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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Exploring nonlinear Rashba effect and spin Hall conductivity in Janus MXenes W 2 ⁢CO ⁢𝑋 (𝑋=S, Se, Te)

Rashba spin-orbit coupling (RSOC) facilitates spin manipulation without relying on an external magnetic field, opening up exciting possibilities for advanced spintronic devices. In this paper, we examine the effects of crystal momentum (𝑘) nonlinearity and anisotropy on the conventional Rashba effect, with a particular focus on their impact on the spin Hall conductivity (SHC) in a newly predicted family of 2D Janus materials, W 2 ⁢CO⁢𝑋 (𝑋 =S, Se, Te). Using first-principles density functional theory calculations, we confirm the dynamical and mechanical stability of the studied 2D materials. Strikingly, this materials family exhibits pronounced nonlinear Rashba spin splitting at the Γ point of Brillouin zone near the Fermi level, which cannot be adequately described by the linear-𝑘 Rashba model. Therefore, third-order momentum contributions (𝑘 3 ) must be incorporated into the Rashba Hamiltonian. Our analysis reveals that among the studied systems, W 2 ⁢COS exhibits the highest 𝑘 3 contribution of −45.9 eV Å 3 , despite having the lowest linear Rashba constant. Here, a detailed analysis of electronic structure reveals topologically nontrivial behavior in these 2D materials, yielding sizable SHC that is primarily governed by the nonlinear Rashba effect. Notably, these materials also exhibit large spin Hall angle (0.018–2.5 at E 𝐹 ), which is comparable to that of in bulk topological insulators like Bi 2 ⁢Se 3 and Bi 2 ⁢Te 3 , and surpassing those in narrow bandgap bulk semiconductors GeTe and SnTe, as well as heavy metals such as Pt. Sizable SHC, large spin Hall angles, and the ability to tune SHC via electric fields without altering the topological properties, rooted in the crystal field splitting, underscore the potential of these materials for spintronic applications.

Electronic structure↗
DOE OSTI2020

Ion irradiation and modification: The role of coupled electronic and nuclear energy dissipation and subsequent nonequilibrium processes in materials

Understanding material responses to energy deposition from energetic charged particles is important for defect engineering, ion-beam processing, ion-beam analysis and modification, geologic aging, space exploration, and nuclear applications. As an incident ion penetrates a solid, its energy is transferred to electrons and to atomic nuclei of the solid. Much of this electronic energy deposition is subsequently transferred to the atomic structure via electron–phonon (e–ph) coupling, leading to local inelastic thermal spikes in which energy dissipation is influenced by the local environment. In addition, intense ionization can lead to high densities of localized electronic excitations in wide-bandgap materials and ceramics that can affect defect dynamics and atomic mobility. Specifically, energy exchange between electrons and atomic nuclei, along with localized electronic excitations, can lead to substantial competitive (ionization-induced annealing), additive (both electronic and nuclear energy depositions contributing to damage production), and synergistic (more damage than the sums of separate damage processes) effects. Although nonmonotonic effects of the e–ph coupling strength and athermal processes are demonstrated for pre-existing defects and residual damage during ion–solid interactions, there is limited understanding of when such electronic effects must be considered in atomic-scale models of damage production and evolution in a broad variety of materials. Complex ceramics and chemically disordered solid solution alloys with different constituent elements allow a systematic evaluation of defect dynamics and irradiation performance with increasing complexity. Current knowledge regarding tuning of bonding characteristics and chemical disorder to control atomic-level dynamics is reviewed. Although a lack of fundamental understanding obstructs the advancement of reliable predictions for ion beam material modification, it highlights challenges and opens research opportunities. Insights into the complex electronic and atomic correlations with extreme energy deposition will strengthen our ability to design materials and predict ion-irradiation-induced damage in a radiation environment, and they may pave the way to better control fundamental processes and design new material functionalities for advanced technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Ensembles of Metastable States Govern Heterogeneous Catalysis on Dynamic Interfaces

