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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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At least 469 records · Page 26

Heat transport in liquid water from first-principles and deep neural network simulations

In this work, we compute the thermal conductivity of water within linear response theory from equilibrium molecular dynamics simulations, by adopting two different approaches. In one, the potential energy surface (PES) is derived on the fly from the electronic ground state of density functional theory (DFT) and the corresponding analytical expression is used for the energy flux. In the other, the PES is represented by a deep neural network (DNN) trained on DFT data, whereby the PES has an explicit local decomposition and the energy flux takes a particularly simple expression. By virtue of a gauge invariance principle, established by Marcolongo, Umari, and Baroni, the two approaches should be equivalent if the PES were reproduced accurately by the DNN model. We test this hypothesis by calculating the thermal conductivity, at the GGA (PBE) level of theory, using the direct formulation and its DNN proxy, finding that both approaches yield the same conductivity, in excess of the experimental value by approximately 60%. Besides being numerically much more efficient than its direct DFT counterpart, the DNN scheme has the advantage of being easily applicable to more sophisticated DFT approximations, such as meta-GGA and hybrid functionals, for which it would be hard to derive analytically the expression of the energy flux. We find in this way that a DNN model, trained on meta-GGA (SCAN) data, reduces the deviation from experiment of the predicted thermal conductivity by about 50%, leaving the question open as to whether the residual error is due to deficiencies of the functional, to a neglect of nuclear quantum effects in the atomic dynamics, or, likely, to a combination of the two.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metastable Clusters and Competitive Solvation Tune Ion Pairing at Liquid Interfaces

The balance of hydrophobic and hydrophilic interactions underlies emergent phenomena in complex multicomponent chemical systems. Here, we show that a supposedly ‘non–interacting’ nonpolar phase can be used to competitively solvate amphiphilic molecules at an oil/aqueous interface. This solvation, as probed by surface specific nonlinear spectroscopy and simulations, results in a molecularly thin corrugated phase boundary featuring metastable assemblies that alter the hydrogen bonding networks of water and the apparent ‘hard/soft’ descriptors used to describe ionic interactions. We show that competitive solvation enhances amphiphile mobility, opening up otherwise energetically inaccessible complexes that transiently interact with aqueous phase ions. These transient species impact ensemble binding affinities and may represent the molecular agents responsible for aspects of ionic transport and function. In conclusion, the result of this work highlights how seemingly unrelated nonpolar interactions feedback onto aqueous phase chemical phenomena, providing a pathway to tune phase separation and self-assembly to access new reaction pathways using interfaces for a range of chemical and biological systems.

Anions↗

Self-assembly of a triply periodic continuous mesophase with Fddd symmetry in simple one-component liquids

Triply periodic continuous morphologies (networks) arising as a result of the microphase separation in block copolymer melts have so far never been observed self-assembled in systems of particles with spherically symmetric interaction. Here, we report a molecular dynamics simulation where two simple one-component liquids form upon cooling an equilibrium network with the Fddd space group symmetry. This complexity reduction in the liquid network formation in terms of the particle geometry and the number of components evidences the generic nature of this class of phase transition suggesting opportunities for producing these structures in a variety of new systems.

36 MATERIALS SCIENCE↗

Syntrophic Co-Cultures of Clostridium Organisms to Produce Higher Alcohols & Other C6-C8 Metabolites (Final Report)

The goal of this project was to advance the systems biology understanding and predictive modeling of synthetic & syntrophic Clostridium microbial consortia, focusing on elucidation of metabolic networks and environmental signals in the consortia. The project has direct applicability to lignocellulosic-biomass based production of higher alcohols as advanced biofuels and C6-C8 metabolites, that can be used as chemicals or serve as biofuel precursors. This project studied and optimized three synthetic syntrophic systems. It examined the population dynamics using flow-cytometry, time-lapse microscopy and PCR analysis. 13C-based tracer analyses was used to examine the metabolite exchange between the syntrophic cell populations and the impact of those interactions on the transcriptome of the individual populations. To enhance our analytical and predictive capabilities, genome-scale models (GSMs) for these syntrophies was developed. RNAseq data for these syntrophic coculture systems were acquired to enable a molecular level understanding of the syntrophies aiming to identify the genetic networks of each organism in the co-culture and compare those against the networks of pure cultures.

