Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “cluster finding”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,099 records · Page 61
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Discovering hidden geothermal signatures using non-negative matrix factorization with customized k-means clustering

Discovery of hidden geothermal resources is challenging. It requires the mining of large datasets with diverse data attributes representing subsurface hydrogeological and geothermal conditions. The commonly used play fairway analysis approach typically incorporates subject-matter expertise to analyze regional data to estimate geothermal characteristics and favorability. We demonstrate an alternative approach based on machine learning (ML) to process a geothermal dataset from southwest New Mexico (SWNM). The study region includes low- and medium-temperature hydrothermal systems. Several of these systems are not well characterized because of insufficient existing data and limited past explorative work. This study discovers hidden patterns and relations in the SWNM geothermal dataset to improve our understanding of the regional hydrothermal conditions and energy-production favorability. This understanding is obtained by applying an unsupervised ML algorithm based on non-negative matrix factorization coupled with customized k-means clustering (NMFk). NMFk can automatically identify (1) hidden signatures characterizing analyzed datasets, (2) the optimal number of these signatures, (3) the dominant data attributes associated with each signature, and (4) the spatial distribution of the extracted signatures. Here, in this study, NMFk is applied to analyze 18 geological, geophysical, hydrogeological, and geothermal attributes at 44 locations in SWNM. Using NMFk, we find data patterns and identify the spatial associations of hydrothermal signatures within two physiographic provinces (Colorado Plateau and Basin and Range) and two sub-regions of these provinces (the Mogollon-Datil volcanic field and the Rio Grande rift) in SWNM. The ML algorithm extracted five hydrothermal signatures in the SWNM datasets that differentiate between low (<90°C) and medium (90-150°C)-temperature hydrothermal systems. The algorithm also suggests that the Rio Grande rift and northern Mogollon-Datil volcanic field are the most favorable regions for future geothermal resource discovery. NMFk also identified critical attributes to identify medium-temperature hydrothermal systems in the study area. The resulting NMFk model can be applied to predict geothermal conditions and their uncertainties at new SWNM locations based on limited data from unexplored regions. The code to execute the performed analyses as well as the corresponding data can be found at https://github.com/SmartTensors/GeoThermalCloud.jl.

15 GEOTHERMAL ENERGY↗
DOE OSTI2026

Reconstruction and Dissolution of Copper Catalysts during Electrocatalytic Nitrate Reduction

Copper-based electrocatalysts are widely explored for electrochemical nitrate remediation, yet their stability under operating conditions remains poorly understood. While nanoscale and subnanoscale Cu motifs are known to restructure during the nitrate reduction reaction (NO 3 RR), how these transformations translate into irreversible material loss remains unclear. Here, we quantify Cu dissolution during NO 3 RR as a function of catalyst architecture and electrolyte chemistry using two model systems: single-atom Cu (Cu 1 ) and Cu nanoparticles (Cu NP ). Time-resolved leaching measurements, integrated with in situ X-ray absorption spectroscopy (XAS), reveal measurable Cu loss for both catalysts during NO 3 RR. Dissolution is concentrated at the initiation of electrolysis, coinciding with rapid restructuring, and depends strongly on morphology, with Cu NP consistently exhibiting greater Cu loss than Cu 1 . In situ XAS reveals that Cu 1 forms transient metallic clusters under reduction that largely redisperse upon returning to open-circuit voltage, whereas Cu NP undergoes reduction of an oxidized surface layer accompanied by sustained Cu loss during electrolysis. Notably, the presence of nitrate significantly intensifies restructuring and Cu loss, highlighting the critical role of electrolyte composition. Furthermore, these findings establish a direct link between electrochemical restructuring and Cu dissolution, unveiling electrolyte-dependent interactions as key determinants of catalyst durability in electrochemical nitrate conversion.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Third-Order Møller–Plesset Theory Made More Useful? The Role of Density Functional Theory Orbitals

