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At least 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

An important need exists to better understand and stratify kidney disease according to its underlying pathophysiology in order to develop more precise and effective therapeutic agents. National collaborative efforts such as the Kidney Precision Medicine Project are working towards this goal through the collection and integration of large, disparate clinical, biological and imaging data from patients with kidney disease. Ontologies are powerful tools that facilitate these efforts by enabling researchers to organize and make sense of different data elements and the relationships between them. Ontologies are critical to support the types of big data analysis necessary for kidney precision medicine, where heterogeneous clinical, imaging and biopsy data from diverse sources must be combined to define a patient’s phenotype. Here, the development of two new ontologies — the Kidney Tissue Atlas Ontology and the Ontology of Precision Medicine and Investigation — will support the creation of the Kidney Tissue Atlas, which aims to provide a comprehensive molecular, cellular and anatomical map of the kidney. These ontologies will improve the annotation of kidney-relevant data, and eventually lead to new definitions of kidney disease in support of precision medicine.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Protein-ligand binding affinity prediction using multi-instance learning with docking structures

Recent advances in 3D structure-based deep learning approaches demonstrate improved accuracy in predicting protein-ligand binding affinity in drug discovery. These methods complement physics-based computational modeling such as molecular docking for virtual high-throughput screening. Despite recent advances and improved predictive performance, most methods in this category primarily rely on utilizing co-crystal complex structures and experimentally measured binding affinities as both input and output data for model training. Nevertheless, co-crystal complex structures are not readily available and the inaccurate predicted structures from molecular docking can degrade the accuracy of the machine learning methods. We introduce a novel structure-based inference method utilizing multiple molecular docking poses for each complex entity. Our proposed method employs multi-instance learning with an attention network to predict binding affinity from a collection of docking poses. We validate our method using multiple datasets, including PDBbind and compounds targeting the main protease of SARS-CoV-2. The results demonstrate that our method leveraging docking poses is competitive with other state-of-the-art inference models that depend on co-crystal structures. This method offers binding affinity prediction without requiring co-crystal structures, thereby increasing its applicability to protein targets lacking such data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

A High-Fidelity Molecular Model of the Cu(111) Repeating Unit

Dynamic processes at surfaces are central to heterogeneous catalysis, but their atomistic mechanism(s) can prove difficult to elucidate due to variations in material structure and the corresponding impact on reactivity. Moreover, disparities between reaction conditions and those employed for spectroscopic characterization at surfaces can inhibit detailed understanding of catalysis-relevant chemistries. Herein, we substantiate the so-called “cluster-surface” analogy by leveraging a low-valent tricopper architecture ( 1 ) as a model system for small molecule activation at Cu(111). Two reaction classes are explored: the adsorption of carbon monoxide (CO) and the dissociative adsorption of dihydrogen (H 2 ). These processes serve as an ideal testbed to compare the reactivity of a molecular cluster ( 1 ) to that of a heterogeneous surface, as both reactions have empirical data from measurements performed on crystalline Cu(111). Cluster 1 reversibly binds CO. Variable temperature NMR analysis with 13 CO reveals a favorable enthalpy but large negative entropy (−5.1 kcal × mol –1 and −22.9 cal × mol –1 × K –1 , respectively) for CO binding, affording a process that is marginally endergonic at room temperature (ΔG ads (298.15 K) = 1.7 ± 0.5 kcal × mol –1 ). Similarly, analogous to a Cu(111) surface, 1 is shown to oxidatively add (chemisorb) H 2 . Kinetic parameters were determined for this process and the activation enthalpy (8.4 ± 0.5 kcal × mol –1 ) closely mirrors that established for H 2 binding at the Cu(111) facet (6.0 to 12.4 kcal × mol –1 ). Together, these results showcase that a trinuclear cluster can reproduce the small molecule binding and activation energetics of a bulk crystalline surface, setting the stage for studying less-defined surface processes in an atomically precise molecular setting.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2006

Aeroheating Analysis for the Mars Reconnaissance Orbiter with Comparison to Flight Data

The aeroheating environment of the Mars Reconnaissance Orbiter (MRO) has been analyzed using the Direct Simulation Monte Carlo and free-molecular techniques. The results of these analyses were used to develop an aeroheating database to be used for the pre-flight planning and the in-flight operations support for the aerobraking phase of the MRO mission. The aeroheating predictions calculated for the MRO include the heat transfer coefficient (C(H)) over a range of angles-of-attack, side-slip angles, and number densities. The effects of flow chemistry were also investigated. Flight heat flux data deduced from surface temperature sensors have been compared to pre-flight predictions and agree favorably.