09 BIOMASS FUELS↗

User Access to Scientific Facilities via 5G: A Cyber Security Thought Experiment

5G is more than an over-the-air radio technology upgrade. It is a strategy to extend Mobile Network Operator service offerings beyond traditional voice, instant messaging and Internet access. 5G Mobile Network Operators will offer new telecommunication services that include enhanced guarantees of confidentiality, integrity and availability. How could such services change the way Science collaborations connect scientists to supercomputers and other scientific facilities? Current scientific collaborations implicitly trust cloud service providers to securely store and process data. The perceived risks of outsourcing Science data security are counterbalanced by assurances that cloud providers operate at a scale that allows them to implement security measures impractical for Science collaborations (e.g. continuous system administrator behavioral monitoring and strict individual separation of duties). If that is true for a cloud service provider like Amazon Web Services (2018 revenue: $25.7 billion), could it also be true for Mobile Network Operators like Verizon Wireless (2018 revenue: $91.7 billion) or AT&T Mobility (2018 revenue: $71.3 billion)? DOE Leadership Class supercomputer facility users currently access them from the public Internet via Secure Shell. The sponsors and operators of the supercomputer facilities have determined that the public Internet path between the Scientist’s Device and the Login Node does not natively provide enough confidentiality or integrity to protect those communications. Therefore, the facilities achieve additional confidentiality and integrity by requiring Secure Shell encryption across those untrusted network paths. Using 5G Network Slice technology, a Mobile Network Operator may offer communication services between supercomputer users and facilities that natively provide confidentiality and integrity guarantees. Sponsors and operators of supercomputer facilities may determine that these guarantees provide enough confidentiality and integrity to protect those communications. If so, a 5G Network Slice could replace an SSH session running over the public Internet. Finally, this use case could be extended to other Office of Science user facility access requirements. Consider microscopy instruments at (e.g.) the Center for Nanoscale Materials or the Environmental Molecular Sciences Laboratory. The embedded systems controlling such instruments may not always support encrypted network access technologies like SSH. 5G Network Slices may offer an alternative to current VPN or SSH tunneling techniques, with additional benefits like guaranteed minimum bandwidth.

5G↗

Advancing density functional tight-binding method for large organic molecules through equivariant neural networks

Semi-empirical quantum-mechanical (QM) methods have become valuable tools for studying complex (bio)molecular systems due to their balance between computational efficiency and accuracy. A key aspect of these methods is their parameterization, which not only governs the reliability of the results but also provides an opportunity to enhance their overall performance. In our previous work [J. Phys. Chem. Lett., 2021, 11, 16], we advanced the third-order semi-empirical density functional tight-binding (DFTB3) method for computing multiple properties of small molecules by developing the machine learning (ML) potential NN rep to bridge the gap between DFTB3 electronic components and those of the hybrid DFT-PBE0 functional. To overcome the limitations of NN rep , we introduce the EquiDTB framework, which leverages physics-inspired equivariant neural networks (NN) to parameterize scalable and transferable many-body Δ TB potentials, replacing the standard pairwise DFTB repulsive potential. This advancement extends the applicability of our ML-corrected DFTB approach to larger molecules and non-covalent systems (including only C, N, O, and H atoms), going beyond the chemical space represented in the training QM datasets. The enhanced performance of EquiDTB over the standard TB methods is demonstrated by the accurate computation of the atomic forces of S66x8 molecular dimers, as well as their interaction energies. Moreover, EquiDTB can be effectively employed to explore the potential energy surfaces of large and flexible drug-like molecules—for example, to determine the minimum energy path between isomers, analyze structural transitions during dynamical simulations, compute vibrational modes, and investigate energetic rankings. The performance for single molecules slightly decreases when the DFTB electronic energy is reduced to first-order but remains superior to standard TB methods. Our work thus demonstrates that an optimal integration of an equivariant NN with QM datasets can advance the DFTB method while maintaining high efficiency, paving the way for reliable (bio)molecular simulations.

Medrano Sandonas, Leonardo [Technische Universität↗

Crystallization of the P 3 Sn 4 Phase upon Cooling P 2 Sn 5 Liquid by Molecular Dynamics Simulation Using a Machine Learning Interatomic Potential

We performed molecular dynamics simulations to study the crystallization of the P3Sn4 phase from P 2 Sn 5 liquid using a machine learning (ML) interatomic potential with desirable efficiency and accuracy. Our results capture the liquid properties of P 2 Sn 5 at 1300 K, which is well above the melting temperature. The phase separation and crystallization are observed when P 2 Sn 5 liquid is cooled down below 832 and 505 K, respectively. The simulation results are in good agreement with the experimentally observed phase transformation behaviors and provide useful insights into the complex nucleation and crystallization process at the details of atomistic scale. Our work also demonstrated that ML interatomic potentials based on neural network deep learning are robust and capable of accurately describing the energetics and kinetics of complex materials through molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ultrafast charge transfer coupled to quantum proton motion at molecule/metal oxide interface

