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At least 595 records · Page 33

Explainable machine learning reveals that local structural motifs encode the thermodynamic state across the CuZr metallic glass-forming range

Metallic glasses derive their properties from the statistics of local atomic motifs rather than from long-range order, yet a quantitative, chemistry-specific link between motif populations and the underlying glassy state has remained elusive. In this work we combine large-scale molecular dynamics, Voronoi tessellation, deep neural networks, and SHapley Additive exPlanations (SHAP) to identify which local structural motifs define the glassy state of Cu—Zr metallic glasses. A dataset of 17,180 atomistic configurations spanning ten compositions (Cu 20 Zr 80 –Cu 80 Zr 20 ) and four quench rates (10 9 –10 12 K/s) is used to train a feed-forward neural network that regresses temperature across the 50–2000 K liquid–supercooled–glass range, achieving a mean absolute error of 19.89 K and R 2 = 0.9974, confirming that the local structural state is faithfully encoded in motif-level structure. SHAP analysis then reveals that a tightly coupled near-icosahedral family of motifs (coordination numbers (CN) 11–13, including the full icosahedron 001200 and its single-atom-perturbation sibling 10930) collectively encodes the thermodynamic state of the system across the full glass-forming range. The CN = 11–13 ordered members carry negative SHAP values at high populations, tracking the most deeply-quenched configurations, while 10930 shows the reversed signature consistent with its role as a soft-spot host whose population shrinks as the icosahedral network deepens. The analysis demonstrates that explainable machine learning can isolate the minimal motif vocabulary defining the glassy state and recovers the near-icosahedral building blocks previously identified by data-driven analyses of Cu—Zr. The approach provides a general, chemistry-specific route for characterizing the structural state of disordered materials.

36 MATERIALS SCIENCE↗

Investigating Bacterial-Fungal Interactions using Fungal Highway Columns in Diverse Environments and Substrates

Bacterial-fungal interactions (BFIs) play an integral role in shaping microbial community composition, biogeochemical functions, spatial dynamics, and microbial dispersal. Mycelial networks created by filamentous fungi or other filamentous microorganisms (e.g., Oomycetes) act as 'fungal highways' that can be utilized by bacteria for transport throughout heterogeneous environments, greatly facilitating their mobility and granting them access to regions that may be challenging or impossible to reach on their own (e.g., due to air pockets within the soil). Several devices and experimental protocols have been created to study these fungal highways, including fungal highway columns. The fungal highway column designed by our group can be used for a variety of in situ or in vitro applications, as well as with diverse environmental and host-associated sample types. Herein, we describe the methods for performing experiments with these columns, including designing, printing, sterilizing, and preparing the devices. The options for analyzing data obtained from the use of these devices are also discussed here, and troubleshooting advice regarding potential pitfalls associated with experiments using fungal highway columns is offered. These devices can be used to gain a more comprehensive understanding of the diversity, mechanisms, and dynamics of fungal highway BFIs to provide valuable insights into the structural and functional dynamics within complex environments (e.g., soils) and across diverse habitats in which bacteria and fungi co-exist.

59 BASIC BIOLOGICAL SCIENCES↗

Superionic conduction using ion aggregates

Project objective: Engineer solid polymeric electrolytes with an optimized, self-assembled, ion network that conducts independently of polymer segmental dynamics. The goal of this project is to engineer an optimized, self-assembled ion aggregate network, by which we can incorporate an aggregate assisted, collective, superionic conduction paradigm into polymeric electrolytes. We do not seek to improve conductivity, although this is a likely result of our approach, but to propose systems in which collective motion is the main conduction mechanism. We believe that once such materials are identified, they will quickly become a subject of research in the solid polymer electrolyte community. With this in mind, we pursue three design strategies: increase ion content in PEG single ion conductors, use mixed anions (including divalent ions as crosslinkers), and introduce swelled polyanion/polycation complexes as a potential ion conducting material.

