at extreme temperatures (65 mK) and magnetic-fields (60 T). A semi-conducting-like conductivity response with temperature becomes temperature-independent approaching absolute-zero, uniquely demonstrating for the first time the necessity of heterogeneous fluctuation induced tunneling; complete de-doping leads to localized hopping, contrasting graphite's pure metallic-like response. High-field magneto-resistance (including novel +22 % longitudinal magneto-resistance near room-temperature) is analyzed with hopping and classical two-band models, both yielding a similar parameter useful for conductor development. Varying field-orientation angle uncovers significant two- and four-fold symmetries that are shown to be from Aharonov-Bohm-like corrections to the curvature-induced bandgap, a first for macroscale CNT fibers. Tight-binding calculations using Green's Function formalism model the largest, coherent transport to-date in commensurate CNT bundles in magnetic-field, revealing non-uniform transmission across bundle cross-sections with doping restoring uniformity; independent of doping, transport in bundle-junction-bundle systems are predominantly from CNTs adjacent to the other bundle—demonstrating that smaller bundles are more efficient for electronic transport. The final impact is predicting the ultimate conductivity of heterogeneous CNT cables using temperature and field-dependent transport, surpassing conductivity of traditional metals.

36 MATERIALS SCIENCE↗

Canonical and noncanonical Hamiltonian operator inference

Here, a method for the nonintrusive and structure-preserving model reduction of canonical and noncanonical Hamiltonian systems is presented. Based on the idea of operator inference, this technique is provably convergent and reduces to a straightforward linear solve given snapshot data and gray-box knowledge of the system Hamiltonian. Examples involving several hyperbolic partial differential equations show that the proposed method yields reduced models which, in addition to being accurate and stable with respect to the addition of basis modes, preserve conserved quantities well outside the range of their training data.

97 MATHEMATICS AND COMPUTING↗

Micro-spectroscopic and freezing characterization of ice-nucleating particles collected in the marine boundary layer in the eastern North Atlantic

Abstract. Formation of atmospheric ice plays a crucial role in the microphysical evolution of mixed-phase and cirrus clouds and thus climate. How aerosol particles impact ice crystal formation by acting as ice-nucleating particles (INPs) is a subject of intense research activities. To improve understanding of atmospheric INPs, we examined daytime and nighttime particles collected during the Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA) field campaign conducted in summer 2017. Collected particles, representative of a remote marine environment, were investigated for their propensity to serve as INPs in the immersion freezing (IMF) and deposition ice nucleation (DIN) modes. The particle population was characterized by chemical imaging techniques such as computer-controlled scanning electron microscopy with energy-dispersive X-ray analysis (CCSEM/EDX) and scanning transmission X-ray microscopy with near-edge X-ray absorption fine-structure spectroscopy (STXM/NEXAFS). Four major particle-type classes were identified where internally mixed inorganic–organic particles make up the majority of the analyzed particles. Following ice nucleation experiments, individual INPs were identified and characterized by SEM/EDX. The identified INP types belong to the major particle-type classes consisting of fresh sea salt with organics or processed sea salt containing dust and sulfur with organics. Ice nucleation experiments show IMF events at temperatures as low as 231 K, including the subsaturated regime. DIN events were observed at lower temperatures of 210 to 231 K. IMF and DIN observations were analyzed with regard to activated INP fraction, ice-nucleation active site (INAS) densities, and a water activity-based immersion freezing model (ABIFM) yielding heterogeneous ice nucleation rate coefficients. Observed IMF and DIN events of ice formation and corresponding derived freezing rates demonstrate that the marine boundary layer aerosol particles can serve as INPs under typical mixed-phase and cirrus cloud conditions. The derived IMF and DIN parameterizations allow for implementation in cloud and climate models to evaluate predictive effects of atmospheric ice crystal formation.

