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At least 433 records · Page 24

Theoretical Calculation Study of Nanomaterials

In recent years, theoretical simulations using computational physics and chemistry models have been used widely to predict the physical, chemical, and structural properties of nanomaterials. To reflect such rapid progress, two Special Issues on the theoretical study of nanomaterials were published. The 36 articles collected cover broad re-search fields and applications. In this Editorial, we provide an overview of these pub-lications and summarize the main findings. Based on these research outcomes, we lay out some future research directions.

First-principles calculations↗

Spike-and-Slab Shrinkage Priors for Structurally Sparse Bayesian Neural Networks

Network complexity and computational efficiency have become increasingly significant aspects of deep learning. Sparse deep learning addresses these challenges by recovering a sparse representation of the underlying target function by reducing heavily overparameterized deep neural networks. Specifically, deep neural architectures compressed via structured sparsity (e.g., node sparsity) provide low-latency inference, higher data throughput, and reduced energy consumption. In this article, we explore two well-established shrinkage techniques, Lasso and Horseshoe, for model compression in Bayesian neural networks (BNNs). To this end, we propose structurally sparse BNNs, which systematically prune excessive nodes with the following: 1) spike-and-slab group Lasso (SS-GL) and 2) SS group Horseshoe (SS-GHS) priors, and develop computationally tractable variational inference, including continuous relaxation of Bernoulli variables. We establish the contraction rates of the variational posterior of our proposed models as a function of the network topology, layerwise node cardinalities, and bounds on the network weights. Furthermore, we empirically demonstrate the competitive performance of our models compared with the baseline models in prediction accuracy, model compression, and inference latency.

97 MATHEMATICS AND COMPUTING↗

Quantum Machine-Learning for Eigenstate Filtration in Two-Dimensional Materials

Quantum machine-learning algorithms have emerged to be a promising alternative to their classical counterparts as they leverage the power of quantum computers. Such algorithms have been developed to solve problems like electronic structure calculations of molecular systems and spin models in magnetic systems. However, the discussion in all these recipes focuses specifically on targeting the ground state. Herein we demonstrate a quantum algorithm that can filter any energy eigenstate of the system based on either symmetry properties or a predefined choice of the user. The workhorse of our technique is a shallow neural network encoding the desired state of the system with the amplitude computed by sampling the Gibbs–Boltzmann distribution using a quantum circuit and the phase information obtained classically from the nonlinear activation of a separate set of neurons. We show that the resource requirements of our algorithm are strictly quadratic. To demonstrate its efficacy, we use state filtration in monolayer transition metal dichalcogenides which are hitherto unexplored in any flavor of quantum simulations. We implement our algorithm not only on quantum simulators but also on actual IBM-Q quantum devices and show good agreement with the results procured from conventional electronic structure calculations. We thus expect our protocol to provide a new alternative in exploring the band structures of exquisite materials to usual electronic structure methods or machine-learning techniques that are implementable solely on a classical computer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unfolding of the Villin Headpiece Domain: Revealing Structural Heterogeneity with Time‐Resolved X‐Ray Solution Scattering and Markov State Modeling

Understanding protein folding pathways is crucial to deciphering the principles of protein structure and function. Here, the unfolding dynamics of the 35‐residue villin headpiece (HP35) and a norleucine‐substituted variant (2F4K) using a combination of experimental and computational techniques is investigated. Time‐resolved X‐ray solution scattering coupled with equilibrium molecular dynamics simulations and Markov state modeling reveals distinct unfolding mechanisms between the two variants: HP35 and 2F4K. Specifically, HP35 exhibits a two‐state unfolding process, whereas an intermediate state is identified for the 2F4K mutant. A Markov state model constructed from simulations is used to map atomic‐level transitions to experimental observations, providing insights into the role of sequence variations in modulating folding pathways. The findings underscore the importance of integrating experimental and computational approaches to unravel protein unfolding mechanisms between heterogenous structural ensembles.

