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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes: Targeted quantification of functional enzyme dynamics

Microbially mediated biogeochemical processes are catalyzed by enzymes that control the transformation of carbon, nitrogen, and other elements in environment. The dynamic linkage between enzymes and biogeochemical species transformation has, however, rarely been investigated because of the lack of analytical approaches to efficiently and reliably quantify enzymes and their dynamics in soils and sediments. Herein, we developed a signature peptide-based technique for sensitively quantifying dissimilatory and assimilatory enzymes using nitrate-reducing enzymes in a hyporheic zone sediment as an example. Moreover, the measured changes in enzyme concentration were found to correlate with the nitrate reduction rate in a way different from that inferred from biogeochemical models based on biomass or functional genes as surrogates for functional enzymes. This phenomenon has important implications for understanding and modeling the dynamics of microbial community functions and biogeochemical processes in environments. Our results also demonstrate the importance of enzyme quantification for the identification and interrogation of those biogeochemical processes with low metabolite concentrations as a result of faster enzyme-catalyzed consumption of metabolites than their production. The dynamic enzyme behaviors provide a basis for the development of enzyme-based models to describe the relationship between the microbial community and biogeochemical processes.

Li, Minjing↗
DOE OSTI2014

Real time quantum dynamics preaveraged over imaginary time path integral: A formal basis for both Centroid Molecular Dynamics and Ring Polymer Molecular Dynamics

An exact real time quantum dynamics preaveraged over imaginary time path integral is formulated for general condensed phase equilibrium ensemble. This formulation results in the well-known centroid dynamics approach upon filtering of centroid constraint, and provides a rigorous framework to understand and analyze a related quantum dynamics approximation method called ring polymer molecular dynamics. The formulation also serves as the basis for developing new kinds of quantum dynamics that utilize the cyclic nature of the imaginary time path integral.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Dynamic Analysis of Hybrid Energy Systems under Flexible Operation and Variable Renewable Generation -- Part I: Dynamic Performance Analysis and Part II: Dynamic Cost

Dynamic analysis of hybrid energy systems (HES) under flexible operation and variable renewable generation is considered in order to better understand various challenges and opportunities associated with the high system variability arising from the integration of renewable energy into the power grid. Unique consequences are addressed by devising advanced HES solutions in which multiple forms of energy commodities, such as electricity and chemical products, may be exchanged. Dynamic models of various unit operations are developed and integrated within two different HES options. One HES option, termed traditional, produces electricity only and consists of a primary heat generator (PHG) (e.g., a small modular reactor), a steam turbine generator, a wind farm, and a battery storage. The other HES option, termed advanced, includes not only the components present in the traditional option but also a chemical plant complex to repurpose excess energy for non-electricity services, such as for the production of chemical goods (e.g., transportation fuel). In either case, a given HES is connected to the power grid at a point of common coupling and requested to deliver a certain electricity generation profile as dictated by a regional power grid operator based on a predicted demand curve. Dynamic analysis of these highly-coupled HES are performed to identify their key dynamical properties and limitations and to prescribe solutions for best managing and mitigating the high variability introduced from incorporating renewable energy into the energy mix. A comparative dynamic cost analysis is also conducted to determine best HES options. The cost function includes a set of metrics for computing fixed costs, such as fixed operations and maintenance (O&M) and overnight capital costs, and also variable operational costs, such as cost of variability, variable O&M cost, and cost of environmental impact, together with revenues. Assuming different options for implementing PHG (e.g., natural gas, coal, nuclear), preliminary results identify the level of renewable penetration at which a given advanced HES option (e.g., a nuclear hybrid) becomes increasingly more economical than a traditional electricity-only generation solution. Conditions are also revealed under which carbon resources may be better utilized as carbon sources for chemical production rather than as combustion material for electricity generation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2015

Communication: Relation of centroid molecular dynamics and ring-polymer molecular dynamics to exact quantum dynamics

We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the “Classical Wigner” approximation. Here, we show that the further approximation of this “Matsubara dynamics” gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Dynamic Stabilization of Metal Oxide–Water Interfaces

