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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

From Protein Design to the Energy Landscape of a Cold Unfolding Protein

Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein–water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ~0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Molecular Level Understanding of the Free Energy Landscape in Early Stages of Metal-Organic Framework Nucleation

The assembly mechanism of hierarchical materials controlled by the choice of solvent and presence of spectator ions. In this paper, we use enhanced sampling molecular dynamics methods to investigate these effects on the configurational landscape of metal-linker interactions in the early stages of synthesis, using MIL-101(Cr) as a prototypical example. Microsecond-long well-tempered metadynamics (WTmetaD) uncover a complex free energy structural landscape, with distinct crystal (C) and non-crystal (NC) like configurations and their equilibrium population. In presence of ions (Na+, F-), we observe a complex effect on the crystallinity of secondary building units (SBUs), by encouraging/suppressing salt bridges between C configurations and consequently controlling the percentage of defects. Solvent effects are assessed by introducing N, N-dimethylformamide (DMF) instead of water, where SBU adducts are appreciably more stable and compact. These results shed light on how solvent nature and ionic strength impact the free energy of nucleation phenomena that ultimately control materials synthesis and defect formation. The work described in this publication was supported by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences and performed at Pacific Northwest National Laboratory (PNNL). The authors acknowledge the use of the UCL Legion High Performance Computing Facility (Legion @ UCL) and associated support services in the completion of this work. This research used resources of the National Energy Research Scientific Computing Centre, a DOE Office of Science User Facility. Battelle operates PNNL for DOE under Contract DE-AC05-76RL01830.

Kollias, Loukas↗
DOE OSTI2017

Influence of landscape heterogeneity on water available to tropical forests in an Amazonian catchment and implications for modeling drought response: Water Available to Tropical Forest

The Amazon basin experienced periodic droughts in the past, and climate models projected more intense and frequent droughts in the future. How tropical forests respond to drought may depend on water availability, which is modulated by landscape heterogeneity. Using the one-dimensional ACME Land Model (ALM) and the three-dimensional ParFlow variably saturated flow model, a series of numerical experiments were performed for the Asu catchment in central Amazon to elucidate processes that influence water available for plant use and provide insights for improving Earth system models. Results from ParFlow show that topography has a dominant influence on groundwater table and runoff through lateral flow. Without any representations of lateral processes, ALM simulates very different seasonal variations in groundwater table and runoff compared to ParFlow even if it is able to reproduce the long-term spatial average groundwater table of ParFlow through simple parameter calibration. In the ParFlow simulations, the groundwater table is evidently deeper and the soil saturation is lower in the plateau compared to the valley. However, even in the plateau during the dry season in the drought year of 2005, plant transpiration is not water stressed in the ParFlow simulations as the soil saturation is still sufficient to maintain a soil matric potential for the stomata to be fully open. This finding is insensitive to uncertainty in atmospheric forcing and soil parameters, but the empirical wilting formulation used in the models is an important factor that should be addressed using observations and modeling of coupled plant hydraulics-soil hydrology processes in future studies.

Fang, Yilin↗
DOE OSTI2017

Microbial diversity in an intensively managed landscape is structured by landscape connectivity

Intensively managed land increases the rate of nutrient and particle transport within a basin, but the impact of these changes on microbial community assembly patterns at the basin scale is not yet understood. The objective of this study was to investigate how landscape connectivity and dispersal impacts microbial diversity in an agricultural-dominated watershed. We characterized soil, sediment and water microbial communities along the Upper Sangamon River basin in Illinois-a 3600 km 2 watershed strongly influenced by human activity, especially landscape modification and extensive fertilization for agriculture. We employed statistical and network analyses to reveal the microbial community structure and interactions in the critical zone (water, soil and sediment media). Using a Bayesian source tracking approach, we predicted microbial community connectivity within and between the environments. We identified strong connectivity within environments (up to 85.4 ± 13.3% of sequences in downstream water samples sourced from upstream samples, and 44.7 ± 26.6% in soil and sediment samples), but negligible connectivity across environments, which indicates that microbial dispersal was successful within but not between environments. Species sorting based on sample media type and environmental parameters was the dominant driver of community dissimilarity. Lastly, we constructed operational taxonomic unit association networks for each environment and identified a number of co-occurrence relationships that were shared between habitats, suggesting that these are likely to be ecologically significant.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Combined Force-Frequency Sampling for Simulation of Systems Having Rugged Free Energy Landscapes.