Liechty, Derek S.↗
NASA NTRS2005

Warm Molecular Gas Traced with CO J = 7 --> 6 in the Galaxy's Central 2 Parsecs: Dynamical Heating of the Circumnuclear Disks

We present an 11" resolution map of the central 2 pc of the Galaxy in the CO J = 7 --> 6 rotational transition. The CO emission shows rotation about Sgr A* but also evidence for noncircular turbulent motion and a clumpy morphology. We combine our data set with available CO measurements to model the physical conditions in the disk. We find that the molecular gas in the region is both warm and dense, with T approx. 200-300 K and n(sub H2) approx. (5-7) x 10(exp 4) cm(exp -3). The mass of warm molecular gas we measure in the central 2 pc is at least 2000 M(solar), about 20 times the UV-excited atomic gas mass, ruling out a UV heating scenario for the molecular material. We compare the available spectral tracers with theoretical models and conclude that molecular gas is heated with magnetohydrodynamic shocks with v approx. 10-20 km s(exp -1) and B approx. 0.3- 0.5 mG. Using the conditions derived with the CO analysis, we include the other important coolants, neutral oxygen and molecular hydrogen, to estimate the total cooling budget of the molecular material. We derive a mass-to-luminosity ratio of approx. 2-3 M(solar)(L(solar)exp -1), which is consistent with the total power dissipated via turbulent decay in 0.1 pc cells with v(sub rms) approx. 15 kilometers per second. These size and velocity scales are comparable to the observed clumping scale and the velocity dispersion. At this rate, the material near Sgr A* is dissipating its orbital energy on an orbital timescale and cannot last for more than a few orbits. Our conclusions support a scenario in which the features near Sgr A* such as the circumnuclear disk and northern arm are generated by infalling clouds with low specific angular momentum.

galatic nuclei↗
DOE OSTI2021

The Atacama Cosmology Telescope: Microwave Intensity and Polarization Maps of the Galactic Center

Herein we present arcminute-resolution intensity and polarization maps of the Galactic center made with the Atacama Cosmology Telescope. The maps cover a 32 deg 2 field at 98, 150, and 224 GHz with |l| ≤ 4°, |b| ≤ 2°. We combine these data with Planck observations at similar frequencies to create coadded maps with increased sensitivity at large angular scales. With the coadded maps, we are able to resolve many known features of the Central Molecular Zone (CMZ) in both total intensity and polarization. We map the orientation of the plane-of-sky component of the Galactic magnetic field inferred from the polarization angle in the CMZ, finding significant changes in morphology in the three frequency bands as the underlying dominant emission mechanism changes from synchrotron to dust emission. Selected Galactic center sources, including Sgr A*, the Brick molecular cloud (G0.253+0.016), the Mouse pulsar wind nebula (G359.23-0.82), and the Tornado supernova remnant candidate (G357.7-0.1), are examined in detail. These data illustrate the potential for leveraging ground-based cosmic microwave background polarization experiments for Galactic science.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Benchmarking structural evolution methods for training of machine learned interatomic potentials

When creating training data for machine-learned interatomic potentials (MLIPs), it is common to create initial structures and evolve them using molecular dynamics (MD) to sample a larger configuration space. Here, we benchmark two other modalities of evolving structures, contour exploration (CE) and dimer-method (DM) searches against MD for their ability to produce diverse and robust density functional theory training data sets for MLIPs. We also discuss the generation of initial structures which are either from known structures or from random structures in detail to further formalize the structure-sourcing processes in the future. The polymorph-rich zirconium-oxygen composition space is used as a rigorous benchmark system for comparing the performance of MLIPs trained on structures generated from these structural evolution methods. Using Behler–Parrinello neural networks as our MLIP models, we find that CE and the DM searches are generally superior to MD in terms of spatial descriptor diversity and statistical accuracy.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1994

CS multitransitional study of density distribution in star-forming regions. 2: The S140 region