36 MATERIALS SCIENCE↗

Dynamic machine learning-based optimization algorithm to improve boiler efficiency

With decreasing computational costs, improvement in algorithms, and the aggregation of large industrial and commercial datasets, machine learning is becoming a ubiquitous tool for process and business innovations. Machine learning is still lacking applications in the field of dynamic optimization for real-time control. This work presents a novel framework for performing constrained dynamic optimization using a recurrent neural network model combined with a metaheuristic optimizer. The framework is designed to augment an existing control system and is purely data-driven, like most industrial Model Predictive Control applications. Several recurrent neural network models are compared as well as several metaheuristic optimizers. Hyperparameters and optimizer parameters are tuned with parameter sweeps, and the resulting values are reported. Further, the best parameters for each optimizer and model combination are demonstrated in closed-loop control of a dynamic simulation, and several recommendations are made for generalizing this framework to other systems. Up to 0.953% improvement is realized over the non-optimized case for a simulated coal-fired boiler. While this is not a large improvement in percentage, the total economic impact is $991,000 per year, and this study builds a foundation for future machine learning with dynamic optimization.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Quantum tensor network algorithms for evaluation of spectral functions on quantum computers

We investigate quantum algorithms derived from tensor networks to simulate the static and dynamic properties of quantum many-body systems. Using a sequentially prepared quantum circuit representation of a matrix product state (MPS) that we call a quantum tensor network (QTN), we demonstrate algorithms to prepare ground and excited states on a quantum computer and apply them to molecular nanomagnets (MNMs) as a paradigmatic example. In this setting, we develop two approaches for extracting the spectral correlation functions measured in neutron-scattering experiments: (a) a generalization of the SWAP test for computing wave function overlaps and, (b) a generalization of the notion of matrix product operators to the QTN setting which generates a linear combination of unitaries. The latter method is discussed in detail for translationally invariant spin-half systems, where it is shown to reduce the qubit resource requirements compared with the SWAP method and may be generalized to other systems. We demonstrate the versatility of our approaches by simulating spin-1/2 and spin-3/2 MNMs, with the latter being an experimentally relevant model of a Cr$^{3+}_{8}$ ring. Here, our approach has qubit requirements that are independent of the number of constituents of the many-body system and scale only logarithmically with the bond dimension of the MPS representation, making them appealing for implementation on near-term quantum hardware with mid-circuit measurement and reset.

Neutron scattering↗

Adaptive nonequilibrium design of actin-based metamaterials: Fundamental and practical limits of control

The adaptive and surprising emergent properties of biological materials self-assembled in far-from-equilibrium environments serve as an inspiration for efforts to design nanomaterials. In particular, controlling the conditions of self-assembly can modulate material properties, but there is no systematic understanding of either how to parameterize external control or how controllable a given material can be. Here, we demonstrate that branched actin networks can be encoded with metamaterial properties by dynamically controlling the applied force under which they grow and that the protocols can be selected using multi-task reinforcement learning. These actin networks have tunable responses over a large dynamic range depending on the chosen external protocol, providing a pathway to encoding “memory” within these structures. Interestingly, we obtain a bound that relates the dissipation rate and the rate of “encoding” that gives insight into the constraints on control—both physical and information theoretical. Taken together, these results emphasize the utility and necessity of nonequilibrium control for designing self-assembled nanostructures.

59 BASIC BIOLOGICAL SCIENCES↗

Transformer Neural Networks with Spatiotemporal Attention for Predictive Control and Optimization of Industrial Processes

In the context of real-time optimization and model predictive control of industrial systems, machine learning, and neural networks represent cutting-edge tools that hold promise for enhancing dynamic modeling. This work presents a novel transformer neural network architecture for real-time optimization and model predictive control. This network design includes a modified attention mechanism inspired by positional embedding attention from vision transformers and task-specific modifications to the input-output structure of the transformer’s decoder stack. Experiments were conducted using data from a 450 MW coal-fired power plant to evaluate this approach's effectiveness. The transformer neural network was compared with conventional recurrent models, including GRU and LSTM. The transformer exhibited a 6% increase in the R-squared (R2) value of predictions and an 83% reduction in mean squared error (MSE). Computation time was also reduced by 84% compared to conventional recurrent models.