An adaptive, machine learning-based sampling method is presented for simulation of systems having rugged, multidimensional free energy landscapes. The method's main strength resides in its ability to learn both from the frequency of visits to distinct states and the generalized force estimates that arise in a system as it evolves in phase space. This is accomplished by introducing a self-integrating artificial neural network, which generates an estimate of the free energy directly from its derivatives. The usefulness of the proposed combined approach is examined in the context of two concrete examples, namely, an alanine dipeptide molecule in water and a polymer diffusing through a narrow pore. This new method is found to be robust, faster, and more accurate than approaches that rely only on frequency-based or generalized force-based estimations. After combining the proposed approach with overfill protection and support for sparse data storage and training, the method is shown to be more effective than comparable, previously available techniques and capable of scaling efficiently to larger numbers of collective variables.

Sevgen, Emre↗
DOE OSTI2018

Free-Energy Landscape of the Dissolution of Gibbsite at High pH

The individual elementary reactions involved in the dissolution of a solid into solution remain mostly speculative due to a lack of direct experimental probes. In this regard, in this paper we have applied atomistic simulations to map the free-energy landscape of the dissolution of gibbsite from a step edge as a model of metal hydroxide dissolution. The overall reaction combines kink formation and kink propagation. Two individual reactions were found to be rate-limiting for kink formation, that is, the displacement of Al from a step site to a ledge adatom site and its detachment from ledge/terrace adatom sites into the solution. Finally, as a result, a pool of mobile and labile adsorbed species, or adatoms, exists before the release of Al into solution. Because of the quasi-hexagonal symmetry of gibbsite, kink site propagation can occur in multiple directions. Overall, our results will enable the development of microscopic mechanistic models of metal oxide dissolution.

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

Bootstrap and amplitudes: a hike in the landscape of quantum field theory

This article is an introduction to two currently very active research programs, the Conformal Bootstrap and Scattering Amplitudes. Rather than attempting full surveys, the emphasis is on common ideas and methods shared by these two seemingly very different programs. In both fields, mathematical and physical constraints are placed directly on the physical observables in order to explore the landscape of possible consistent quantum field theories. We give explicit examples from both programs: the reader can expect to encounter boiling water, ferromagnets, pion scattering, and emergent symmetries on this journey into the landscape of local relativistic quantum field theories. Here, the first part is written for a general physics audience. The second part includes further details, including a new on-shell bottom-up reconstruction of the CP 1 model with the Fubini-Study metric arising from re-summation of the n-point interaction terms derived from amplitudes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Local random potentials of high differentiability to model the Landscape

We generate random functions locally via a novel generalization of Dyson Brownian motion, such that the functions are in a desired differentiability class C{sup k}, while ensuring that the Hessian is a member of the Gaussian orthogonal ensemble (other ensembles might be chosen if desired). Potentials in such higher differentiability classes (k≥2) are required/desirable to model string theoretical landscapes, for instance to compute cosmological perturbations (e.g., k=2 for the power-spectrum) or to search for minima (e.g., suitable de Sitter vacua for our universe). Since potentials are created locally, numerical studies become feasible even if the dimension of field space is large (D∼100). In addition to the theoretical prescription, we provide some numerical examples to highlight properties of such potentials; concrete cosmological applications will be discussed in companion publications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Tundra landscape heterogeneity, not interannual variability, controls the decadal regional carbon balance in the Western Russian Arctic