Understanding how the nuclear quantum effects (NQEs) in the hydrogen bond (H-bond) network influence the photoexcited charge transfer at semiconductor/molecule interface is a challenging problem. By combining two kinds of emerging molecular dynamics methods at the ab initio level, the path integral–based molecular dynamics and time-dependent nonadiabatic molecular dynamics, and choosing CH 3 OH/TiO 2 as a prototypical system to study, we find that the quantum proton motion in the H-bond network is strongly coupled with the ultrafast photoexcited charge dynamics at the interface. The hole trapping ability of the adsorbed methanol molecule is notably enhanced by the NQEs, and thus, it behaves as a hole scavenger on titanium dioxide. The critical role of the H-bond network is confirmed by in situ scanning tunneling microscope measurements with ultraviolet light illumination. It is concluded the quantum proton motion in the H-bond network plays a critical role in influencing the energy conversion efficiency based on photoexcitation.

74 ATOMIC AND MOLECULAR PHYSICS↗

Helium Bubble Growth and Retention Characteristics in Aging Palladium Tritide

The helium-related characteristics of aged palladium tritide, including tritium loss, the formation of He bubbles from tritium decay-induced He atoms, and He thermal desorption behavior are computed using a continuum model of bubble evolution that incorporates the log-normal bubble spacing distribution deduced from 3 He nuclear magnetic resonance (NMR) measurements. This spacing distribution produces significant differences between mean (expectation) values of the bubble size and pressure and the average (median) values of these aging characteristics obtained by a previous calculation. The new calculations find much of the He is retained in a large quantity of smaller bubbles with higher bubble pressures, improving the overall stability of the bubbles and extending the age of He retention. By contrast, the integrated tritide material characteristics of swelling and tritium pressure are found relatively insensitive to details of the bubble spacing distribution. Inter-bubble fracture is predicted to begin with small, closely-spaced bubbles and progress to include larger bubbles near the onset of rapid He release. The critical concentration for this onset increases almost linearly with material tensile strength and decreases with shear modulus. Release of He from the aging solid is modeled as a growing network of fractured inter-bubble ligaments. For small particle or small grain material, the physical size of the fracture cluster, relative to the material dimensions, becomes important. In contrast with normal aging, inter-bubble fracture occurring during thermal desorption appears to begin with large, widely-spaced bubbles, indicating elevated temperature techniques may be of limited use for evaluating development of the bubble fracture network.

74 ATOMIC AND MOLECULAR PHYSICS↗

In Silico Insights into Protein–Protein Interaction Disruptive Mutations in the PCSK9-LDLR Complex

Gain-of-function mutations in PCSK9 (proprotein convertase subtilisin/kexin type 9) lead to reduced uptake of LDL (low density lipoprotein) cholesterol and, therefore, increased plasma LDL levels. However, the mechanism by which these mutants reduce LDL reuptake is not fully understood. Here, we have used molecular dynamics simulations, MM/PBSA (Molecular Mechanics/Poisson–Boltzmann Surface Area) binding affinity calculations, and residue interaction networks, to investigate the protein–protein interaction (PPI) disruptive effects of two of PCSK9's gain-of-function mutations, Ser127Arg and Asp374Tyr on the PCSK9 and LDL receptor complex. In addition to these PPI disruptive mutants, a third, non-interface mutation (Arg496Trp) is included as a positive control. Our results indicate that Ser127Arg and Asp374Tyr confer significantly improved binding affinity, as well as different binding modes, when compared to the wild-type. These PPI disruptive mutations lie between the EGF(A) (epidermal growth factor precursor homology domain A) of the LDL receptor and the catalytic domain of PCSK9 (Asp374Tyr) and between the prodomain of PCSK9 and the β-propeller of the LDL receptor (Ser127Arg). The interactions involved in these two interfaces result in an LDL receptor that is sterically inhibited from entering its closed conformation. This could potentially implicate the prodomain as a target for small molecule inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

Controlled Fabrication of Quality ZnO NWs/CNTs and ZnO NWs/Gr Heterostructures via Direct Two-Step CVD Method