Heterogeneous catalysis is at the heart of chemical industry. Being able to tune and design efficient catalysts for processes of interest is of an utmost importance, and for this, the molecular-level understanding of heterogeneous catalysts is the first step, and indeed a prime focus of the modern catalysis research. For a long time, a single most thermodynamically stable structure of the catalytic interface attained in reaction conditions had been envisioned as the reactive phase. However, some catalytic interfaces continue to undergo structural dynamics in the steady state, triggered by high temperatures, pressures, and binding and changing reagents. Among particularly dynamic interfaces are such widely-used catalysts as crystalline and amorphous surfaced supporting (sub-)nano metallic clusters. Recently, it became clear that this dynamic fluxionality causes the supported clusters to populate many distinct structural and stoichiometric states in catalytic conditions. Hence, the catalytic interface should be viewed as an evolving statistical ensemble of many (not one) structures. As such, every member in the ensemble contributes to the properties of the catalyst differently, and in proportion to its probability to be populated. This new notion flips the established paradigm and calls for new theory, modeling approaches, operando measurements, and updated design strategies. The statistical ensemble nature of surface-supported sub-nano cluster catalysts can be exemplified by oxide-supported and adsorbate-covered Pt, Pd, Cu, CuPd clusters, catalytic toward oxidative and non-oxidative dehydrogenation. They have access to a variety of 3D and quasi-2D shapes. The compositions of their thermal ensembles are dependent on the cluster size, leading to size-specific catalytic activities and the famous “every atom counts” phenomenon. The support and adsorbates affect catalyst structures, and state of the reacting species causes the ensemble to change in every reaction intermediate. The most stable member of the ensemble dominates the thermodynamic properties of the corresponding intermediate, whereas the kinetics can be determined by more active but less populated metastable catalyst states, and that suggests that many earlier studies might have overlooked the actual active sites. Both effects depend on the relative time-scales of catalyst restructuring and reaction dynamics. The catalyst may routinely operate off-equilibrium. Ensemble phenomena lead to surprising exceptions from established rules of catalysis, such as scaling relations, and Arrhenius behavior. Catalyst deactivation is also an ensemble property, and its extent of mitigation can be predicted through the new paradigm. These findings were enabled by advances in theory, such as global optimization and subsequent utilization of multiple local minima, and pathways sampling, as well as operando catalyst characterization. The fact that the per-site and per-species resolution is needed for the description and predicting of catalyst properties gives theory the central role in catalysis research, as most experiments provide ensemble-average information and cannot detect the crucial minority species that may be responsible for the catalytic activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Small Polarons and Surface Defects in Metal Oxide Photocatalysts Studied Using XUV Reflection–Absorption Spectroscopy

In photocatalytic transition metal oxides, the surface electronic structure and carrier kinetics are complicated by both charge trapping at defects and self-trapping by small polaron formation. These effects are specific to both the material and the type of defect or surface states involved. Here we review recent studies on ultrafast photoexcited charge carrier dynamics at the surfaces of alpha-Fe 2 O 3 (hematite) and NiO and at the interface of a alpha-Fe 2 O 3 /NiO heterojunction using extreme ultraviolet (XUV) reflection-absorption spectroscopy. We study dynamics of small polaron formation at hematite surfaces showing that the rate of carrier self-trapping is slower than in the bulk due to a greater lattice reorganization energy required for surface polaron formation. We also show that surface dynamics of hematite can be systematically tuned to control carrier transport properties through surface functionalization. To better understand the impact of defects on carrier events, we study charge carrier recombination of NiO. It is shown that O vacancies have no detrimental effect on carrier lifetime while grain boundaries cause fast recombination. Finally, we study a model heterojunction consisting of alpha-Fe 2 O 3 and NiO and find that interfacial charge transfer across these two materials occurs by a two-step mechanism where the interfacial electric field drives fast exciton dissociation followed by hole injection from alpha-Fe2O3 to NiO. Finally, these examples illustrate future opportunities to observe surface electron dynamics in photocatalytic materials with element and chemical state resolution using ultrafast XUV spectroscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Probing the Local Site Disorder and Distortion in Pyrochlore High-Entropy Oxides