Gallup, Ethan R.↗

Generative Thermodynamic Computing

Here, we introduce a generative modeling framework for thermodynamic computing, in which structured data are synthesized from noise by the natural time evolution of a physical system governed by Langevin dynamics. While conventional diffusion models use neural networks to perform denoising, here the information needed to generate structure from noise is encoded by the dynamics of a thermodynamic system. Training proceeds by maximizing the probability with which the computer generates the reverse of a noising trajectory, which ensures that the computer generates data with minimal heat emission. We demonstrate this framework within a digital simulation of a thermodynamic computer. If realized in analog hardware, such a system would function as a generative model that produces structured samples without the need for artificially injected noise or active control of denoising.

Whitelam, Stephen [Lawrence Berkeley National Labo↗

A two-equation soot-in-flamelet modeling approach applied under Spray A conditions

Soot production (including formation and oxidation) is studied in the transient, high-pressure and turbulent n-dodecane Spray A flames from the Engine Combustion Network (ECN) using computational fluid dynamics (CFD) simulations. A two-equation soot-in-flamelet modeling approach is applied within the framework of the Unsteady Flamelet Progress Variable (UFPV) model and results are validated against experimental data. Equations for soot mass fraction and soot number density derived in the mixture fraction space are solved in the context of detailed flamelet calculations. Source terms for the different steps in the soot chemistry are tabulated and incorporated in the flamelet manifold. For the reference condition, the modeling approach based on the tabulated flamelet manifold reduces the computational cost of a CFD calculation by approximately 40 times compared to a non-tabulated well-mixed (WM) modeling approach. The soot-in-flamelet approach is then extended to study the effect of ambient oxygen concentration, ambient mixture composition and ambient temperature on soot production. Results show that the modeling approach is able to capture the experimental trends for the soot volume fraction (SVF) with good quantitative agreement, especially in the soot ramp-up region.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Performance of multifunctional piezoelectric energy harvesting microgyroscopes with material degradation

Most microelectromechanical systems (MEMS) are made from brittle materials that are prone to cracking. Damage from the formation of cracks can occur anytime during the manufacturing process or due to mechanical loading of MEMS devices. Cracks can increase the structures flexibility and lead to changes in performance or total failure. Understanding the potential influences cracks in MEMS is necessary for the longevity of these systems. The energy harvesting microgyroscope studied in this work is susceptible to crack propagation in its silicon substrate and lead zirconate titanate piezoelectric patch. To this end, an electromechanical model is developed to capture the impacts of cracks on the performance of a damaged energy harvesting microgyroscope. Numerical methods are used to approximate the damage associated with distributed crack networks. Then, the static and dynamic responses of the damaged microgyroscope are analyzed for two possible multifunctional setups. Here, the current study revealed that cracks can significantly affect the static and dynamic behaviors of the microgyroscope energy harvester. Combinations of cracking and piezoelectric property degradation cause a decrease in the static pull-in voltage and shift the resonance frequencies of the system. Additionally, it is shown that the systems sensitivity to changes in the base rotation and energy harvesting capabilities vary widely depending on the severity of material degradation.