54 ENVIRONMENTAL SCIENCES↗

Hypertriton puzzle in relativistic heavy-ion collisions

The yields of hadrons and light nuclei in relativistic collisions of heavy-nuclei at a center of mass energy of $\sqrt{s_{NN}}$ = 2.6 TeV can be described remarkably well by a thermal distribution of an ideal gas of hadrons and light nuclei interacting only via the decay of resonances. Given the particularly small binding energy of hypertritons relative to the temperature describing the yields (about 156 MeV), one might naturally expect hypertrions to dissociate in medium, making the agreement of hypertriton yields with thermal predictions highly puzzling. The puzzle is compounded by the fact that small binding energy is associated with the large size of the hypertriton. This size is on a similar scale to the overall size of the fireball and much larger than the length scale over which temperatures in the fireball vary over phenomenologically relevant amounts. Here, this paper quantifies the tension this effect causes and shows that it is sufficiently large to render the thermal model inconsistent: its natural assumptions are in conflict with its outputs. The possibility that hypertritons are formed at freeze out as compact objects, quark droplets, that subsequently evolve into hypertritons is considered as a way to resolve the puzzle. It is noted that beyond making the assumption that compact quark droplets form, additional detailed dynamical assumptions which have not been justified are needed to make the thermal model work. The issue of why, despite these issues, the hypertriton is well described by a simple statistical description at freeze out is unresolved. Resolving the hypertriton puzzle is important as it may clarify whether the phenomenological success of the simple thermal model for yields accurately reflects the simple picture of the underlying physics on which it is based.

hydrodynamic models↗

ChIMES: A Machine-Learned Interatomic Model Targeting Improved Description of Condensed Phase Chemistry in Energetic Materials

In this report we detail completion of a Physics and Engineering Model Level Two Milestone targeting improved reactive interatomic potentials (IAPs) for energetic materials (EM) through machine learning. The specific goals of this milestone were to develop, validate, and document a new reactive molecular dynamics method for EM, based on machine learning by (1) generating databases of first-principles-derived forces, stresses, and energies for HN3 and 3,4-bis(3-nitrofurazan- 4-yl)furoxan (DNTF) (2) generate atomistic force fields from these databases via ML, and (3) benchmark model performance against first principles calculations. These goals were achieved by (1) further developing a machine learned reactive IAP and generation approach (i.e. the Chebyshev Interaction Model for Efficient Simulation or “ChIMES”), for which resulting IAPs can approach the predictive power of quantum-mechanical approaches at a fraction of the computational expense, and (2) applying the ChIMES framework to develop models for HN3 and DNTF. We find that for simple energetic materials like HN3, high accuracy ChIMES models can be obtained through application of a fitting approach that does not use active machine learning. We demonstrate the suitability of ChIMES models for simulations involving EM by using the HN3 model in multiscale shock technique simulations to predict the HN3 Chapman-Jouguet detonation state and investigate chemical evolution out to 1 ns following shock compression. This model is then used in larger direct shock (DS) simulations for a preliminary investigation of how bubbles (i.e. voids) influence material response under shock compression. We find that more complex EM (i.e. DNTF) necessitate a more sophisticated fitting approach, and develop a new active learning method and python tool to meet this challenge. We demonstrate that this fitting approach yields ChIMES models that out-perform commonly used standard reactive IAPs as well as semi-empirical quantum methods, and discuss the systematic improvability of these actively learned ChIMES models. We also describe challenges related to model development for EM such as DNTF, for which few experimental or previous simulation data are available (e.g. which could otherwise inform generation of training data). To overcome this issue, we establish a semi-empirical quantum ChIMES capability which can be used to efficiently map out relevant thermodynamic and configurational space, and generate ChIMES-IAP training data in a multiscale manner. We also show that these semi-empirical quantum ChIMES models can be used to generate predictions for the shock Hugoniot (the Hugoniot is the locus of thermodynamic states found in a shocked material) equation of state, investigate related thermochemistry, and explore carbon condensation following shock compression. This work represents a substantial advance in our atomistic modeling capability for EM that will provide much needed information on the chemistry of detonation for continued development of continuum models based on the Cheetah thermochemical code.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Data‐Efficient Generation of Synthetic Microstructures of Polymer‐Bonded Energetic Material With Fine‐Tuned Stable Diffusion