High-entropy oxides (HEOs) have attracted great interest in diverse fields because of their inherent opportunities to tailor and combine materials functionalities. The control of local order/disorder in the class is by extension a grand challenge toward realizing their vast potential. In this paper, we report the first examples of pyrochlore HEOs with five M-site cations, for Nd 2 M 2 O 7 , in which the local structure has been investigated by neutron diffraction and pair distribution function (PDF) analysis. The average structure of the pyrochlores is found to be orthorhombic Imma, in agreement with radius-ratio rules governing the structural archetype. The computed PDFs from density functional theory relaxed special quasirandom structure models are compared with real space PDFs in this work to evaluate M-site order/disorder. Reverse Monte Carlo combined with ab initio molecular dynamics and Metropolis Monte Carlo simulations demonstrates that Nd 2 (Ta 0.2 Sc 0.2 Sn 0.2 Hf 0.2 Zr 0.2 ) 2 O 7 is synthesized with its M-site local to nanoscale order highly randomized/disordered, while Nd 2 (Ti 0.2 Nb 0.2 Sn 0.2 Hf 0.2 Zr 0.2 ) 2 O 7+x exhibits a strong distortion of the TiO 6 octahedron and small degree of Ti chemical short-range order (SRO) on the subnanometer scale. Calculations suggest that this may be intrinsic, energetically favored SRO rather than due to sample processing. These results offer an important demonstration that the engineered variation of participating ions in HEOs, even among those with very similar radii, provides richly diverse opportunities to control local order/disorder motifs—and therefore materials properties for future designs. This work also hints at the exquisite level of detail that may be needed in computational and experimental data analysis to guide structure–property tuning in the emerging HEO materials class.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Thiol post-translational modifications modulate allosteric regulation of the OpcA–G6PDH complex through conformational gate control

In cyanobacteria, the redox-sensitive protein OpcA acts as a metabolic switch for G6PDH, enabling rapid adjustment of reducing power generation from glycogen catabolism and thereby precisely regulating carbon flux between anabolic and catabolic pathways. Although redox-sensitive cysteines in OpcA are known to regulate G6PDH, the mechanisms by which redox post-translational modifications (PTMs) on OpcA control G6PDH structure and activity remain unclear. Here, we combine computational modeling with experimental redox proteomics in Synechococcus elongatus PCC 7942 to dissect this mechanism. Experimentally, redox proteome analysis revealed differential redox PTM patterns, particularly on cysteines within the G6PDH-binding site of OpcA. These environmentally sensitive PTM changes at the interface suggest that thiol modifications in this region form a key regulatory node. More broadly, redox proteomics identified site-specific cysteine modifications under light/dark transitions and circadian cycling, linking distinct redox regimes to discrete PTM states. We employed PTM-Psi simulations to show that thiol PTMs near the OpcA–G6PDH interface are critical for allosteric regulation of G6PDH. The thiol PTMs on OpcA affect a putative gate region in G6PDH for substrate ingress and product egress as well as key hydrogen-bond networks within the active site. We infer that PTMs on OpcA tune the conformational landscapes of individual G6PDH subunits toward functionally relevant configurations according to environmental gradients, biasing the enzyme toward catalytically favorable states. Together, our results reveal a molecular mechanism in which thiol PTMs on OpcA modulate G6PDH structure and function through PTM-induced reorganization of conformational dynamics and allosteric communication. These findings demonstrate that PTM-level regulation provides a critical control layer from genotypes to phenotypes that enables cyanobacteria to rapidly adapt to environmental fluctuations through precise metabolic fine-tuning.

Allosteric regulation↗
DOE OSTI2020

Coordinated Multiscale Modeling and Synthesis of Novel Nanostructured Composite Membranes for Solar Fuels Generation (Final Report)