The S140 molecular cloud was observed in five transitions of CS with resolutions of 11 to 45 arcsec. The data were analyzed with both the LVG and microturbulent models of radiative transfer to derive the density structure. It was found that the CS emission comes from three components of gas: a spherical component centered on the infrared cluster, an arc component along the ionization front between the S140 H II region and the dense molecular cloud core, and a high-velocity component from the dense part of a molecular outflow. The spherical component contributes most to the CS emission and was analyzed in more detail than the other components. Using a temperature distribution derived from an analysis of the dust emission from S140, we fit a power-law density distribution of n(r) = n(sub i)(r/r(sub i))(exp -alpha) to the spherical component. The best fit was for n(sub i) = 1.4 x 10(exp 6) (density at r(sub i) = 0.026 pc) and alpha = 0.8. The density (n(sub i)) was found to be greater than or equal to the density required to account for the dust emission, depending on the dust opacity laws adopted. The presence of optical emission (Dinerstein, Lester, & Rank 1979) suggests a clumpy structure for the dense gas. Considerations of the virial mass and the lowest amount of column density required to produce dust emission put the volume filling factor (f(sub nu)) of the dense gas at approximately 0.14-0.5. We compared S140 with other regions of star formation where the density structure has been derived from excitation analysis. Source-source variations in density gradients and clumpiness clearly exist, ranging from alpha = 2 and f(sub nu) approximately 1 in B335 to alpha approximately 0, f(sub nu) approximately 0.1 in M17. There is a tendency for more massive star-forming regions to have a flatter density distribution, a more clumpy structure, and a large number of young stars. The implications of this tendency are discussed.

Zhou, Shudong↗
DOE OSTI2024

In-Depth Proteome Profiling of the Hippocampus of LDLR Knockout Mice Reveals Alternation in Synaptic Signaling Pathway

The low-density lipoprotein receptor (LDLR) is a major apolipoprotein receptor that regulates cholesterol homeostasis. LDLR deficiency is associated with cognitive impairment by the induction of synaptopathy in the hippocampus. Despite the close relationship between LDLR and neurodegenerative disorders, proteomics research for protein profiling in the LDLR knockout (KO) model remains insufficient. Therefore, understanding LDLR KO-mediated differential protein expression within the hippocampus is crucial for elucidating a role of LDLR in neurodegenerative disorders. In this study, we conducted first-time proteomic profiling of hippocampus tissue from LDLR KO mice using tandem mass tag (TMT)-based MS analysis. LDLR deficiency induces changes in proteins associated with the transport of diverse molecules, and activity of kinase and catalyst within the hippocampus. Additionally, significant alterations in the expression of components in the major synaptic pathways were found. Furthermore, these synaptic effects were verified using a data-independent acquisition (DIA)-based proteomic method. In conclusion, our data will serve as a valuable resource for further studies to discover the molecular function of LDLR in neurodegenerative disorders.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

A methodology for selection of solid desiccants in energy recovery ventilators

Controlling indoor humidity levels is essential for maintaining acceptable indoor air quality in buildings. The use of energy recovery ventilators (ERVs) is an energy-efficient way to regulate indoor air humidity. Fixed-bed regenerators and rotary wheels are widely used ERVs because of their high sensible and latent effectiveness. These ERVs are made of desiccant-coated substrates, which enable them to transfer moisture between the supply and exhaust air streams. However, the moisture transfer ability of ERVs depends on the physiochemical and sorption properties of desiccants. Extensive, full-scale experiments are required to determine the best desiccant material for these systems. This paper presents a simplified method of selecting suitable desiccant materials for ERVs. The methodology involves important characterization methods, literature correlations for performance prediction, and cost-effective testing methods prior to full-scale testing, and full-scale test methods are discussed in detail. Furthermore, the performance of a few newly derived materials is evaluated and compared with that of conventional desiccants such as silica gel and molecular sieves. The highest latent effectiveness was obtained for composite of super absorbent polymer (SAP) with potassium formate (SAP-HCO2K-50 %), all-polymer porous solid desiccant (APPSD) and metal organic framework (MOF)–MIL–101 (Cr), followed by activated carbon fibre felt (ACFF) Silica sol-LiCl30, SAP, silica gel, MOF–303, and molecular sieve. Researchers and manufacturers would benefit from the proposed methodology and presented data in developing new desiccant materials for ERV applications.

Energy recovery↗
DOE OSTI2021

Desalination metamodels and a framework for cross-comparative performance simulations

There is an opportunity to save energy and reduce operational expenses when choosing a suitable desalination method aided by computational modeling. Existing models are not conducive to generalized comparisons between different desalination methods. Therefore, the work in this study developed metamodels for six desalination methods, grouped them into thermal and molecular transport families, and validated their predictive performance within 9% difference from published data. This validated framework allowed comparisons of desalination methods at their prescribed ranges of operational conditions that they were designed for. These conditions specify feed salinity ranges of 1.6 to 2.4 g/kg for Capacitive Deionization and Reverse Osmosis (RO), 2.8 to 4.2 g/kg for Electrodialysis, 28 to 42 g/kg for Thermovapor Compression and Humidification-Dehumidification, and 37 to 55 g/kg for Multi-Effect Distillation (MED). Despite different operational conditions, all models exhibit non-linear, positive correlation between energy consumption and system size in response to feed salinity and production rate. The framework is also employed in a cross-comparative analysis between MED and RO whose results suggest that energy intensity for MED is an order of magnitude greater than RO for the same operational conditions, but actual operational costs are comparable. Overall, the framework is ready for deployment in case studies of actual desalination plants.