36 MATERIALS SCIENCE↗

Magnetic charge and geometry confluence for ultra-low forward voltage diode in artificial honeycomb lattice

We report spin diode is important prerequisite to practical manifestation of spin electronics. Yet, a functioning magnetic diode at room temperature is still illusive. Here, we reveal diode-type phenomena due to magnetic charge mediated conduction in artificial honeycomb geometry, made of concave shape single domain permalloy element. We find that honeycomb lattice defies symmetry by populating vertices with low and high multiplicity magnetic charges, causing asymmetric magnetization, in applied current of opposite polarity. High multiplicity units create highly resistive network, thereby inhibiting magnetic charge dynamics propelled electrical conduction. However, practical realization of this effect requires modest demagnetization factor in constituting element. Concave structure fulfills the condition. Subsequently, magnetic diode behavior emerges across broad thermal range of T = 40 K–300 K. The finding is a departure from the prevailing notion of spin-charge interaction as the sole guiding principle behind spintronics. Consequently, a new vista, mediated by magnetic charge interaction, is envisaged for spintronic research.

36 MATERIALS SCIENCE↗

Lagrangian Characterization of Surface Transport From the Equatorial Atlantic to the Caribbean Sea Using Climatological Lagrangian Coherent Structures and Self‐Organizing Maps

Abstract This study presents an assessment of the transport of suspended material by surface ocean currents, which have a critical role in determining the connectivity and distribution of living and non‐living material. Lagrangian experiments reveal pathways from the Equatorial Atlantic to 10 strategic regions within the Caribbean Sea, determined by considering the space‐time variability of climatological Lagrangian Coherent Structures, which act as recurrent attracting pathways and transport barriers. Due to windage or Stokes drift, wind forcing is a significant factor in determining the spatial locations where particles cluster and the time needed to reach the Caribbean from the Equatorial Atlantic. Pathways shift westward within the Caribbean and take less time to arrive with increasing wind influence. Depending on the wind effect, the particles show higher confluence in different areas of the Caribbean. A case study is presented for the Mexican Caribbean nearshore area, isolated from ocean‐current trajectories. Here, wind weakens the transport barrier responsible for this isolation and causes particle confluence toward that region. Spatial patterns of the Eulerian velocity identified through Self‐Organizing Maps, with time dependence given by their best matching units, can reproduce the characteristic Lagrangian patterns of surface current climate variability. Our study demonstrates the application of tools from dynamical systems and unsupervised neural networks to understand Lagrangian patterns and identify the processes that drive them. These findings improve our understanding of transport mechanisms of suspended material by surface ocean currents in the Western Atlantic and the Caribbean Sea, which is essential for managing and conserving marine ecosystems.

Allende‐Arandía, Ma. Eugenia↗

Parallel measurement of transcriptomes and proteomes from same single cells using nanodroplet splitting

Single-cell multiomics provides comprehensive insights into gene regulatory networks, cellular diversity, and temporal dynamics. Here, we introduce nanoSPLITS (nanodroplet SPlitting for Linked-multimodal Investigations of Trace Samples), an integrated platform that enables global profiling of the transcriptome and proteome from same single cells via RNA sequencing and mass spectrometry-based proteomics, respectively. Benchmarking of nanoSPLITS demonstrates high measurement precision with deep proteomic and transcriptomic profiling of single-cells. We apply nanoSPLITS to cyclin-dependent kinase 1 inhibited cells and found phospho-signaling events could be quantified alongside global protein and mRNA measurements, providing insights into cell cycle regulation. We extend nanoSPLITS to primary cells isolated from human pancreatic islets, introducing an efficient approach for facile identification of unknown cell types and their protein markers by mapping transcriptomic data to existing large-scale single-cell RNA sequencing reference databases. Accordingly, we establish nanoSPLITS as a multiomic technology incorporating global proteomics and anticipate the approach will be critical to furthering our understanding of biological systems.