The practical utility of Møller–Plesset (MP) perturbation theory is severely constrained by the use of Hartree–Fock (HF) orbitals. It has recently been shown that the use of regularized orbital-optimized MP2 orbitals and scaling of MP3 energy could lead to a significant reduction in MP3 error. In this work, we examine whether density functional theory (DFT)-optimized orbitals can be similarly employed to improve the performance of MP theory at both the MP2 and MP3 levels. We find that the use of DFT orbitals leads to significantly improved performance for prediction of thermochemistry, barrier heights, noncovalent interactions, and dipole moments relative to the standard HF-based MP theory. Indeed, MP3 (with or without scaling) with DFT orbitals is found to surpass the accuracy of coupled-cluster singles and doubles (CCSD) for several data sets. We also found that the results are not particularly functional sensitive in most cases (although range-separated hybrid functionals with low delocalization error perform the best). As such, MP3 based on DFT orbitals thus appears to be an efficient, noniterative O(N 6 ) scaling wave-function approach for single-reference electronic structure computations. Scaled MP2 with DFT orbitals is also found to be quite accurate in many cases, although modern double hybrid functionals are likely to be considerably more accurate.

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

Using Density-Corrected DFT to Understand Density-Driven and Functional-Dependent Errors in Ab Initio Simulations of the Hydrated Electron

The hydrated electron, an excess electron in liquid water, plays a crucial role in a plethora of chemical processes, motivating extensive research efforts to characterize its structure, dynamics, and reactivity in solution. Recent theoretical approaches to understanding this intriguing object have involved ab initio simulations based on density functional theory (DFT). Although DFT allows for the study of hydrated electron reactivity and quantum mechanical behavior, it is well-known that anionic systems can suffer from significant density-driven errors (DDEs). Density-corrected DFT (DC-DFT) provides a framework to mitigate such errors; the method reduces DDEs by replacing the self-consistent (SC) density associated with a given density functional with the Hartree–Fock (HF) density. Since HF densities tend to be more localized than DFT SC densities, the DC-DFT scheme significantly improves errors in calculations where the SC density is spuriously delocalized. Here, we investigate how the use of density correction affects the calculated properties of the DFT-simulated (PBEh) hydrated electron, a particularly challenging diffuse anionic system to simulate. First, we analyze charge delocalization in a system consisting of a model octahedral hydrated electron water cluster (the so-called Kevan structure) along with a spatially separated sulfur atom. We show that the use of density correction indeed reduces DDEs in comparison to a standard DFT global hybrid functional. We then propagate molecular dynamics trajectories of the hydrated electron using DC-DFT, where we find that DC further localizes electron density in the cavity region, a signature of reduced charge delocalization. Unfortunately, the decreased radius of gyration of the spin density and corresponding tightening of the local solvation structure from density correction causes predicted observables to deviate further from experimental measurements than when density correction is not employed. Here, we argue that DC’s worse agreement with experiment results from the removal of a fortuitous cancellation of errors that is intrinsic to the PBEh functional. This indicates that the difficulties with DFT to simulate hydrated electrons are primarily due to the inherent approximations in DFT rather than to density-driven errors.

Density functional theory↗
DOE OSTI2023

Mastering morphology of non-fullerene acceptors towards long-term stable organic solar cells

Despite the rapid progress of organic solar cells based on non-fullerene acceptors, simultaneously achieving high power conversion efficiency and long-term stability for commercialization requires sustainable research effort. Here, we demonstrate stable devices by integrating a wide bandgap electron-donating polymer (namely PTzBI-dF) and two acceptors (namely L8BO and Y6) that feature similar structures yet different thermal and morphological properties. The organic solar cell based on PTzBI-dF:L8BO:Y6 could achieve a promising efficiency of 18.26% in the conventional device structure. In the inverted structure, excellent long-term thermal stability over 1400 h under 85 °C continuous heating is obtained. The improved performance can be ascribed to suppressed charge recombination along with appropriate charge transport. We find that the morphological features in terms of crystalline coherence length of fresh and aged films can be gradually regulated by the weight ratio of L8BO:Y6. Additionally, the occurrence of melting point decrease and reduced enthalpy in PTzBI-dF:L8BO:Y6 films could prohibit the amorphous phase to cluster, and consequently overcome the energetic traps accumulation aroused by thermal stress, which is a critical issue in high efficiency non-fullerene acceptors-based devices. This work provides insight into understanding non-fullerene acceptors-based organic solar cells for improved efficiency and stability.