The interaction of water with metal oxide surfaces plays a crucial role in the catalytic and geochemical behavior of metal oxides. In a vast majority of studies, the interfacial structure is assumed to arise from a relatively static lowest energy configuration of atoms, even at room temperature. Using hematite (α-Fe 2 O 3 ) as a model oxide, we show through a direct comparison of in situ synchrotron X-ray scattering with density functional theory-based molecular dynamics simulations that the structure of the ($1\bar{10}2 $) termination is dynamically stabilized by picosecond water exchange. Simulations show frequent exchanges between terminal aquo groups and adsorbed water in locations and with partial residence times consistent with experimentally determined atomic sites and fractional occupancies. Frequent water exchange occurs even for an ultrathin adsorbed water film persisting on the surface under a dry atmosphere. The resulting time-averaged interfacial structure consists of a ridged lateral arrangement of adsorbed water molecules hydrogen bonded to terminal aquo groups. Surface pK a prediction based on bond valence analysis suggests that water exchange will influence the proton-transfer reactions underlying the acid/base reactivity at the interface. Our findings provide important new insights for understanding complex interfacial chemical processes at metal oxide–water interfaces.

58 GEOSCIENCES↗
DOE OSTI2013

Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling

Here, neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Two-temperature model in molecular dynamics simulations of cascades in Ni-based alloys

In high-energy irradiation events, energy from the fast moving ion is transferred to the system via nuclear and electronic energy loss mechanisms. The nuclear energy loss results in the creation of point defects and clusters, while the energy transferred to the electrons results in the creation of high electronic temperatures, which can affect the damage evolution. We perform molecular dynamics simulations of 30 keV and 50 keV Ni ion cascades in nickel-based alloys without and with the electronic effects taken into account. We compare the results of classical molecular dynamics (MD) simulations, where the electronic effects are ignored, with results from simulations that include the electronic stopping only, as well as simulations where both the electronic stopping and the electron-phonon coupling are incorporated, as described by the two temperature model (2T-MD). Our results indicate that the 2T-MD leads to a smaller amount of damage, more isolated defects and smaller defect clusters.

Zarkadoula, Eva↗
DOE OSTI2015

Solution Phase Exciton Diffusion Dynamics of a Charge-Transfer Copolymer PTB7 and a Homopolymer P3HT

Using ultrafast polarization-controlled transient absorption (TA) measurements, dynamics of the initial exciton states were investigated on the time scale of tens of femtoseconds to about 80 ps in two different types of conjugated polymers extensively used in active layers of organic photovoltaic devices. These polymers are poly(3-fluorothienothiophenebenzodithiophene) (PTB7) and poly-3-hexylthiophene (P3HT), which are charge-transfer polymers and homopolymers, respectively. In PTB7, the initial excitons with excess vibrational energy display two observable ultrafast time constants, corresponding to coherent exciton diffusion before the vibrational relaxation, and followed by incoherent exciton diffusion processes to a neighboring local state after the vibrational relaxation. In contrast, P3HT shows only one exciton diffusion or conformational motion time constant of 34 ps, even though its exciton decay kinetics are multiexponential. Based on the experimental results, an exciton dynamics mechanism is conceived taking into account the excitation energy and structural dependence in coherent and incoherent exciton diffusion processes, as well as other possible deactivation processes including the formation of the pseudo-charge-transfer and charge separate states, as well as interchain exciton hopping or coherent diffusion.