Generation of carbon-based liquid fuels from reduction of CO 2 using solar energy requires the development of improved membranes that provide good ionic conductivity and mechanical properties while minimizing the crossover of gases and reduction products. Using closely coordinated multiscale modeling, synthesis and characterization studies we propose to investigate and develop novel nanostructured composite membranes with applications to conversion of carbon dioxide to storable chemical fuels. The envisioned proton exchange membranes (PEMs) will be based on a support of self- assembling polymer-modified nanoparticles with controllable porosity and tortuosity. The use of a nanoparticle support will provide control of transport and mechanical properties of the membranes. Tuning the copolymer modification of nanoparticles (polymer architectures, brush grafting density) will allow to optimize the ion (proton) transport via the Grotthuss mechanism through narrow hydrated channels while minimizing crossover of gases and reaction products due to the high density of the grafted brush and use of a non-ionic conducting glassy polymers to fill spaces between polymer-grafted nanoparticles. In Phase I synthesis of the copolymers and their attachment to the nanoparticle support will be guided by multiscale simulations that include atomistic molecular dynamics and continuum-level transport simulations. The former will include reactive and non-reactive atomistic simulations that will provide key insight into nanoscale polymer morphology and ion/molecular transport mechanisms need to optimize the copolymer structure. The latter will provide insight into the role of nanoparticle self-assembly on the global transport of ionic and molecular species. The proton conduction and CO 2 /methanol permeability of the membranes will be experimentally characterized as well as simulated and will be correlated with morphology and polymer structure. Prototypes of optimal membranes will be fabricated and characterized at the end of the project. Successful development of improved nanostructured composite PEMs and demonstration of the simulation-guided materials-by-design paradigm will result in our ability to design and synthesize membranes for a wide variety of solar fuels generation and related electrochemical applications.

14 SOLAR ENERGY↗
DOE OSTI2021

Investigation of post-injection strategies for diesel engine Catalyst Heating Operation using a vapor-liquid-equilibrium-based spray model

Most multidimensional engine simulations spend much time solving for non-equilibrium spray dynamics (atomization, collision, vaporization). However, their accuracy is limited by significant grid dependency, and the need for extensive calibration. This is critical for modeling cold-start diesel fuel post injections, which occur at low temperatures and pressures, far from typical model validation ranges. At the same time, resolving micron-scale spray phenomena would render full Eulerian multiphase calculations prohibitive. In this study, an improved phase equilibrium based approach was implemented and assessed for simulating diesel catalyst heating operation strategies. A phase equilibrium solver based on the model by Yue and Reitz [1] was implemented: a fully multiphase CFD solver is employed with an engineering-size engine grid, and fuel injection is modeled using the standard Lagrangian parcels approach. Mass and energy from the liquid parcels are released to the Eulerian multiphase mixture according to an equilibrium-based liquid jet model. An improved phase equilibrium solver was developed to handle large real-gas mixtures such as those from accurate chemical kinetics mechanisms. The liquid-jet model was improved such that momentum transfer to the Eulerian solver better reproduces the physical spray jet structure. Validation of liquid/vapor penetration predictions showed that the model yields accurate results with very limited tuning and low sensitivity to the few calibration constants. In-cylinder simulations of diesel catalyst heating operation strategies showed that capturing spray structure is paramount when short, transient injection pulses and low temperatures are present. Furthermore, the EP model provides improved predictions of post-injection spray structure and ignitability, while conventional spray modeling does not capture the increase of liquid penetration during the expansion stroke. Finally, the only important EP model calibration constant, Cliq, does not affect momentum transfer, but it changes the local charge cooling distribution through the local energy transfer, which makes it candidate to additional research. The results confirm that non-equilibrium spray processes do not need to be resolved in engineering simulations of high-pressure diesel sprays.

42 ENGINEERING↗
DOE OSTI2023

Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies

Within-host HIV evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is re-activation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in bifurcating trees. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an Ancestral Recombination Graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time-signals or population bottlenecks. Further, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an Approximate Bayesian Computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally-sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Dynamic behavior of chemically tunable mechano-responsive hydrogels

Here, using theory and simulation, we model the mechanical behavior of gels that encompass loops and dangling chain ends. If the loops remain folded and dangling ends are chemically inert, then these topological features just serve as defects. If, however, the loops unfold to expose the hidden (“cryptic”) binding sites and the ends of the dangling chains are reactive, these moieties can form bonds that improve the gel's mechanical properties. For gels with a lower critical solubility temperature (LCST), we systematically switch on the possible unfolding and binding events. To quantify the resulting effects, we derive equations for the gel's equilibrium and dynamic elastic moduli. We also use a finite element approach to simulate the gel's response to deformation and validate the analytic calculations. Herein, we show that the equilibrium moduli are highly sensitive to the presence of unfolding and binding transitions. The dynamical moduli are sensitive not only to these structural changes, but also to the frequency of deformation. For example, when reactive ends bind to exposed cryptic sites at T = 29 °C and relatively high frequency, the storage shear modulus is 119% greater than the corresponding equilibrium value, while the storage Young's modulus is 109% greater than at equilibrium. These findings provide guidelines for tuning the chemical reactivity of loops and dangling ends and the frequency of deformation to tailor the mechano-responsive behavior of polymer networks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