A novel and advanced approach of growing zinc oxide nanowires (ZnO NWs) directly on single-walled carbon nanotubes (SWCNTs) and graphene (Gr) surfaces has been demonstrated through the successful formation of 1D–1D and 1D–2D heterostructure interfaces. The direct two-step chemical vapor deposition (CVD) method was utilized to ensure high-quality materials’ synthesis and scalable production of different architectures. Iron-based universal compound molecular ink was used as a catalyst in both processes (a) to form a monolayer of horizontally defined networks of SWCNTs interfaced with vertically oriented ZnO NWs and (b) to grow densely packed ZnO NWs directly on a graphene surface. We show here that our universal compound molecular ink is efficient and selective in the direct synthesis of ZnO NWs/CNTs and ZnO NWs/Gr heterostructures. Heterostructures were also selectively patterned through different fabrication techniques and grown in predefined locations, demonstrating an ability to control materials’ placement and morphology. Several characterization tools were employed to interrogate the prepared heterostructures. ZnO NWs were shown to grow uniformly over the network of SWCNTs, and much denser packed vertically oriented ZnO NWs were produced on graphene thin films. Such heterostructures can be used widely in many potential applications, such as photocatalysts, supercapacitors, solar cells, piezoelectric or thermal actuators, as well as chemical or biological sensors.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DancePartner: Python Package to Mine Multiomics Relationship Networks from Literature and Databases

A goal of multi-omics experiments is to understand how mechanistic molecular biology is altered between conditions, typically a control group and experimental groups. Oftentimes this involves studying changes in biomolecule relationships (e.g. interactions, metabolic relationships) of several types of biomolecules (e.g. proteins, lipids, metabolites). Though several databases contain relationships between biomolecules, understudied species may have little to no relationship information in databases and thus must be mined from literature. There are several challenges to literature mining, including automated full-text extraction, duplicate biomolecule term collapsing, and implementing complex machine learning tools. To make relationship extraction more accessible to the community, a python package called DancePartner was developed to allow for the extraction of relationships from literature and databases, with functions to map biomolecule synonyms to standardized identifiers and visualize and characterize the resulting multi-omics network. Here, in this study, an example dataset involving Caenorhabditis elegans is presented, where relationships are mined from 1443 publications using DancePartner. These relationships are combined with relationships from KEGG, WikiPathways, UniProt, and LipidMaps, and visualized.

BERT↗

Wavelength conversion for single-photon polarization qubits through continuous-variable quantum teleportation

A quantum internet connects remote quantum processors that need to interact and exchange quantum signals over a long distance through photonic channels. However, these quantum nodes operate at the wavelength ranges unsuitable for long-distance transmission. Therefore, quantum wavelength conversion to telecom bands is crucial for long-distance quantum networks based on optical fiber. Here, we propose wavelength conversion devices for single-photon polarization qubits using continuous-variable quantum teleportation that can efficiently convert qubits between near-infrared (780–795 nm suitable for interacting with atomic quantum nodes) and telecom wavelength (1300–1500 nm suitable for long-distance transmission). The teleportation uses entangled photon fields (i.e., nondegenerate two-mode squeezed state) that can be generated by four-wave mixing in a rubidium atomic gas using a diamond configuration of atomic transitions. The entangled fields can be emitted in two orthogonal polarizations with locked relative phase, making them especially suitable for interfacing with single- photon polarization qubits. Furthermore, our work may pave the way for the realization of long-distance quantum networks.

74 ATOMIC AND MOLECULAR PHYSICS↗

Prediction of plant complex traits via integration of multi-omics data

The formation of complex traits is the consequence of genotype and activities at multiple molecular levels. However, connecting genotypes and these activities to complex traits remains challenging. Here, we investigate whether integrating genomic, transcriptomic, and methylomic data can improve prediction for six Arabidopsis traits. We find that transcriptome- and methylome-based models have performances comparable to those of genome-based models. However, models built for flowering time using different omics data identify different benchmark genes. Nine additional genes identified as important for flowering time from our models are experimentally validated as regulating flowering. Gene contributions to flowering time prediction are accession-dependent and distinct genes contribute to trait prediction in different genotypes. Models integrating multi-omics data perform best and reveal known and additional gene interactions, extending knowledge about existing regulatory networks underlying flowering time determination. These results demonstrate the feasibility of revealing molecular mechanisms underlying complex traits through multi-omics data integration.

59 BASIC BIOLOGICAL SCIENCES↗

Breakthrough Conductivity Enhancement in Deep Eutectic Solvents via Grotthuss–Type Proton Transport

There is an increasing demand for the development of ion-conducting electrolytes for energy storage systems. Much attention is directed toward deep eutectic solvents as potential candidates. In the search for highly conductive systems, the possibility of designing deep eutectic solvents with Grotthuss-type proton transport is widely overlooked. Herein, ethaline, a mixture of choline chloride and ethylene glycol is used in a 1:2 molar ratio, to induce a significant conductivity increase with the addition of water and sulfuric acid (H 2 SO 4 ). The achieved breakthrough conductivity is analyzed experimentally and simulated with ab initio molecular dynamics (AIMD). At sufficient water content, an H-bonding network is formed that leads to a significant breakthrough conductivity based on H 2 SO 4 -derived proton transfer following the long-established Grotthuss proton transport mechanism. This result is substantiated by the positive deviation from the ideal KCl line in the Walden plot. Specifically, the data series positioned above the reference line indicates a Grotthuss mechanism in action. The AIMD simulations demonstrate proton transfer between water and ethylene glycol, supported by simulation frames captured at various times.