36 MATERIALS SCIENCE↗
DOE OSTI2014

A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

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

Lattice dynamics and thermoelectric properties of nanocrystalline silicon-germanium alloys: Lattice dynamics and thermoelectric properties of nc Si-Ge alloys

The lattice dynamics and thermoelectric properties of sintered phosphorus-doped nanostructured silicon–germanium alloys obtained by gas-phase synthesis were studied. Measurements of the density of phonon states by inelastic neutron scattering were combined with measurements of the elastic constants and the low-temperature heat capacity. A strong influence of nanostructuring and alloying on the lattice dynamics was observed. The thermoelectric transport properties of samples with different doping as well as samples sintered at different temperature were characterized between room temperature and 1000°C. A peak figure of merit zT=0.88 at 900°C is observed and is comparatively insensitive to the aforementioned parameter variations.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structure, Dynamics, and Hydrogen Transport in Amorphous Polymers: An Analysis of the Interplay between Free Volume Element Distribution and Local Segmental Dynamics from Molecular Dynamics Simulations

Polymers are attractive membrane materials owing to their mechanical robustness and relatively inexpensive fabrication. An important indicator of membrane performance are free volume elements (FVE): microporous void spaces created by the inefficient packing of bulky groups along the polymer chain. FVEs tend to degrade over time, as polymer chains reorganize irreversibly. While it is widely accepted that polymer flexibility has an impact on membrane transport properties, the molecular nature of this impact is still not well understood. By the establishment of a correlation between local chain dynamics and the distribution of free volume elements (FVEs), penetrant transport can be regulated more efficiently in amorphous polymer membranes. In this work, we implement all-atom molecular dynamics (MD) simulations to explore the relationship between chain dynamics and free volume in three polymers with different levels of backbone flexibility: polymethylpentene (PMP), polystyrene (PS), and HAB-6FDA thermally rearranged polymer (TRP). We construct these polymers at different temperatures and examine how temperature impacts the FVE distribution and segmental mobility. Our analysis shows that chain segments near FVEs have higher mobility compared with the atoms in the bulk; the extent of this difference increases with chain flexibility. Increasing the chain flexibility by increasing the temperature results in a broader FVE distribution. Rigid polymers such as TRP show the most robust FVE distribution and are not significantly affected by the temperature change. To capture penetrant diffusion through the polymer matrix, hydrogen is inserted and the diffusion is measured at different temperatures; hydrogen mobility is influenced by the FVE structure and overall mobility of polymer chains. Lastly, at low temperatures, hydrogen mobility is influenced by void distribution, while at high temperatures, polymer dynamics dictate hydrogen transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Lattice thermal conductivity of UO{sub 2} using ab-initio and classical molecular dynamics

We applied the non-equilibrium ab-initio molecular dynamics and predict the lattice thermal conductivity of the pristine uranium dioxide for up to 2000 K. We also use the equilibrium classical molecular dynamics and heat-current autocorrelation decay theory to decompose the lattice thermal conductivity into acoustic and optical components. The predicted optical phonon transport is temperature independent and small, while the acoustic component follows the Slack relation and is in good agreement with the limited single-crystal experimental results. Considering the phonon grain-boundary and pore scatterings, the effective lattice thermal conductivity is reduced, and we show it is in general agreement with the sintered-powder experimental results. The charge and photon thermal conductivities are also addressed, and we find small roles for electron, surface polaron, and photon in the defect-free structures and for temperatures below 1500 K.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Nanoscale dynamics and aging of fibrous peptide-based gels

Solutions of the aromatic dipeptide derivative molecule fluorenylmethoxycarbonyl-diphenylalanine (Fmoc-FF) in dimethyl sulfoxide produce fibrous gels when mixed with water. We study the evolution of density fluctuations of this three-component system using X-ray photon correlation spectroscopy (XPCS) and compare these results to the macroscopic rheology of the gels and optical observations of the microstructure evolution. At the investigated scattering angles, the intensity autocorrelation functions do not follow behavior expected for simple diffusion of individual Fmoc-FF molecules localized within cages of nearest neighbors. Instead, the dynamics are associated with density fluctuations on length scales of ∼10–100 nm arising from disaggregation and reformation of fibers, leading to an increasingly uniform network. This process is correlated with the growth of the elastic modulus, which saturates at long times. Autocorrelation functions and relaxation times acquired from XPCS measurements are consistent with relaxation rates of structures at dynamic equilibrium. This study provides further support to the concept of exploring peptide-based gelators as valence-limited patchy particles capable of forming equilibrium gels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