A foundation model for atomistic materials chemistry

Atomistic simulations of matter, especially those that leverage first-principles (ab initio) electronic structure theory, provide a microscopic view of the world, underpinning much of our understanding of chemistry and materials science. Over the last decade or so, machine-learned force fields have transformed atomistic modeling by enabling simulations of ab initio quality over unprecedented time and length scales. However, early machine-learning (ML) force fields have largely been limited by (i) the substantial computational and human effort required to develop and validate potentials for each particular system of interest and (ii) a general lack of transferability from one chemical system to the next. Here, we show that it is possible to create a general-purpose atomistic ML model, trained on a public dataset of moderate size, that is capable of running stable molecular dynamics for a wide range of molecules and materials. We demonstrate the power of the MACE-MP-0 model-and its qualitative and at times quantitative accuracy-on a diverse set of problems in the physical sciences, including properties of solids, liquids, gases, chemical reactions, interfaces, and even the dynamics of a small protein. The model can be applied out of the box as a starting or "foundation" model for any atomistic system of interest and, when desired, can be fine-tuned on just a handful of application-specific data points to reach ab initio accuracy. Establishing that a stable force-field model can cover almost all materials changes atomistic modeling in a fundamental way: experienced users obtain reliable results much faster, and beginners face a lower barrier to entry. Foundation models thus represent a step toward democratizing the revolution in atomic-scale modeling that has been brought about by ML force fields.

Batatia, Ilyes↗
DOE OSTI2021

via machinae : Searching for stellar streams using unsupervised machine learning

ABSTRACT We develop a new machine learning algorithm, via machinae, to identify cold stellar streams in data from the Gaia telescope. via machinae is based on ANODE, a general method that uses conditional density estimation and sideband interpolation to detect local overdensities in the data in a model agnostic way. By applying ANODE to the positions, proper motions, and photometry of stars observed by Gaia, via machinae obtains a collection of those stars deemed most likely to belong to a stellar stream. We further apply an automated line-finding method based on the Hough transform to search for line-like features in patches of the sky. In this paper, we describe the via machinae algorithm in detail and demonstrate our approach on the prominent stream GD-1. Though some parts of the algorithm are tuned to increase sensitivity to cold streams, the via machinae technique itself does not rely on astrophysical assumptions, such as the potential of the Milky Way or stellar isochrones. This flexibility suggests that it may have further applications in identifying other anomalous structures within the Gaia data set, for example debris flow and globular clusters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Influence of the Graft Length on Nanocomposite Structure and Interfacial Dynamics

Both the dispersion state of nanoparticles (NPs) within polymer nanocomposites (PNCs) and the dynamical state of the polymer altered by the presence of the NP/polymer interfaces have a strong impact on the macroscopic properties of PNCs. In particular, mechanical properties are strongly affected by percolation of hard phases, which may be NP networks, dynamically modified polymer regions, or combinations of both. In this article, the impact on dispersion and dynamics of surface modification of the NPs by short monomethoxysilanes with eight carbons in the alkyl part (C 8 ) is studied. As a function of grafting density and particle content, polymer dynamics is followed by broadband dielectric spectroscopy and analyzed by an interfacial layer model, whereas the particle dispersion is investigated by small-angle X-ray scattering and analyzed by reverse Monte Carlo simulations. NP dispersions are found to be destabilized only at the highest grafting. The interfacial layer formalism allows the clear identification of the volume fraction of interfacial polymer, with its characteristic time. The strongest dynamical slow-down in the polymer is found for unmodified NPs, while grafting weakens this effect progressively. The combination of all three techniques enables a unique measurement of the true thickness of the interfacial layer, which is ca. 5 nm. Finally, the comparison between longer (C 18 ) and shorter (C 8 ) grafts provides unprecedented insight into the efficacy and tunability of surface modification. It is shown that C 8 -grafting allows for a more progressive tuning, which goes beyond a pure mass effect.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Base pairing, structural and functional insights into N 4 -methylcytidine (m 4 C) and N 4 ,N 4 -dimethylcytidine (m 4 2 C) modified RNA