36 MATERIALS SCIENCE↗

Short- and medium-range orders in Al90Tb10 glass and their relation to the structures of competing crystalline phases

Molecular dynamics simulations using an interatomic potential developed by artificial neural network deep machine learning are performed to study the local structural order in Al90Tb10 metallic glass. We show that more than 80% of the Tb-centered clusters in Al90Tb10 glass have short-range order (SRO) with their 17 first coordination shell atoms stacked in a ‘3661’ or ‘15551’ sequence. Medium-range order (MRO) in Bergman-type packing extended out to the second and third coordination shells is also clearly observed. Analysis of the network formed by the ‘3661’ and ‘15551’ clusters show that ~82% of such SRO units share their faces or vertexes, while only ~6% of neighboring SRO pairs are interpenetrating. Such a network topology is consistent with the Bergman-type MRO around the Tb-centers. Moreover, crystal structure searches using genetic algorithm and the neural network interatomic potential reveal several low-energy metastable crystalline structures in the composition range close to Al 90 Tb 10 . Some of these crystalline structures have the ‘3661’ SRO while others have the ‘15551’ SRO. While the crystalline structures with the ‘3661’ SRO also exhibit the MRO very similar to that observed in the glass, the ones with the ‘15551’ SRO have very different atomic packing in the second and third shells around the Tb centers from that of the Bergman-type MRO observed in the glassy phase.

36 MATERIALS SCIENCE↗

Polyphenols Weaken Pea Protein Gel by Formation of Large Aggregates with Diminished Noncovalent Interactions

Polyphenols are well-known native cross-linkers and gel strengthening agents for many animal proteins. However, their role in modifying plant protein gels remains unclear. In this study, multiple techniques were applied to unravel the influence of green tea polyphenols (GTP) on pea protein gels and the underlying mechanisms. We found that the elasticity and viscosity of pea protein gels decreased with increased GTP. The protein backbone became less rigid when GTP was present based on shortened T 1ρ H in relaxation solid-state NMR measurements. Electron microscopy and small-angle X-ray scattering showed that gels weakened by GTP possessed disrupted networks with the presence of large protein aggregates. Solvent extraction and molecular dynamic simulation revealed a reduction in hydrophobic interactions and hydrogen bonds among proteins in gels containing GTP. The current findings may be applicable to other plant proteins for greater control of gel structures in the presence of polyphenols, expanding their utilization in food and biomedical applications.

59 BASIC BIOLOGICAL SCIENCES↗

Influence of Rigidity–Hydration Coupling on Size-Dependent Diffusion in Hydrated Polymer Membranes

Selective ion transport in polymer membranes depends critically on how penetrant motion couples to polymer dynamics and hydration. Yet, the mechanistic interplay between polymer rigidity, water content, and penetrant size remains poorly understood, especially in the regime where the penetrant diameter, polymer Kuhn length, and correlation length are comparable. Here, we employ coarse-grained molecular dynamics simulations to systematically investigate penetrant diffusion in hydrated polymer networks across a broad range of water volume fractions, chain rigidities, and penetrant sizes. The results reveal a transition from a decoupled regime, where small penetrants diffuse nearly independently of polymer relaxation, to a coupled regime in which large penetrants require cooperative polymer motion for transport. Increasing polymer rigidity amplifies the sensitivity of diffusivity to hydration, particularly at low water content, leading to pronounced deviations from Stokes−Einstein scaling. Comparison with scaling theories and free-volume models shows that classical nanoparticle-based frameworks fail to capture this intermediate regime. To address this gap, we extend the Yasuda model to incorporate polymer rigidity through a single parameter that quantifies the dynamic contribution of chain stiffness to free-volume fluctuations. The resulting model collapses diffusivity data across all sizes, water contents, and rigidities, providing a unified description of penetrant transport in hydrated polymer matrices. Furthermore, these findings establish polymer rigidity as a key, tunable determinant of diffusion and offer a framework for interpreting size-dependent transport in ion-selective membranes.

diffusion↗