Nijhawan, Adam K. [Department of Chemistry Northwe↗

Machine learning with persistent homology and chemical word embeddings improves prediction accuracy and interpretability in metal-organic frameworks

Machine learning has emerged as a powerful approach in materials discovery. Its major challenge is selecting features that create interpretable representations of materials, useful across multiple prediction tasks. We introduce an end-to-end machine learning model that automatically generates descriptors that capture a complex representation of a material’s structure and chemistry. This approach builds on computational topology techniques (namely, persistent homology) and word embeddings from natural language processing. It automatically encapsulates geometric and chemical information directly from the material system. We demonstrate our approach on multiple nanoporous metal–organic framework datasets by predicting methane and carbon dioxide adsorption across different conditions. Our results show considerable improvement in both accuracy and transferability across targets compared to models constructed from the commonly-used, manually-curated features, consistently achieving an average 25–30% decrease in root-mean-squared-deviation and an average increase of 40–50% in R 2 scores. A key advantage of our approach is interpretability: Our model identifies the pores that correlate best to adsorption at different pressures, which contributes to understanding atomic-level structure–property relationships for materials design.

97 MATHEMATICS AND COMPUTING↗

Computational modeling of phononic pseudocrystal isolators

Methods for the efficient computational prediction of the performance of phononic pseudocrystals (structured materials capable of blocking extraordinary ranges of frequency) in COMSOL and other comparable finite element method codes are set forth. These methods include boundary conditions that make possible halving the size of the computational domain. Also included is an introduction of elastic energy density methods for assessing the extinction of elastic waves within the patterned region.

Swift, Stephen Hales↗

Synchrotron CT imaging of lattice structures with engineered defects

Understanding mechanical failure, crack propagation, and compressive behavior at the micrometer scale is essential for tailoring material properties for structural performance in cellular materials. Typically, modeling of traditional polymer foam materials is clouded by the lack of control in material morphology and its inherent stochastic structure. Additive manufacturing with sub-micrometer resolution provides a direct path for experimenters to specifically tailor structures needed by modelers to explicitly probe mechanical performance. Using laboratory-based 3D X-ray computed tomographic imaging (CT), the examination of deformation and damage provides a critical path to understand how these soft materials behave. Additionally, synchrotron CT yields realistic information at higher strain rates to directly validate the robustness of our finite element modeling. For this study, nanolithographic printing was employed to generate a series of engineered lattices with increasing levels of defects through the random removal of ligaments. These structures were mechanically tested and imaged with laboratory-based microCT. Additionally, synchrotron experiments were conducted in which the structures were imaged in 3D at 14 Hz during compression at a 0.4 s –1 strain rate. These 3D images show the changes in the structure as the ligaments bend, buckle and fracture in real time. This technique provides a robust framework for developing our methodologies and future exploration of engineered structures.

36 MATERIALS SCIENCE↗

Synergy of semiempirical models and machine learning in computational chemistry

Catalyzed by enormous success in the industrial sector, many research programs have been exploring data-driven, machine learning approaches. Performance can be poor when the model is extrapolated to new regions of chemical space, e.g., new bonding types, new many-body interactions. Another important limitation is the spatial locality assumption in model architecture, and this limitation cannot be overcome with larger or more diverse datasets. The outlined challenges are primarily associated with the lack of electronic structure information in surrogate models such as interatomic potentials. Given the fast development of machine learning and computational chemistry methods, we expect some limitations of surrogate models to be addressed in the near future; nevertheless spatial locality assumption will likely remain a limiting factor for their transferability. Here, we suggest focusing on an equally important effort—design of physics-informed models that leverage the domain knowledge and employ machine learning only as a corrective tool. In the context of material science, we will focus on semi-empirical quantum mechanics, using machine learning to predict corrections to the reduced-order Hamiltonian model parameters. The resulting models are broadly applicable, retain the speed of semiempirical chemistry, and frequently achieve accuracy on par with much more expensive ab initio calculations. These early results indicate that future work, in which machine learning and quantum chemistry methods are developed jointly, may provide the best of all worlds for chemistry applications that demand both high accuracy and high numerical efficiency.

36 MATERIALS SCIENCE↗

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↗

Fostering a Guiding Multiscale Model for the Development of Advanced MgB 2 Hydrogen Storage Materials (Final Technical Report)