Among current deep learning approaches for synthetic image generation, diffusion-based models stand out in terms of algorithmic stability and ability to retain high-fidelity image features with detailed resolution. Here, in this work, we employ Dreambooth, a method for fine-tuning Stable Diffusion, on X-ray CT images of microstructure of the polymer-bonded form (PBX) of a commonly used high explosive, Pentaerythritol tetranitrate (PETN), which yields generative models for creating synthetic PBX images. The models developed here represent five classes (or ‘lots’) of microstructures and demonstrate successful generation of images of each class with high fidelity, as verified by computed classification accuracy of ∼ 94% or higher. Data augmentation afforded by such image synthesis can be used to more reliably decipher underlying statistics, build processing-structure correlations, recognize off-normal structural anomalies, and identify age-related changes. Ideas related to converting image data into appropriate density mapping and performing mesoscale simulation or surrogate modeling of detonation are also discussed.

Dreambooth↗

Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium

Abstract Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.

59 BASIC BIOLOGICAL SCIENCES↗

GCAM–GLORY v1.0: representing global reservoir water storage in a multi-sector human–Earth system model

Abstract. Reservoirs play a significant role in modifying the spatiotemporal availability of surface water to meet multi-sector human demands, despite representing a relatively small fraction of the global water budget. Yet the integrated modeling frameworks that explore the interactions among climate, land, energy, water, and socioeconomic systems at a global scale often contain limited representations of water storage dynamics that incorporate feedbacks from other systems. In this study, we implement a representation of water storage in the Global Change Analysis Model (GCAM) to enable the exploration of the future role (e.g., expansion) of reservoir water storage globally in meeting demands for, and evolving in response to interactions with, the climate, land, and energy systems. GCAM represents 235 global water basins, operates at 5-year time steps, and uses supply curves to capture economic competition among renewable water (now including reservoirs), non-renewable groundwater, and desalination. Our approach consists of developing the GLObal Reservoir Yield (GLORY) model, which uses a linear programming (LP)-based optimization algorithm and dynamically linking GLORY with GCAM. The new coupled GCAM–GLORY approach improves the representation of reservoir water storage in GCAM in several ways. First, the GLORY model identifies the cost of supplying increasing levels of water supply from reservoir storage by considering regional physical and economic factors, such as evolving monthly reservoir inflows and demands, and the leveled cost of constructing additional reservoir storage capacity. Second, by passing those costs to GCAM, GLORY enables the exploration of future regional reservoir expansion pathways and their response to climate and socioeconomic drivers. To guide the model toward reasonable reservoir expansion pathways, GLORY applies a diverse array of feasibility constraints related to protected land, population, water sources, and cropland. Finally, the GLORY–GCAM feedback loop allows evolving water demands from GCAM to inform GLORY, resulting in an updated supply curve at each time step, thus enabling GCAM to establish a more meaningful economic value of water. This study improves our understanding of the sensitivity of reservoir water supply to multiple physical and economic dimensions, such as sub-annual variations in climate conditions and human water demands, especially for basins experiencing socioeconomic droughts.

54 ENVIRONMENTAL SCIENCES↗

An Exploration of the Equation of State Dependence of Core-collapse Supernova Explosion Outcomes and Signatures

We explore, using a state-of-the-art simulation code in 3D and late-enough times to witness final observables, the dependence of core-collapse supernova explosions on the nuclear equation of state (EOS). Going beyond questions of explodability, we compare final explosion energies, nucleosynthetic yields, recoil kicks, and gravitational-wave and neutrino signatures using the SFHo and DD2 nuclear EOSs for a 9 M ⊙ /solar-metallicity progenitor star. The DD2 EOS is stiffer and has a lower effective nucleon mass. The result is a more extended protoneutron star (PNS) and lower central densities. As a consequence, the mean neutrino energies, final explosion energy, and recoil kick speed are lower. Moreover, the evolution of PNS convection differs between the two EOS models in significant ways. This translates in part into interestingly altered neutrino “light” curves and noticeably altered gravitational-wave signal strengths and frequency characteristics that may be diagnostic. The faster exploding model (SFHo) yields slightly more neutron-rich ejecta and more species with atomic weights between 60 and 90 and a weak r-process. However, this is merely a preliminary study. The next step is a more comprehensive and multiprogenitor set of 3D supernova simulations for various EOSs to late times when the observables have asymptoted. Such a future investigation will have a direct bearing on the neutron star and black hole birth mass functions and the quest toward a fully quantitative theory of supernova observables.