The N 4 -methylation of cytidine (m 4 C and m 4 2 C) in RNA plays important roles in both bacterial and eukaryotic cells. In this work, we synthesized a series of m 4 C and m 4 2 C modified RNA oligonucleotides, conducted their base pairing and bioactivity studies, and solved three new crystal structures of the RNA duplexes containing these two modifications. Our thermostability and X-ray crystallography studies, together with the molecular dynamic simulation studies, demonstrated that m 4 C retains a regular C:G base pairing pattern in RNA duplex and has a relatively small effect on its base pairing stability and specificity. By contrast, the m 4 2 C modification disrupts the C:G pair and significantly decreases the duplex stability through a conformational shift of native Watson-Crick pair to a wobble-like pattern with the formation of two hydrogen bonds. This double-methylated m 4 2 C also results in the loss of base pairing discrimination between C:G and other mismatched pairs like C:A, C:T and C:C. The biochemical investigation of these two modified residues in the reverse transcription model shows that both mono- or di-methylated cytosine bases could specify the C:T pair and induce the G to T mutation using HIV-1 RT. In the presence of other reverse transcriptases with higher fidelity like AMV-RT, the methylation could either retain the normal nucleotide incorporation or completely inhibit the DNA synthesis. These results indicate the methylation at N 4 -position of cytidine is a molecular mechanism to fine tune base pairing specificity and affect the coding efficiency and fidelity during gene replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Assessing electrogenetic activation via a network model of biological signal propagation

Introduction: Molecular communication is the transfer of information encoded by molecular structure and activity. We examine molecular communication within bacterial consortia as cells with diverse biosynthetic capabilities can be assembled for enhanced function. Their coordination, both in terms of engineered genetic circuits within individual cells as well as their population-scale functions, is needed to ensure robust performance. We have suggested that “electrogenetics,” the use of electronics to activate specific genetic circuits, is a means by which electronic devices can mediate molecular communication, ultimately enabling programmable control. Methods: Here, we have developed a graphical network model for dynamically assessing electronic and molecular signal propagation schemes wherein nodes represent individual cells, and their edges represent communication channels by which signaling molecules are transferred. We utilize graph properties such as edge dynamics and graph topology to interrogate the signaling dynamics of specific engineered bacterial consortia. Results: We were able to recapitulate previous experimental systems with our model. In addition, we found that networks with more distinct subpopulations (high network modularity) propagated signals more slowly than randomized networks, while strategic arrangement of subpopulations with respect to the inducer source (an electrode) can increase signal output and outperform otherwise homogeneous networks. Discussion: We developed this model to better understand our previous experimental results, but also to enable future designs wherein subpopulation composition, genetic circuits, and spatial configurations can be varied to tune performance. We suggest that this work may provide insight into the signaling which occurs in synthetically assembled systems as well as native microbial communities.

Chun, Kayla↗
DOE OSTI2024

Bridging the time scale in exascale computing of chemical systems (Final Technical Report)

