Engineering topics

Bell, David R.

Publications and source records attributed to Bell, David R..

6 records

DOE OSTI2022

Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes

We report two-dimensional (2D) nanomaterials such as graphene are increasingly used in research and industry for various biomedical applications. Extensive experimental and theoretical studies have revealed that 2D nanomaterials are promising drug delivery vehicles, yet certain materials exhibit toxicity under biological conditions. So far, it is known that 2D nanomaterials possess strong adsorption propensities for biomolecules. To mitigate potential toxicity and retain favorable physical and chemical properties of 2D nanomaterials, it is necessary to explore the underlying mechanisms of interactions between biomolecules and nanomaterials for the subsequent design of biocompatible 2D nanomaterials for nanomedicine. The purpose of this review is to integrate experimental findings with theoretical observations and facilitate the study of 2D nanomaterial interaction with biomolecules at the molecular level. We discuss the current understanding and progress of 2D nanomaterial interaction with proteins, lipid membranes, and DNA based on molecular dynamics (MD) simulation. In this review, we focus on the 2D graphene nanosheet and briefly discuss other 2D nanomaterials. With the ever-growing computing power, we can image nanoscale processes using MD simulation that are otherwise not observable in experiment. We expect that molecular characterization of the complex behavior between 2D nanomaterials and biomolecules will help fulfill the goal of designing effective 2D nanomaterials as drug delivery platforms.

2D nanomaterials↗

DOE OSTI2021

Dynamics-Based Peptide–MHC Binding Optimization by a Convolutional Variational Autoencoder: A Use-Case Model for CASTELO

An unsolved challenge in the development of antigen-specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen–major histocompatibility complex (MHC) binding is paramount toward achieving this goal. Here, we apply CASTELO, a combined machine learning-molecular dynamics (ML-MD) approach, to identify per-residue antigen binding contributions and then design novel antigens of increased MHC-II binding affinity for a type 1 diabetes-implicated system. We build upon a small-molecule lead optimization algorithm by training a convolutional variational autoencoder (CVAE) on MD trajectories of 48 different systems across four antigens and four HLA serotypes. We develop several new machine learning metrics including a structure-based anchor residue classification model as well as cluster comparison scores. ML-MD predictions agree well with experimental binding results and free energy perturbation-predicted binding affinities. Moreover, ML-MD metrics are independent of traditional MD stability metrics such as contact area and root-mean-square fluctuations (RMSF), which do not reflect binding affinity data. Finally, our work supports the role of structure-based deep learning techniques in antigen-specific immunotherapy design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2014

Water Content of Earth's Continental Mantle Is Controlled by the Circulation of Fluids or Melts

A key mission of the ARES Directorate at JSC is to constrain models of the formation and geological history of terrestrial planets. Water is a crucial parameter to be measured with the aim to determine its amount and distribution in the interior of Earth, Mars, and the Moon. Most of that "water" is not liquid water per se, but rather hydrogen dissolved as a trace element in the minerals of the rocks at depth. Even so, the middle layer of differentiated planets, the mantle, occupies such a large volume and mass of each planet that when it is added at the planetary scale, oceans worth of water could be stored in its interior. The mantle is where magmas originate. Moreover, on Earth, the mantle is where the boundary between tectonic plates and the underlying asthenosphere is located. Even if mantle rocks in Earth typically contain less than 200 ppm H2O, such small quantities have tremendous influence on how easily they melt (i.e., the more water there is, the more magma is produced) and deform (the more water there is, the less viscous they are). These two properties alone emphasize that to understand the distribution of volcanism and the mechanism of plate tectonics, the water content of the mantle must be determined - Earth being a template to which all other terrestrial planets can be compared.

Peslier, Anne↗

NASA NTRS2012

Metasomatic Control of Water in Garnet and Pyroxene from Kaapvaal Craton Mantle Xenoliths