Project Goal and Objective. The demand for energy and for an upgraded energy infrastructure has steadily grown, as have the needs for energy independence and alternatives to our reliance on petroleum. Hydrogen is considered the most viable fuels for wide-scale implementation in the near future as it is less-polluting, non-toxic, and has more stored energy than petroleum. It is envisioned that hydrogen can eventually become the prime energy carrier, integrating the transportation, grid, and chemical sectors in a way that improves resiliency, diversifies feedstocks, and affords new economic opportunities. A key remaining challenge is the development materials with enhanced gravimetric and volumetric hydrogen storage capacities that offer a higher performance than compressed gas. These materials would eliminate the need for large-scale compression, thereby dramatically reducing the footprint and cost of gas storage. The high gravimetric and volumetric hydrogen capacities of complex hydrides has prompted an intensive investigation of the potential of this class of materials as hydrogen storage media over the past 25 years. Among the many complex hydrides that have been explored, magnesium borohydride, Mg(BH 4 ) 2 , has been found to possess the best combination of practical thermodynamic properties. These include a gravimetric H 2 density of 14.9 wt% H 2 and thermodynamics for the dehydrogenation of Mg(BH 4 ) 2 to MgB 2 (equation 1) (ΔH° = 39 kJ/mol H 2 , ΔS = 112 J/K mol H 2 ) which lie in the narrow window required Mg(BH 4 ) 2 $\Leftrightarrow$ MgB 2 + 4 H 2 (1) for reversibility under moderate pressure and temperature. However, overcoming the extremely slow kinetics of the reversible release of hydrogen by this material in the solid state is a daunting challenge. At temperatures greater than 400 °C, the borohydride releases up to 14 wt% hydrogen giving MgB 2 . We discovered that the direct re-hydrogenation of MgB 2 to Mg(BH 4 ) 2 can be accomplished under 950 bar H 2 at 400 °C. While this demonstrated that complete reversibility can be achieved, the conditions employed are far too extreme for commercial hydrogen storage applications. More recently, we found through US DOE funded research projects (EERE HyMARC and HySCOR), that hydrogen cycling, can be accomplish at much milder conditions upon modification of the borohydride or boride. Guided by these discoveries these discoveries, the objective of this research project was to obtain key information that will enable the development of a model of reversible hydrogenation of MgB 2 to Mg(BH 4 ) 2 . The ultimate goal of our efforts is to attain a model of this transformation that can be utilized to accelerate development further advanced materials. This project directly follows on discoveries that were made over the course of a US DOE, EERE HyMARC project that was focused on improvement of the hydrogen cycling kinetics of modified MgB 2 . We found that that mechanical milling with graphene results the desired, pronounced kinetic enhancement. The dramatic lowering of the conditions required for the hydrogenation of MgB 2 is a significant step towards overcoming its chemical inertness allowing its development as a practical onboard hydrogen storage material. However, the exact nature of the modification(s) of MgB 2 that is responsible for its activation towards hydrogenation is completely unknown. This situation is not unique, as efforts to develop hydrogen storage materials typically have a narrow focus rather than a comprehensive approach that takes atomic level bonding and structure; molecular dynamics; long range, nano- and mesoscale-structure and their interconnection all into account. The goal of this project was the development of a comprehensive, multi-scale computational model of reversible hydrogenation of MgB 2 to Mg(BH 4 ) 2 that can be utilized for development of higher performance versions of the modified material. Development of the model requires determination of: 1) the bulk, nano-scale, and meso-scale structural changes occurring at elevated pressure following mechano-chemical modification of MgB 2 ; 2) the reaction pathway of the reversible hydrogenation of MgB 2 to Mg(BH 4 ) 2 ; 3) the effect of elevated pressure and mechano-chemical modification on the chemical reaction pathways; 4) the interactions at solid-gas interfaces; and particle surfaces; and 5) the kinetics and thermodynamic parameters associated with each step of the hydrogenation reaction pathway. This investigation required advanced techniques as preliminary, standard XRD, 11 B NMR, and FTIR analysis showed no signs of material modification. In order to gain this level of understanding of modified MgB 2 , required the teaming of a diverse group of experts and state-of-the art experimental capabilities at the University of Hawaii at Manoa (UHM) and collaborating National Laboratories: Craig Jensen , Department of Chemistry (PI and Project Director), solid state, solution, and high pressure NMR spectroscopy; solid-state synthesis; and high pressure hydrogenation (collaboration with SNL); Godwin Severa , Hawaii Natural Energy Institute (co-PI) calorimetry; infrared and Raman spectroscopy (collaboration with NREL); Dera , high pressure X-ray diffraction including in situ experiments (collaboration with ANL); Hope Ishii , Hawaii Institute of Geophysics electron microscopy investigations (collaboration with LBNL); and Joe Brown , Mechanical Engineering , material electronic structure and electric field effects.