Across the Arctic, the net ecosystem carbon (C) balance of tundra ecosystems is highly uncertain due to substantial temporal variability of C fluxes and to landscape heterogeneity. We modeled both carbon dioxide (CO2) and methane (CH4) fluxes for the dominant regional land cover types in a sub-Arctic tundra region in northeast European Russia for the period of 2006-2015 using coupled biogeochemical and permafrost models. Modeled net annual CO2 fluxes ranged from -300 g C m-2 y-1 [net uptake] in a willow fen to 3 g C m-2 y-1 [net source] in dry lichen tundra. Modeled annual CH4 emissions ranged from -0.2 to 22.3 g C m-2 y-1 at a peat plateau site and a willow fen site, respectively. Interannual variability over the decade was relatively small (20-30%) in comparison to variability among the land cover types (120-225%). Using high-resolution land cover classification, the region was a net sink of atmospheric CO2 across most land cover types but a net source of CH4 to the atmosphere due to high emissions from permafrost-free fens. Using a lower-resolution for land cover classification resulted in a 20-65% underestimation of regional CH4 flux and smaller (10%) overestimation of regional CO2 uptake, leading to an overall overestimation of the regional GHG sink by 90% due to the underestimation of wetland extent by 60%. Accurately capturing the relative fraction of uplands versus wetlands was key to determining the net regional C balance but required high (<25-30 m) spatial resolution.

Treat, Claire↗
DOE OSTI2014

The Energy Landscape of Uranyl-Peroxide Species

Nanoscale uranyl peroxide clusters containing UO22+ groups bonded through peroxide bridges to form polynuclear molecular species (polyoxometalates) exist both in solution and in the solid state. There is an extensive family of clusters containing 28 uranium atoms (U28 clusters), with an encapsulated anion in the center, for example, [UO2(O2)3-x(OH)x4-], [Nb(O2)43-], or [Ta(O2)43-]. The negative charge of these clusters is balanced by alkali ions, both encapsulated, and located exterior to the cluster. The present study reports measurement of enthalpy of formation for two such U28 compounds, one of which is uranyl centered and the other is peroxotantalate centered. The [(Ta(O2)4]-centered U28 capsule is energetically more stable than the [(UO2)(O2)3]-centered capsule. These data, along with our prior studies on other uranyl–peroxide solids, are used to explore the energy landscape and define thermochemical trends in alkali–uranyl–peroxide systems. It was suggested that the energetic role of charge-balancing alkali ions and their electrostatic interactions with the negatively charged uranyl–peroxide species is the dominant factor in defining energetic stability. These experimental data were supported by DFT calculations, which agree that the [(Ta(O2)4]-centered U28 capsule is more stable than the uranyl-centered capsule. Moreover, the relative stability is controlled by the interactions of the encapsulated alkalis with the encapsulated anion. Thus, the role of alkali-anion interactions was shown to be important at all length scales of uranyl–peroxide species: in both comparing clusters to clusters; and clusters to monomers or extended solids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Communication: Theoretical prediction of free-energy landscapes for complex self-assembly

We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity of the target assembly. By considering the designed interactions separately from weaker, incidental interactions, our approach yields predictions for the equilibrium yield and nucleation barriers. These predictions are in good agreement with corresponding Monte Carlo simulations. We show that a few fundamental properties of the connectivity graph determine the most prominent features of the assembly thermodynamics. Surprisingly, we find that polydispersity in the strengths of the designed interactions stabilizes intermediate structures and can be used to sculpt the free-energy landscape for self-assembly. Finally, we demonstrate that weak incidental interactions can preclude assembly at equilibrium due to the combinatorial possibilities for incorrect association.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Developing a landscape of urban building energy use with improved spatiotemporal representations in a cool-humid climate

Urban buildings account for up to 75% of total energy use in the United States (U.S.). Understanding urban building energy use is important for developing feasible options to mitigate energy use and greenhouse gas emissions. In this study, an improved bottom-up building energy use model, named City Building Energy Use Model (City-BEUM), was developed to estimate building energy use for all buildings in Polk County, Iowa. First, 28 commercial and 6 residential building prototypes were designed by combing Assessor's parcel data and building footprint data. Then, the EnergyPlus in the CityBEUM was calibrated for all building prototypes using the U.S. Energy Information Administration's survey data, monthly utility meter data, and actual weather data. Finally, spatial and temporal variations of building energy use in the study area were estimated using the CityBEUM. Results indicate that the spatial variation of building energy use in the study area can be captured using the CityBEUM. With the monthly-calibrated model, the temporal pattern of urban building energy use can be well represented. The comparison of building energy use using the Typical Meteorological Year and actual weather data demonstrates the importance of using actual weather data in building energy modeling for an improved temporal representation.

CityBEUM, Urban building energy use, High spatiote↗