59 BASIC BIOLOGICAL SCIENCES↗

Temperature and composition dependent screw dislocation mobility in austenitic stainless steels from large-scale molecular dynamics

Abstract Extensive molecular dynamics simulations are performed to determine screw dislocation mobility in austenitic Fe 0.7 Ni x Cr 0.3-x stainless steels as a function of temperature ranging from 100 to 1300 K, resolved shear stress from 30 to 140 MPa, and Ni composition from 0.0 to 30.0 at%. These mobility data are fitted to a linear mobility law with a nonzero stress offset, referred to as the threshold stress. We find that both the linear drag coefficient and the threshold stress increase with Ni composition. The drag coefficient increases with temperature, whereas the threshold stress decreases with temperature. Based on these calculations, we determine fitting functions for the linear solute drag coefficient as a function of temperature and composition. The mobility laws determined in this study may serve to inform dislocation dynamics simulations pertinent to dislocation network evolution at elevated temperatures for a wide composition range of austenitic stainless steels.

Chu, Kevin (ORCID:000000031929710X)↗

Data-driven modeling of dislocation mobility from atomistics using physics-informed machine learning

Dislocation mobility, which dictates the response of dislocations to an applied stress, is a fundamental property of crystalline materials that governs the evolution of plastic deformation. Traditional approaches for deriving mobility laws rely on phenomenological models of the underlying physics, whose free parameters are in turn fitted to a small number of intuition-driven atomic scale simulations under varying conditions of temperature and stress. This tedious and time-consuming approach becomes particularly cumbersome for materials with complex dependencies on stress, temperature, and local environment, such as body-centered cubic crystals (BCC) metals and alloys. In this paper, we present a novel, uncertainty quantification-driven active learning paradigm for learning dislocation mobility laws from automated high-throughput large-scale molecular dynamics simulations, using Graph Neural Networks (GNN) with a physics-informed architecture. We demonstrate that this Physics-informed Graph Neural Network (PI-GNN) framework captures the underlying physics more accurately compared to existing phenomenological mobility laws in BCC metals.

36 MATERIALS SCIENCE↗

Characterization of the structural forces governing the reversibility of the thermal unfolding of the human acidic fibroblast growth factor

Human acidic fibroblast growth factor (hFGF1) is an all beta-sheet protein that is involved in the regulation of key cellular processes including cell proliferation and wound healing. hFGF1 is known to aggregate when subjected to thermal unfolding. In this study, we investigate the equilibrium unfolding of hFGF1 using a wide array of biophysical and biochemical techniques. Systematic analyses of the thermal and chemical denaturation data on hFGF1 variants (Q54P, K126N, R136E, K126N/R136E, Q54P/K126N, Q54P/R136E, and Q54P/K126N/R136E) indicate that nullification of charges in the heparin-binding pocket can significantly increase the stability of wtFGF1. Triple variant (Q54P/K126N/R136E) was found to be the most stable of all the hFGF1 variants studied. With the exception of triple variant, thermal unfolding of wtFGF1 and the other variants is irreversible. Thermally unfolded triple variant refolds completely to its biologically native conformation. Microsecond-level molecular dynamic simulations reveal that a network of hydrogen bonds and salt bridges linked to Q54P, K126N, and R136E mutations, are responsible for the high stability and reversibility of thermal unfolding of the triple variant. In our opinion, the findings of the study provide valuable clues for the rational design of a stable hFGF1 variant that exhibits potent wound healing properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Operating-Envelopes-Aware Decentralized Welfare Maximization for Energy Communities

We propose an operating-envelope-aware, prosumer-centric, and efficient energy community that aggregates individual and shared community distributed energy resources and transacts with a regulated distribution system operator (DSO) under a generalized net energy metering tariff design. To ensure safe network operation, the DSO imposes dynamic export and import limits, known as dynamic operating envelopes, on end-users' revenue meters. Given the operating envelopes, we propose an incentive-aligned community pricing mechanism under which the decentralized optimization of community members' benefit implies the optimization of overall community welfare. The proposed pricing mechanism satisfies the cost-causation principle and ensures the stability of the energy community in a coalition game setting. Numerical examples provide insights into the characteristics of the proposed pricing mechanism and quantitative measures of its performance.

distributed energy resources aggregation↗