Rusakov, Aleksandr [Princeton University, NJ (Unit↗

Modeling of Magnetic Properties of Magnetorheological Elastomers Using JA Hysteresis Model

Magnetorheological elastomers (MREs) are composite materials that consist of magnetically permeable particles in a nonmagnetic polymeric matrix. Under the influence of an external magnetic field, a reversible deformation change occurs in the mechanical properties of these materials. Due to their coupled magnetomechanical response, these materials have been found suitable for a range of applications including tunable vibration absorbers, sensors, and actuators. Notably, improvement of such devices are prerequisites to efficient energy conversion systems, hence the need to understand further the MRE technology. The Jiles-Atherton (JA) theory takes into consideration the magneto-coupling experienced by effective domains in a magnetic material. Algorithm based on the theory yields five model parameters; saturation magnetization (M s ), domain density (a), domain coupling (α), loss coefficient (k), and reversibility (c). Using JA theory, model parameters were calculated and linked to the physical attributes of Fe powder and isotropic MRE. The results show that the calculated Ms for the MRE is reasonably related to that of the Fe powder by a factor of the particle's volume fraction used in the MRE. Further, the calculated k, a, and α provided support for the reduced pinning factor, domain density, and increased domain coupling in the MRE due to the changes in the domain structure between the two materials. From the calculated JA parameters, finite-element modeling (FEM) of the MRE hysteresis loop was performed. The analysis showed that the modeled magnetic properties including coercivity, remanence, and coordinates of the hysteresis loop tip vary with geometric position.

42 ENGINEERING↗

AQuaRef: machine learning accelerated quantum refinement of protein structures

Cryo-EM and X-ray crystallography provide crucial experimental data for obtaining atomic-detail models of biomacromolecules. Refining these models relies on library-based stereochemical data, which, in addition to being limited to known chemical entities, do not include meaningful noncovalent interactions. Quantum mechanical (QM) calculations could alleviate these issues but are too expensive for large molecules. Here we present a novel AI-enabled Quantum Refinement (AQuaRef) based on AIMNet2 machine learned interatomic potential (MLIP) mimicking QM at substantially lower computational costs. By refining 41 cryo-EM and 30 X-ray structures, we show that this approach yields atomic models with superior geometric quality compared to standard techniques, while maintaining an equal or better fit to experimental data. Notably, AQuaRef aids in determining proton positions, as illustrated in the challenging case of short hydrogen bonds in the parkinsonism-associated human protein DJ-1 and its bacterial homolog YajL.

Zubatyuk, Roman [Carnegie Mellon University, Pitts↗

A computationally-efficient method for flamelet calculations

A new open-source code for the simulation of the diffusion flamelet equations is proposed. Emphasis is placed on using an approximate Jacobian to reduce the computational cost of the matrix operations. Performance of the proposed solvers is tested by performing flamelet calculations with kinetic mechanisms of varying sizes. For the unity Lewis number equations, the present iterative Newton solver using an approximate Jacobian greatly outperforms direct Newton solvers using exact Jacobians. The computation cost scales linearly with the number of species, leading to a reduction in solution times by two orders of magnitude for mechanisms containing thousands of species. The applicability of the Jacobian approximations to the solution of the non-unity Lewis number flamelet equations is assessed. The approximations are generally inadequate to solve the full non-unity Lewis number equations but can be used in some applications depending on the balance of terms in the flamelet equations. As an example, the flamelet solver is applied to the study of sooting tendencies in laminar co-flow diffusion flames where modified non-unity Lewis number flamelet equations, previously shown to accurately reproduce experimentally-measured Yield Sooting Indices (YSI), are solved. Here, the accelerated flamelet solver is well suited for sensitivity analysis and uncertainty quantification with large detailed kinetic mechanisms, tasks for which the computational cost was previously prohibitive.

42 ENGINEERING↗