14 SOLAR ENERGY↗
DOE OSTI2022

Variational quantum eigensolver with reduced circuit complexity

Abstract The variational quantum eigensolver (VQE) is one of the most promising algorithms to find eigenstates of a given Hamiltonian on noisy intermediate-scale quantum devices (NISQ). The practical realization is limited by the complexity of quantum circuits. Here we present an approach to reduce quantum circuit complexity in VQE for electronic structure calculations. Our ClusterVQE algorithm splits the initial qubit space into clusters which are further distributed on individual (shallower) quantum circuits. The clusters are obtained based on mutual information reflecting maximal entanglement between qubits, whereas inter-cluster correlation is taken into account via a new “dressed” Hamiltonian. ClusterVQE therefore allows exact simulation of the problem by using fewer qubits and shallower circuit depth at the cost of additional classical resources, making it a potential leader for quantum chemistry simulations on NISQ devices. Proof-of-principle demonstrations are presented for several molecular systems based on quantum simulators as well as IBM quantum devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Computational multiphysics modeling of radioactive aerosol deposition in diverse human respiratory tract geometries

The evaluation of aerosol exposure relies on generic mathematical models that assume uniform particle deposition profiles over the human respiratory tract and do not account for subject-specific characteristics. Here we introduce a hybrid-automated computational workflow that generates personalized particle deposition profiles in 3D reconstructed human airways from computed tomography scans using Computational Fluid and Particle Dynamics simulations. This is the first large-scale study to consider realistic airways variability, where 380 lower and 40 upper human respiratory tract 3D geometries are reconstructed and parameterized. The data is clustered into nine groups using random forest regression. Computational fluid and particle dynamics simulations are conducted on these representative geometries using a realistic heavy-breathing respiratory cycle and radioactive iodine-131 as a source term. Monte Carlo radiation transport simulations are performed to obtain detailed energy deposition maps. Our findings emphasize the importance of personalized studies, as minor respiratory tract variations notably influence deposition patterns rather than global parameters of the lower airways, observing more than 30% variance in the mass deposition fraction.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Accurate core excitation and ionization energies from a state-specific coupled-cluster singles and doubles approach

Here, we investigate the use of orbital-optimized references in conjunction with single-reference coupled-cluster theory with single and double substitutions (CCSD) for the study of core excitations and ionizations of 18 small organic molecules, without the use of response theory or equation-of-motion (EOM) formalisms. Three schemes are employed to successfully address the convergence difficulties associated with the coupled-cluster equations, and the spin contamination resulting from the use of a spin symmetry-broken reference, in the case of excitations. In order to gauge the inherent potential of the methods studied, an effort is made to provide reasonable basis set limit estimates for the transition energies. Overall, we find that the two best-performing schemes studied here for ΔCCSD are capable of predicting excitation and ionization energies with errors comparable to experimental accuracies. The proposed ΔCCSD schemes reduces statistical errors against experimental excitation energies by more than a factor of two when compared to the frozen-core core–valence separated (FC-CVS) EOM-CCSD approach – a successful variant of EOM-CCSD tailored towards core excitations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Primordial non-Gaussianities with weak lensing: information on non-linear scales in the Ulagam full-sky simulations