This report summarizes the work carried out with support of the United States Department of Energy under Award DE-SC0019441. The theme of this project was to develop and apply methods that allowed for the acceleration of atomistic calculations, particularly in challenging areas such as multiphase systems, electrified interfaces, uncertainty estimation, and applications requiring chemical accuracy, which tend to be applications where simulation time is severely bottlenecked by the computational time requirements. Much of the focus was on the application of emerging machine-learning methodologies, although a wide range of methodologies were employed. This report has two major sections. The first focuses on the methodological advances themselves. Within this part, we report a number of major advances, a few examples of which are described here. We report the first machine-learning scheme for the acceleration of electronically grand-canonical calculations (that is, those applicable to electrochemistry). We report new methods of performing transfer learning, in which physics-based priors can be used to provide predictions, often with uncertainty estimates, of images well outside of training sets; we also offer ways to fine-tune these transfer-learning models. We provide a new systematic means to generate and apply minimal training data sets to very large (10,000’s of atoms) systems, with only small training sets appropriate for electronic structure. We developed new methodologies to integrate surface vibrations into surface adsorption calculations. We made advances to the applicability of diffusion Monte Carlo methods to allow (learned) force prediction, finite-size error correction, and force-free means of searching for transition states. We integrated machine-learned atomistic predictions into mechanism generation codes. Additionally, we released new software including AmpTorch, a modernized version of our original atomistic machine-learning code Amp. The second part of this report focuses on the scientific applications that accompanied, and were often enabled by, the methodological advances described earlier. A few examples follow, but full details are in the individual chapters of the report. For example, we developed a general theory of phonon-induced friction on molecular adsorbates. We showed fundamentally how solvent influences the adsorption and desorption process and how it differs from the processes typically involved at the solid–gas interface, making aqueous-phase and electrocatalysis different from traditional thermocatalysis. We examined how metal–insulator and magnetic transitions can be probed, and accelerated exciton dynamics via Frenkel Hamiltonian parameters. We showed that the nearsighted force-training approach, developed within this project, can predict both the stability and reactivity of large nanoparticles, and can also lead to insights on catalyst coverage on binding energies and entropies. These applied studies, which generally integrated with our method development, allowed us to push forward the theoretical understanding of several reaction classes.

08 HYDROGEN↗
DOE OSTI2024

Rapid curing dynamics of PEG-thiol-ene resins allow facile 3D bioprinting and in-air cell-laden microgel fabrication

Thiol-norbornene photoclick hydrogels are highly efficient in tissue engineering applications due to their fast gelation, cytocompatibility, and tunability. In this work, we utilized the advantageous features of polyethylene glycol (PEG)-thiol-ene resins to enable fabrication of complex and heterogeneous tissue scaffolds using 3D bioprinting and in-air drop encapsulation techniques. We demonstrated that photoclickable PEG-thiol-ene resins could be tuned by varying the ratio of PEG-dithiol to PEG norbornene to generate a wide range of mechanical stiffness (0.5–12 kPa) and swelling ratios. Importantly, all formulations maintained a constant, rapid gelation time (<0.5 s). We used this resin in biological projection microstereolithography (BioPµSL) to print complex structures with geometric fidelity and demonstrated biocompatibility by printing cell-laden microgrids. Moreover, the rapid gelling kinetics of this resin permitted high-throughput fabrication of tunable, cell-laden microgels in air using a biological in-air drop encapsulation apparatus (BioIDEA). We demonstrated that these microgels could support cell viability and be assembled into a gradient structure. This PEG-thiol-ene resin, along with BioPµSL and BioIDEA technology, will allow rapid fabrication of complex and heterogeneous tissues that mimic native tissues with cellular and mechanical gradients. The engineered tissue scaffolds with a controlled microscale porosity could be utilized in applications including gradient tissue engineering, biosensing, and in vitro tissue models.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Multi-fidelity modeling to predict the rheological properties of a suspension of fibers using neural networks and Gaussian processes

Unveiling the rheological properties of fiber suspensions is of paramount interest to many industrial applications. There are multiple factors, such as fiber aspect ratio and volume fraction, that play a significant role in altering the rheological behavior of suspensions. Three-dimensional (3D) numerical simulations of coupled differential equations of the suspension of fibers are computationally expensive and time-consuming. Machine learning algorithms can be trained on the available data and make predictions for the cases where no numerical data are available. However, some widely used machine learning surrogates, such as neural networks, require a relatively large training dataset to produce accurate predictions. Multi-fidelity models, which combine high-fidelity data from numerical simulations and less expensive lower fidelity data from resources such as simplified constitutive equations, can pave the way for more accurate predictions. Here, we focus on neural networks and the Gaussian processes with two levels of fidelity, i.e., high and low fidelity networks, to predict the steady-state rheological properties, and compare them to the single-fidelity network. High-fidelity data are obtained from direct numerical simulations based on an immersed boundary method to couple the fluid and solid motion. The low-fidelity data are produced by using constitutive equations. Multiple neural networks and the Gaussian process structures are used for the hyperparameter tuning purpose. Results indicate that with the best choice of hyperparameters, both the multi-fidelity Gaussian processes and neural networks are capable of making predictions with a high level of accuracy with neural networks demonstrating marginally better performance.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