42 ENGINEERING↗
DOE OSTI2024

Local Electric Field Effects on Water Dissociation in Bipolar Membranes Studied Using Core–Shell Catalysts

The local electric field strength is thought to affect the rate of water dissociation (WD) in bipolar membranes (BPMs) at the catalyst–nanoparticle surfaces. Here, we study core–shell nanoparticles, where the core is metallic, semiconducting, or insulating, to understand this effect. The nanoparticle cores were coated with a WD catalyst layer (TiO2 or HfO2) via atomic layer deposition (ALD), and the morphology was imaged with transmission electron microscopy. Irrespective of the core material, these core–shell catalysts displayed comparable WD overpotentials at optimal mass loading, despite the hypothesized differences in the electric field strength across the catalyst particle suggested by continuum electrostatic simulations. Substantial atomic interdiffusion between the core and shell was ruled out by X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, and diffuse reflectance optical measurements. However, the optimal mass loading of catalyst was roughly 1 order of magnitude higher for the conductive and high dielectric core materials than for the low dielectric insulating cores. These findings are consistent with the hypothesis that electric field screening within the core material focuses the electric field drop between particles such that larger film thicknesses can be tolerated. Collectively, these data support the idea that it is the local electric field at the molecular level that controls proton-transfer rates and that the metal core/dielectric-shell constructs introduced here modulate that field. Further materials and synthetic design may enable optimization of the electric field strength across the proton-transfer trajectory at the material surface.

Sarma, Prasad V↗
DOE OSTI2026

One-Body Properties and Their Perturbative Accuracy with Aufbau Suppressed Coupled Cluster Theory

In this work we derived and implemented the calculation of the one-body reduced density matrix for Aufbau suppressed coupled cluster theory, from which excited state natural orbitals and one-body properties, like atomic populations and dipole moments, are obtained. We utilized the natural orbitals to refine the ASCC solution for simple valence and Rydberg systems, exploring the process of repeatedly solving the ASCC equations in successive natural orbital bases to achieve independence from the starting molecular orbitals. For dipole moments in small molecules where high-level comparison data is available, we find that the accuracy of ASCC essentially matches that of linear response and equation-of-motion coupled cluster as long as care is taken to preserve the response's perturbative completeness.

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

Comparing the Effects of Side Chain Dipole–Dipole Interactions and Hydrogen Bonding on the Mechanical and Electrical Properties of Poly(3-hexylthiophene)

Poly(3-alkylthiophenes) are simple conjugated polymers with good electrical properties, but tend to be brittle, limiting their application. Here, we investigate how side chain modifications can improve their toughness without compromising their charge transport. Specifically, we compare a weak dipole–dipole interaction of ester groups with a stronger hydrogen-bonding interaction of the hydroxyl groups. Two copolymers with targeted 5 and 10 mol % ester-functionalized side chains were synthesized and hydrolyzed in the solid state to introduce hydroxyl groups. Both hydrolyzed polymers became insoluble in most organic solvents, providing a path to layer-by-layer solution processing. All polymers’ optical, thermal, structural, electrical, and mechanical properties were investigated. Optical spectroscopy revealed that functionalization at these low levels did not significantly affect aggregation or π–π stacking. Differential scanning calorimetry indicated reduced crystallinity in the functionalized copolymers compared to that of P3HT. Grazing-incidence wide-angle X-ray diffraction data showed that functionalization led to an increase in lamellar spacing without altering molecular orientation or π–π stacking. Mechanical testing highlighted that at the lower functionalization level, both ester and hydroxyl groups similarly enhanced toughness, suggesting that disorder, rather than the specific nature of the functional group, was responsible for these improvements. At the higher functionalization level, hydroxyl groups significantly increased the elastic modulus while also negatively impacting charge carrier mobility. This study suggests that with stronger hydrogen-bonding groups, only very small amounts can improve P3HT’s toughness. For a wider tunable range, it may be a better strategy to use weak interactions such as dipole–dipole interactions of ester groups.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Synchronous RNA conformational changes trigger ordered phase transitions in crystals