Abstract Primordial non-Gaussianities (PNGs) are signatures in the density field that encode particle physics processes from the inflationary epoch. Such signatures have been extensively studied using the Cosmic Microwave Background, through constraining their amplitudes,f X NL , with future improvements expected from large-scale structure surveys; specifically, the galaxy correlation functions. We show that weak lensing fields can be used to achieve competitive and complementary constraints. This is shown via theUlagamsuite of N-body simulations, a subset of which evolves primordial fields with four types of PNGs. We create full-sky lensing maps and estimate the Fisher information from three summary statistics measured on the maps: the moments, the cumulative distribution function, and the 3-point correlation function. We find that the year 10 sample from the Rubin Observatory Legacy Survey of Space and Time (LSST) can constrain PNGs toσ(f NL eq ) ≈ 110,σ(f NL or, lss ) ≈ 120,σ(f NL loc ) ≈ 40. For the former two, this is better than or comparable to expected galaxy clustering-based constraints from the Dark Energy Spectroscopic Instrument (DESI). The PNG information in lensing fields is on non-linear scales and at low redshifts (z≲ 1.25), with a clear origin in the evolution history of massive halos. The constraining power degrades by ∼60% under scale cuts of ≳ 20 Mpc, showing there is still significant information on scales mostly insensitive to small-scale systematic effects (e.g., baryons). We publicly release theUlagamsuite to enable more survey-focused analyses.

Astronomy & Astrophysics↗
DOE OSTI2021

Characterizing the target selection pipeline for the Dark Energy Spectroscopic Instrument Bright Galaxy Survey

ABSTRACT We present the steps taken to produce a reliable and complete input galaxy catalogue for the Dark Energy Spectroscopic Instrument (DESI) Bright Galaxy Survey (BGS) using the photometric Legacy Survey DR8 DECam. We analyse some of the main issues faced in the selection of targets for the DESI BGS, such as star–galaxy separation, contamination by fragmented stars and bright galaxies. Our pipeline utilizes a new way to select BGS galaxies using Gaia photometry and we implement geometrical and photometric masks that reduce the number of spurious objects. The resulting catalogue is cross-matched with the Galaxy And Mass Assembly (GAMA) survey to assess the completeness of the galaxy catalogue and the performance of the target selection. We also validate the clustering of the sources in our BGS catalogue by comparing with mock catalogues and the Sloan Digital Sky Survey (SDSS) data. Finally, the robustness of the BGS selection criteria is assessed by quantifying the dependence of the target galaxy density on imaging and other properties. The largest systematic correlation we find is a 7 per cent suppression of the target density in regions of high stellar density.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Gravothermal collapse and the diversity of galactic rotation curves

The rotation curves of spiral galaxies exhibit a great diversity that challenges our understanding of galaxy formation and the nature of dark matter. Previous studies showed that in self-interacting dark matter (SIDM) models with a cross section per unit mass of σ/m ≈ $\mathscr{O}$(1) cm 2 /g, the predicted dark matter central densities are a good match to the observed densities in galaxies. Here, in this work, we explore a regime with a larger cross section of σ/m ≈ 20−40 cm 2 /g in dwarf galactic halos. We will show that such strong dark matter self-interactions can further amplify the diversity of halo densities inherited from their assembly history. High concentration halos can enter the gravothermal collapse phase within 10 Gyr, resulting in a high density, while low concentration ones remain in the expansion phase and have a low density. We fit the rotation curves of 14 representative low surface brightness galaxies and demonstrate how the large range of observed central densities is naturally accommodated in the strong SIDM regime of σ/m ≈ 20 – 40 cm 2 /g. Galaxies that are outliers in the previous studies, due to their high halo central densities, are no longer outliers in this SIDM regime as their halos would be in the collapse phase. For galaxies with a low density, the SIDM fits are robust to the variation of the cross section. Our findings open up a new window for testing gravothermal collapse, the unique signature of strong dark matter self-interactions, and exploring a broader SIDM model space. As an example, we illustrate how the larger cross sections favored by our fits, together with upper limits from strong lensing observations in clusters, pick out the preferred SIDM model space for a dark matter particle coupled to a light gauge boson in the Born regime.