08 HYDROGEN↗

Heuristic Computational Model for Predicting Lignin Solubility in Tailored Organic Solvents

Lignin is a random heteropolymer that has been extensively studied as a renewable source of aromatic precursors for high-value chemicals, biofuels, and bioplastics. A key challenge in lignin valorization is the structural and compositional heterogeneity of lignin feedstocks. Solvent-based approaches are commonly used to fractionate lignin to reduce this heterogeneity, but solvent selection can be challenging due to variability in lignin composition. In this work, we developed computational methods to predict good and poor organic solvents as a function of lignin composition. We analyzed 28 different linear pentamer structures, 18 from known libraries and 10 hypothetical polymers, and calculated their activity coefficients in 50 different organic solvents by using the conductor-like screening model for realistic solvents. We used these data to train a regression model that enabled the extensive investigation of the impact of solvent and monolignol compositions on predicted lignin solubility. The exhaustive exploration of solubility trends using model predictions revealed sets of solvents, identified using Kamlet–Taft parameters, that are predicted to promote lignin dissolution regardless of lignin composition. We further identified solvents expected to selectively isolate lignin fractions enriched in certain subunits. Furthermore, these results establish heuristic guidelines for solvent selection that can be used to tailor fractionation processes for lignin feedstocks of distinct composition or to design new processes that isolate fractions with higher proportions of selected subunits.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

How the Size and Density of Charge-Transfer Excitons Depend on Heterojunction’s Architecture

We have characterized the size, intensity, density, and distribution of charge-transfer (CT) excitons as a function of the acceptor–donor architecture of prototypical organic interfaces. This characterization was done by computational analysis of 17 models of varying numbers, positions, and orientations of the donor and acceptor molecules. The models’ building blocks were phenyl-C61-butyric acid methyl ester (PCBM) fullerene acceptors and dual-band donor polymers composed of thiophene, benzothiadiazole, and benzotriazole subunits. The electronic structure of the donor–acceptor complexes was computed with the time-dependent long-range-corrected density-functional tight-binding method and analyzed with the fragment-based one-electron transition density matrix. In all models, the complexes with edge-on orientation have denser spectra of low-energy CT states lying below the absorption bands compared to the complexes with face-on orientation. This CT-state distribution in edge-on complexes provides a gate to efficiently populate cold CT excitons. Moreover, the cold CT excitons have a higher degree of charge separation in the edge-on than in the face-on complexes. The CT amount and the CT exciton size generally increase with the energy of the CT states, although the electron remains localized on a single molecule in cold CT states. Delocalization over two PCBM molecules was observed for high-energy CT states. The exciton size also depends on the orientation. Larger excitons are produced by the delocalization of the electrons perpendicularly to the interface. When the delocalization is parallel, the smaller electron–hole distances yield moderately sized CT excitons.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High–Energy Earth–Abundant Cathodes with Enhanced Cationic/Anionic Redox for Sustainable and Long–Lasting Na–Ion Batteries

Layered iron/manganese-based oxides are a class of promising cathode materials for sustainable batteries due to their high energy densities and earth abundance. However, the stabilization of cationic and anionic redox reactions in these cathodes during cycling at high voltage remain elusive. Here, an electrochemically/thermally stable P2-Na 0.67 Fe 0.3 Mn 0.5 Mg 0.1 Ti 0.1 O 2 cathode material with zero critical elements is designed for sodium-ion batteries (NIBs) to realize a highly reversible capacity of ≈210 mAh g –1 at 20 mA g –1 and good cycling stability with a capacity retention of 74% after 300 cycles at 200 mA g –1 , even when operated with a high charge cut-off voltage of 4.5 V versus sodium metal. Combining a suite of cutting-edge characterizations and computational modeling, it is shown that Mg/Ti co-doping leads to stabilized surface/bulk structure at high voltage and high temperature, and more importantly, enhances cationic/anionic redox reaction reversibility over extended cycles with the suppression of other undesired oxygen activities. This work fundamentally deepens the failure mechanism of Fe/Mn-based layered cathodes and highlights the importance of dopant engineering to achieve high-energy and earth-abundant cathode material for sustainable and long-lasting NIBs.