Time-resolved studies of biomacromolecular crystals have been limited to systems involving only minute conformational changes within the same lattice. Ligand-induced changes greater than several angstroms, however, are likely to result in solid-solid phase transitions, which require a detailed understanding of the mechanistic interplay between conformational and lattice transitions. Here we report the synchronous behavior of the adenine riboswitch aptamer RNA in crystal during ligand-triggered isothermal phase transitions. Direct visualization using polarized video microscopy and atomic force microscopy shows that the RNA molecules undergo cooperative rearrangements that maintain lattice order, whose cell parameters change distinctly as a function of time. The bulk lattice order throughout the transition is further supported by time-resolved diffraction data from crystals using an X-ray free electron laser. The synchronous molecular rearrangements in crystal provide the physical basis for studying large conformational changes using time-resolved crystallography and micro/nanocrystals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Na ion dynamics in P2-Na x [Ni 1/3 Ti 2/3 ]O 2 : a combination of quasi-elastic neutron scattering and first-principles molecular dynamics study

In this work, the P2-type layered material Na 2/3 [Ni 1/3 Ti 2/3 ]O 2 was studied as a promising bi-functional electrode material for sodium-ion batteries. To assess the electrochemical performance of this material, we investigated the diffusion mechanism as well as ionic and electronic conductivity with a combination of experimental and computational techniques. The quasi-elastic neutron scattering (QENS) experiments and first-principles molecular dynamics (FPMD) simulations were performed to identify the diffusion mechanism. The QENS data showed that Na ion diffusion can be well described by the Singwi–Sjölander jump diffusion model, where the obtained mean jump length matched the distances between the neighboring edge-share and face-share Na sites. FPMD predicted diffusivity values similar to those from QENS. The computed composition dependence of ionic and electronic conductivity of Na x [Ni 1/3 Ti 2/3 ]O 2 suggested that electronic conductivity changes significantly when x deviates from 2/3 as the redox couple of Ni and Ti is activated, while the change of ionic conductivity with x is relatively small.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Porting fragmentation methods to GPUs using an OpenMP API: Offloading the resolution-of-the-identity second-order Møller–Plesset perturbation method

Here, using an OpenMP Application Programming Interface, the resolution-of-the-identity second-order Møller–Plesset perturbation (RI-MP2) method has been off-loaded onto graphical processing units (GPUs), both as a standalone method in the GAMESS electronic structure program and as an electron correlation energy component in the effective fragment molecular orbital (EFMO) framework. First, a new scheme has been proposed to maximize data digestion on GPUs that subsequently linearizes data transfer from central processing units (CPUs) to GPUs. Second, the GAMESS Fortran code has been interfaced with GPU numerical libraries (e.g., NVIDIA cuBLAS and cuSOLVER) for efficient matrix operations (e.g., matrix multiplication, matrix decomposition, and matrix inversion). The standalone GPU RI-MP2 code shows an increasing speedup of up to 7.5× using one NVIDIA V100 GPU with one IBM 42-core P9 CPU for calculations on fullerenes of increasing size from 40 to 260 carbon atoms using the 6-31G(d)/cc-pVDZ-RI basis sets. A single Summit node with six V100s can compute the RI-MP2 correlation energy of a cluster of 175 water molecules using the correlation consistent basis sets cc-pVDZ/cc-pVDZ-RI containing 4375 atomic orbitals and 14 700 auxiliary basis functions in ~0.85 h. In the EFMO framework, the GPU RI-MP2 component shows near linear scaling for a large number of V100s when computing the energy of an 1800-atom mesoporous silica nanoparticle in a bath of 4000 water molecules. The parallel efficiencies of the GPU RI-MP2 component with 2304 and 4608 V100s are 98.0% and 96.1%, respectively.

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

Time-resolved atomic-resolution Brownian tomography of single nanocrystals reveals size-dependent dynamics

Atomic-resolution structure identification of nanocrystals by graphene liquid cell electron microscopy (GLC-EM) has revealed that small, solubilized platinum nanocrystals consist of an ordered crystalline core surrounded by mobile surface atoms, which dissociate during oxidative etching, resulting in distinct temporal structural states. Requirements imposed by the 3D reconstruction algorithm limit the number of structural states that can be resolved. We introduce a regularized 3D reconstruction algorithm that exploits the redundancy inherent in the experimental data, allowing us to improve the time resolution. Our developments provide a comprehensive molecular picture at unprecedented spatial and temporal resolution of the nonlinear, linear, and fluctuating dynamic phenomena that single nanocrystals undergo during the GLC-EM experiment. We determined atomic structures of 66 temporal structural states, extracted from 15 time trajectories of individual nanocrystals. Large (478 to 698 atoms) and small (<300 atoms) nanocrystals show etching that preserves a stable core, whereas mid-sized (351 to 571 atoms) nanocrystals present dynamics that change the coordination of the core.

Meana-Pañeda, Rubén↗