dark matter↗
DOE OSTI2020

Collective effects and pattern formation for directional locking of disks moving through obstacle arrays

We examine directional locking effects in an assembly of disks driven through a square array of obstacles as the angle of drive rotates from 0° to 90°. For increasing disk densities, the system exhibits a series of different dynamic patterns along certain locking directions, including one-dimensional or multiple-row chain phases and density-modulated phases. For nonlocking driving directions, the disks form disordered patterns or clusters. Here, when the obstacles are small or far apart, a large number of locking phases appear; however, as the number of disks increases, the number of possible locking phases drops due to the increasing frequency of collisions between the disks and obstacles. For dense arrays or large obstacles, we find an increased clogging effect in which immobile and moving disks coexist.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Chemomechanics in alloy phase stability

We describe a first-principles statistical mechanics method to calculate the free energies of crystalline alloys that depend on temperature, composition, and strain. The approach relies on an extension of the alloy cluster expansion to include an explicit dependence on homogeneous strain in addition to site occupation variables that track the degree of chemical ordering. The method is applied to the Si-Ge binary alloy and is used to calculate free energies that describe phase stability under arbitrary epitaxial constraints. We find that while the incoherent phase diagram (in which coexisting phases are not affected by coherency constraints) hosts a miscibility gap, coherent phase equilibrium predicts ordering and negative enthalpies of mixing. Instead of chemical instability, the chemomechanical free energy exhibits instabilities along directions that couple the composition of the alloy with a volumetric strain order parameter. Furthermore, this has fundamental implications for phase field models of spinodal decomposition as it indicates the importance of gradient energy coefficients that couple gradients in composition with gradients in strain.

Materials Science↗
DOE OSTI2021

Detection of significant antiviral drug effects on COVID-19 with reasonable sample sizes in randomized controlled trials: A modeling study

Development of an effective antiviral drug for Coronavirus Disease 2019 (COVID-19) is a global health priority. Although several candidate drugs have been identified through in vitro and in vivo models, consistent and compelling evidence from clinical studies is limited. The lack of evidence from clinical trials may stem in part from the imperfect design of the trials. We investigated how clinical trials for antivirals need to be designed, especially focusing on the sample size in randomized controlled trials. A modeling study was conducted to help understand the reasons behind inconsistent clinical trial findings and to design better clinical trials. We first analyzed longitudinal viral load data for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) without antiviral treatment by use of a within-host virus dynamics model. The fitted viral load was categorized into 3 different groups by a clustering approach. Comparison of the estimated parameters showed that the 3 distinct groups were characterized by different virus decay rates (p-value < 0.001). The mean decay rates were 1.17 d -1 (95% CI: 1.06 to 1.27 d -1 ), 0.777 d -1 (0.716 to 0.838 d -1 ), and 0.450 d -1 (0.378 to 0.522 d -1 ) for the 3 groups, respectively. Such heterogeneity in virus dynamics could be a confounding variable if it is associated with treatment allocation in compassionate use programs (i.e., observational studies). Subsequently, we mimicked randomized controlled trials of antivirals by simulation. An antiviral effect causing a 95% to 99% reduction in viral replication was added to the model. To be realistic, we assumed that randomization and treatment are initiated with some time lag after symptom onset. Using the duration of virus shedding as an outcome, the sample size to detect a statistically significant mean difference between the treatment and placebo groups (1:1 allocation) was 13,603 and 11,670 (when the antiviral effect was 95% and 99%, respectively) per group if all patients are enrolled regardless of timing of randomization. The sample size was reduced to 584 and 458 (when the antiviral effect was 95% and 99%, respectively) if only patients who are treated within 1 day of symptom onset are enrolled. We confirmed the sample size was similarly reduced when using cumulative viral load in log scale as an outcome. We used a conventional virus dynamics model, which may not fully reflect the detailed mechanisms of viral dynamics of SARS-CoV-2. The model needs to be calibrated in terms of both parameter settings and model structure, which would yield more reliable sample size calculation. In this study, we found that estimated association in observational studies can be biased due to large heterogeneity in viral dynamics among infected individuals, and statistically significant effect in randomized controlled trials may be difficult to be detected due to small sample size. The sample size can be dramatically reduced by recruiting patients immediately after developing symptoms. We believe this is the first study investigated the study design of clinical trials for antiviral treatment using the viral dynamics model.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Uncertainty in Synthetic Tropical Cyclone Hazard and Risk Estimates: Insights from RAFT, CHAZ, MIT, STORM, and CLIMADA