25 ENERGY STORAGE↗

A Lanthanum‐Filled Carbon–Boron Clathrate

Abstract We report a carbon‐boron clathrate with composition 2 La@B 6 C 6 (LaB 3 C 3 ). Like recently reported SrB 3 C 3 , [1] single‐crystal X‐ray diffraction and computational modelling indicate that the isostructural La member crystallizes in the cubic bipartite sodalite structure (Type‐VII clathrate) with La atoms encapsulated within truncated octahedral cages composed of alternating carbon and boron atoms. The covalent nature of the B−C bonding results in a hard, incompressible framework, and owing to the balanced electron count, La 3+ [B 3 C 3 ] 3− exhibits markedly improved pressure stability and is a semiconductor with an indirect band gap predicted near 1.3 eV. A variety of different guest atoms may potentially be substituted within Type‐VII clathrate cages, presenting opportunities for a large family of boron‐stabilized, carbon‐based clathrates with ranging physical properties.

Strobel, Timothy A.↗

Mesoporous peptide frameworks engineered from crystallizable collagen-mimetic peptide amphiphiles

The rational design of porous frameworks with tunable pore dimensions and chemical functionalities is a critical step toward their implementation in diverse applications. While traditional porous materials are typically constructed from abiotic components, there is increasing interest in employing biologically derived building blocks (e.g., peptides and proteins) that offer unmatched structural and functional diversity. Here, we report the construction of crystalline mesoporous frameworks that are self-assembled from amphiphilic collagen-mimetic peptides. Comprehensive structural characterization via microscopy, spectroscopy, and computational techniques provides insights into the assembly packing model, in which hexagonally packed channels are interconnected by antiparallel-aligned collagen triple helices via hydrophobic and electrostatic interactions. Lastly, we demonstrate the functional potential of aCMP frameworks through the encapsulation of various molecular guests, including doxorubicin, an anti-cancer drug. Overall, this work establishes a class of mesoporous frameworks, derived from synthetically engineerable peptide conjugates, marking a significant step forward in broadening the architectural scope and application potential of peptide-based materials.

Perez, Anthony R↗

TransPolymer: a Transformer-based language model for polymer property predictions

Accurate and efficient prediction of polymer properties is of great significance in polymer design. Conventionally, expensive and time-consuming experiments or simulations are required to evaluate polymer functions. Recently, Transformer models, equipped with self-attention mechanisms, have exhibited superior performance in natural language processing. However, such methods have not been investigated in polymer sciences. Herein, we report TransPolymer, a Transformer-based language model for polymer property prediction. Our proposed polymer tokenizer with chemical awareness enables learning representations from polymer sequences. Rigorous experiments on ten polymer property prediction benchmarks demonstrate the superior performance of TransPolymer. Moreover, we show that TransPolymer benefits from pretraining on large unlabeled dataset via Masked Language Modeling. Experimental results further manifest the important role of self-attention in modeling polymer sequences. We highlight this model as a promising computational tool for promoting rational polymer design and understanding structure-property relationships from a data science view.

36 MATERIALS SCIENCE↗

Challenges and approaches to interpretive modeling of boundary plasma and neutral transport in a closed, pumped divertor

An experimental discharge from the DIII-D tokamak is modeled using the SOLPS-ITER code suite and compared against measurements in the pumped and relatively closed upper divertor. Uncertainties of boundary plasma simulations are identified by attempting to match code inputs to experimental conditions, including iteratively solving transport coefficients to match upstream experimental profiles using varying quantities of core particle flux, different pumping models, and various assumptions of ion thermal transport. Simulated boundary conditions for particle injection at the core interface are shown to be relevant to the plasma solution at the divertor targets, even if upstream transport is modified so that plasma profiles are comparatively similar, although seperatrix density is not held constant. When upstream plasma profiles are matched to experimental measurements by varying diffusive transport coefficients, using either poloidally symmetric or ballooning structure, the model finds a majority of injected energy being transported radially off the computational domain, in conflict with experimental radiated power measurements and heat flux measurements at the divertor target. Imposing a maximum thermal diffusivity or radially shifting the experimental separatrix location of the fitted profiles to increase power conducted to the targets by increasing the upstream electron temperature does not significantly modify this result. Including a thermalizing plenum volume in the simulation domain is shown to maintain the experimental volumetric pumping rate without knowing the neutral energy distribution incident on the pump duct a priori. By modifying transport parameters to match different assumptions for ion temperature, downstream neutral pressure changes by more than a factor of two, suggesting that attention to ion thermal transport may be a critical parameter for simulations to accurately resolve recycling and neutral transport, particularly in a closed divertor geometry. In addition to quantifying various modeling uncertainties, this work motivates both further experimental study and modeling improvements to improve predictive capabilities.

divertor↗