Fourier transform infrared spectrometry (FTIR) and laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) were used to determine water, rare earth (REE), lithophile (LILE), and high field strength (HFSE) element contents in garnet and pyroxene from mantle xenoliths, Kaapvaal craton, southern Africa. Water enters these nominally anhydrous minerals as protons bonded to structural oxygen in lattice defects. Pyroxene water contents (150-400 ppm in clinopyroxene; 40-250 ppm in orthopyroxene) correlate with their Al, Fe, Ca and Na and are homogeneous within a mineral grains and a xenolith. Garnets from Jagersfontein are chemically zoned for Cr, Ca, Ti and water contents. Garnets contain 0 to 20 ppm H2 Despite the fast diffusion rate of H in mantle m inerals, the observations above indicate that the water contents of mantle xenolith minerals were not disturbed during kimberlite entrainment and that the measured water data represent mantle values. Trace elements in all minerals show various degrees of light REE and LILE enrichments indicative of minimal to strong metasomatism. Water contents of peridotite minerals from the Kaapvaal lithosphere are not related to the degree of depletion of the peridotites. Instead, metasomatism exerts a clear control on the amount of water of mantle minerals. Xenoliths from each location record specific types of metasomatism with different outcomes for the water contents of mantle minerals. At pressures . 5.5 GPa, highly alkaline melts metasomatized Liqhobong and Kimberley peridotites, and increased the water contents of their olivine, pyroxenes and garnet. At higher pressures, the circulation of ultramafic melts reacting with peridotite resulted in co-variation of Ca, Ti and water at the edge of garnets at Jagersfontein, overall decreasing their water content, and lowered the water content of olivines at Finsch Mine. The calculated water content of these melts varies depending on whether the water content of the peridotite (2 wt% HO. 2O) or individual m inerals (<0.5-13 wt% H2O) are used, and also depend on the mineral-melt water partition coefficients. These metasomatic events are thought to have occurred during the Archean and Proterozoic, meaning that the water contents measured here have been preserved since that time and can be used to investigate viscocity and longevity of cratonic mantle roots.

Peslier, Anne H.↗

NASA NTRS2011

The Role of Water in the Stability of Cratonic Keels

Cratons are typically underlain by large, deep, and old lithospheric keels (to greater than 200 km depth, greater than 2.5 Ga old) projecting into the asthenosphere (e.g., Jordan, 1978; Richardson et al., 1984). This has mystified Earth scientists as the dynamic and relatively hot asthenosphere should have eroded away these keels over time (e.g., Sleep, 2003; O'Neill et al., 2008; Karato, 2010). Three key factors have been invoked to explain cratonic root survival: 1) Low density makes the cratonic mantle buoyant (e.g., Poudjom Djomani et al., 2001). 2) Low temperatures (e.g., Pollack, 1986; Boyd, 1987), and 3) low water contents (e.g., Pollack, 1986), would make cratonic roots mechanically strong. Here we address the mechanism of the longevity of continental mantle lithosphere by focusing on the water parameter. Although nominally anhydrous , olivine, pyroxene and garnet can accommodate trace amounts of water in the form of H bonded to structural O in mineral defects (e.g., Bell and Rossman, 1992). Olivine softens by orders of magnitude if water (1-1000 ppm H2O) is added to its structure (e.g., Mackwell et al., 1985). Our recent work has placed constraints on the distribution of water measured in peridotite minerals in the cratonic root beneath the Kaapvaal in southern Africa (Peslier et al., 2010). At P greater than 5 GPa, the water contents of pyroxene remain relatively constant while those of olivine systematically decrease from 50 to less than 10 ppm H2O at 6.4 GPa. We hypothesized that at P greater than 6.4 GPa, i.e. at the bottom of the cratonic lithosphere, olivines are essentially dry (greater than 10 ppm H2O). As olivine likely controls the rheology of the mantle, we calculated that the dry olivines could be responsible for a contrast in viscosity between cratonic lithosphere and surrounding asthenosphere large enough to explain the resistance of cratonic root to asthenospheric delamination.

Peslier, Anne H.↗

NASA NTRS1994

D/H ratios and H2O contents of mantle-derived amphibole megacrysts from Dish Hill, California

D/H ratios are, in principle, useful in characterizing reservoirs of mantle hydrogen and as tracers of volatile transfer processes in Earth's interior. In practice, however, interpretation of isotopic measurements on mantle derived H is complicated by surface processes such as contamination and degassing which may alter the primary D/H ratio. Although there are indications that water associated with subduction zones and certain chemically enriched basalts is enriched in D relative to 'typical' upper mantle water, the extent of isotopic heterogeneity of mantle H remains uncertain. Kaersutitic amphibole megacrysts in alkaline basalts are one of the most widespread sources of mantle water and are therefore potentially useful for large-scale regional studies of D/H variation. However, D/H ratios of these amphiboles vary widely (from plus 8 to minus 113 percent), even in samples from the same locality, so that this potential has yet to be realized. In order to investigate the origin of this variability, and to explore the possibility that primary mantle D/H ratios may be deduced from these amphiboles, we analyzed the D/H ratios and chemical compositions of a suite of 17 kaersutitic amphiboles from Dish Hill, California. This work contrasts with previous studies in which sampling is widespread, but representatives from any given locality are few. Samples were collected from a restricted area on the southern flank of the volcanic center and are associated with the basal volcanic breccia. Fourteen of the samples were large single crystals or crystal fragments (megacrysts, 0.4 to 30 grams), believed to derive from pegmatitic veins crystallized from melts in the mantle. Two were coarse-grained intergrowths of amphibole with olivine and spinel, and one was a thin (2 mm) selvage on a peridotite xenolith.

Bell, David R.↗