We synthesize five complementary tropical cyclone (TC) hazard frameworks—RAFT (physics-based machine learning), CHAZ and MIT (statistical–dynamical), STORM (fully statistical), and CLIMADA (observation-driven resampling)—to characterize uncertainty in wind-related TC metrics relevant to energy applications. All datasets and the IBTrACS observational record are harmonized to a common 6-hourly, 2.5° grid. We compare basin-wide and coastal properties using consistent definitions for TC frequency, mean and maximum intensity, 24-hour intensification, and 6-hour translation speed, and quantify agreement with Pearson r, RMSE, and Kling–Gupta efficiency (KGE) alongside resampling-based confidence intervals. CLIMADA is included for basin context but excluded from coastal skill scoring because it resamples historical IBTrACS; if supplied with projected future tracks from an external hazard model, CLIMADA can be used to simulate future TC scenarios. Results show robust, cross-model signals: (i) a corridor of activity from the tropical Atlantic through the Caribbean into the Bahamas and western subtropical Atlantic; (ii) a meridional dipole in 24-hour intensification (low-latitude strengthening, subtropical weakening); and (iii) a transition from slower tropical motion to faster midlatitude translation. Coastal winds (mean and maximum) consistently cluster from the eastern Gulf into the Bahamas–western Atlantic transition. The largest structural spread occurs in the amplitude and footprint of lifetime maximum intensity and, secondarily, in translation speed; intensification exhibits similar central behavior across frameworks with variability in extremes. Translation speed shows the most uniform coastal agreement. These findings provide a decision envelope for wind-focused risk screening and clarify where uncertainty should be carried forward; wind-only results represent a lower bound on total hazard, motivating integration of surge and rainfall modules and a companion, asset-level damage analysis.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2024

Functional analysis of the methylerythritol phosphate pathway terminal enzymes IspG and IspH from Zymomonas mobilis

ABSTRACT Isoprenoids are a diverse family of compounds that are synthesized from two isomeric compounds, isopentenyl diphosphate and dimethylallyl diphosphate. In most bacteria, isoprenoids are produced from the essential methylerythritol phosphate (MEP) pathway. The terminal enzymes of the MEP pathway IspG and IspH are [4Fe-4S] cluster proteins, and in Zymomonas mobilis, the substrates of IspG and IspH accumulate in cells in response to O 2 , suggesting possible lability of their [4Fe-4S] clusters. Here, we show using complementation assays in Escherichia coli that even under anaerobic conditions, Z. mobilis IspG and IspH are not as functional as their E. coli counterparts, requiring higher levels of expression to rescue viability. A deficit of the sulfur utilization factor (SUF) Fe-S cluster biogenesis pathway did not explain the reduced function of Z. mobilis IspG and IspH since no improvement in viability was observed in E. coli expressing the Z. mobilis SUF pathway or having increased expression of the E. coli SUF pathway. Complementation of single and double mutants with various combinations of Z. mobilis and E. coli IspG and IspH indicated that optimal growth required the pairing of IspG and IspH from the same species. Furthermore, Z. mobilis IspH conferred an O 2 -sensitive growth defect to E. coli that could be partially rescued by co-expression of Z. mobilis IspG. In vitro analysis showed O 2 sensitivity of the [4Fe-4S] cluster of both Z. mobilis IspG and IspH. Altogether, our data indicate an important role of the cognate protein IspG in Z. mobilis IspH function under both aerobic and anaerobic conditions. IMPORTANCE Isoprenoids are one of the largest classes of natural products, exhibiting diversity in structure and function. They also include compounds that are essential for cellular life across the biological world. In bacteria, isoprenoids are derived from two precursors, isopentenyl diphosphate and dimethylallyl diphosphate, synthesized primarily by the methylerythritol phosphate pathway. The aerotolerant Z. mobilis has the potential for methylerythritol phosphate pathway engineering by diverting some of the glucose that is typically efficiently converted into ethanol to produce isoprenoid precursors to make bioproducts and biofuels. Our data revealed the surprising finding that Z. mobilis IspG and IspH need to be co-optimized to improve flux via the methyl erythritol phosphate pathway in part to evade the oxygen sensitivity of IspH.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Highly Basic Clusters in the Herpes Simplex Virus 1 Nuclear Egress Complex Drive Membrane Budding by Inducing Lipid Ordering

During replication of herpesviruses, capsids escape from the nucleus into the cytoplasm by budding at the inner nuclear membrane. This unusual process is mediated by the viral nuclear egress complex (NEC) that deforms the membrane around the capsid by oligomerizing into a hexagonal, membrane-bound scaffold. Here, we found that highly basic membrane-proximal regions (MPRs) of the NEC alter lipid order by inserting into the lipid headgroups and promote negative Gaussian curvature. We also find that the electrostatic interactions between the MPRs and the membranes are essential for membrane deformation. One of the MPRs is phosphorylated by a viral kinase during infection, and the corresponding phosphomimicking mutations block capsid nuclear egress. We show that the same phosphomimicking mutations disrupt the NEC-membrane interactions and inhibit NEC-mediated budding in vitro, providing a biophysical explanation for the in vivo phenomenon. Our data suggest that the NEC generates negative membrane curvature by both lipid ordering and protein scaffolding and that phosphorylation acts as an off switch that inhibits the membrane-budding activity of the NEC to prevent capsid-less budding.

membrane curvature↗
DOE OSTI2022

Rare Earth and Transition Metal Containing Glasses

Transition metal (TM) and rare earth (RE) ions have been incorporated into many glass systems such as silicate, phosphate, and borosilicate-based oxide glasses, as well as in halide and chalcogenide glasses, that find applications ranging from optical, photonic, and magnetic devices, solid-state battery, to nuclear waste disposal. Understanding the structural role of RE and TM in these glasses can help to develop glass compositions for targeted applications with either high-optical emission efficiency, electrical conductivity, or chemical durability. In this chapter, we first provide a general introduction of the applications and structural features of RE and TM in glasses, then the critical aspects of molecular dynamics (MD) simulations of these glasses such as interatomic potentials, structural analysis tools to study RE and TM ions in glasses and their clustering behaviors, Quantitative Structure–Property Analysis (QSPR), diffusion and dynamic property calculations, and electronic structure calculations to understand electronic defects such as charge trapping and radiation effects are introduced. Three representative case studies are presented: the first one is on MD simulations of erbium- and europium-doped silica and silicate glasses, as well as cerium doped aluminophosphate glasses, that revealed the effect of glass composition on RE ion local structure and clustering behavior. Electronic structure calculations of cerium-doped glass show how the existence of multioxidation states help to mediate radiation-induced damages caused by excited electron–hole pairs was also discussed. The second one focuses on alkali vanadophosphate glasses where the existence of two vanadium oxidation states help to provide electronic conduction in the glasses while alkali ions provide ionic conduction. MD simulations were used to understand vanadium environments and other structural aspects in the phosphate glasses, as well as the ionic transport behaviors of alkali ions. The third case study is on zirconium-containing borosilicate and aluminosilicate glasses that find wide applications in nuclear waste disposal. MD simulations help to provide structural details of zirconium ions that are validated by diffraction and EXAFS spectra. The structural information was used to interpret changes of mechanical properties and chemical durability by using QSPR and other analyses-based MD-generated structure models.

Du, Jincheng↗