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At least 37 records · Page 2

Modulating factors of hydrologic exchanges in a large-scale river reach: Insights from three-dimensional computational fluid dynamics simulations

Hyporheic exchange is a critical mechanism shaping hydrological and biogeochemical processes along a river corridor. Recent studies on quantifying the hyporheic exchange were mostly limited to local scales due to field inaccessibility, computational demand, and complexity of geomorphology and subsurface geology. Surface flow conditions and subsurface physical properties are well known factors on modulating the hyporheic exchange, but quantitative understanding of their impacts on the strength and direction of hyporheic exchanges at reach scales is absent. In this study, a high resolution computational fluid dynamics (CFD) model that couples surface and subsurface flow and transport is employed to simulate hyporheic exchanges in a 7-km long reach along the main-stem of the Columbia River. Assuming that the hyporheic exchange does not affect surface water flow conditions due to its negligible magnitude compared to the volume and velocity of river water, we developed a one-way coupled surface and subsurface water flow model using the commercial CFD software STAR-CCM+. The model integrates the Reynolds-averaged Navier-Stokes (RANS) equation solver with a realizable k-e two-layer turbulence model, a two-layer all y^+ wall treatment, and the volume of fluid (VOF) method, and is used to simulate hyporheic exchanges by tracking the free water-air interface as well as flow in the river and the subsurface porous media. The model is validated against measurements from acoustic Doppler current profiler (ADCP) in the stream water and hyporheic fluxes derived from a set of temperature profilers installed across the riverbed. The validated model is then employed to systematically investigate how hyporheic exchanges are influenced by surface water fluid dynamics strongly regulated by upstream dam operations, as well as subsurface structures (e.g. thickness of riverbed and subsurface formation layers) and hydrogeological properties (e.g. permeability). The results suggest that the thickness of riverbed alluvium layer is the dominant factor for reach-scale hyporheic exchanges, followed by the alluvium permeability, the depth of the underlying impermeable layer, and the assumption of hydrostatic pressure.

Bao, Jie↗

Modeling light-induced charge transfer dynamics across a metal-molecule-metal junction: Bridging classical electrodynamics and quantum dynamics

We develop a numerical approach for simulating light-induced charge transport dynamics across a metal-molecule-metal conductance junction. The finite-difference time-domain method is used to simulate the plasmonic response of the metal structures. The Huygens subgridding technique, as adapted to Lorentz media, is used to bridge the vastly disparate length scales of the plasmonic metal electrodes and the molecular system, maintaining accuracy. The charge and current densities calculated with classical electrodynamics are transformed to an electronic wavefunction, which is then propagated through the molecular linker via the Heisenberg equations of motion. We focus mainly on development of the theory and exemplify our approach by a numerical illustration of a simple system consisting of two silver cylinders bridged by a three-site molecular linker. The electronic subsystem exhibits fascinating light driven dynamics, wherein the charge density oscillates at the driving optical frequency, exhibiting also the natural system timescales, and a resonance phenomenon leads to strong conductance enhancement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mode specific dynamics of the H{sub 2} + CH{sub 3} → H + CH{sub 4} reaction studied using quasi-classical trajectory and eight-dimensional quantum dynamics methods

An eight-dimensional quantum dynamical model is proposed and applied to the title reaction. The reaction probabilities and integral cross sections have been determined for both the ground and excited vibrational states of the two reactants. The results indicate that the H{sub 2} stretching and CH{sub 3} umbrella modes, along with the translational energy, strongly promote the reactivity, while the CH{sub 3} symmetric stretching mode has a negligible effect. The observed mode specificity is confirmed by full-dimensional quasi-classical trajectory calculations. The mode specificity can be interpreted by the recently proposed sudden vector projection model, which attributes the enhancement effects of the reactant modes to their strong couplings with the reaction coordinate at the transition state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Controlling Proton Delivery with Catalyst Structural Dynamics

The fastest synthetic molecular catalysts for production and oxidation of H2 emulate components of the active site of natural hydrogenases. The role of controlled structural dynamics is recognized as a critical component in the catalytic performance of many enzymes, including hydrogenases, but is largely neglected in the design of synthetic molecular cata-lysts. In this work, the impact of controlling structural dynamics on the rate of production of H2 was studied for a series of [Ni(PPh2NC6H4-R2)2]2+ catalysts including R = n-hexyl, n-decyl, n-tetradecyl, n-octadecyl, phenyl, or cyclohexyl. A strong correlation was observed between the ligand structural dynamics and the rates of electrocatalytic hydrogen production in acetonitrile, acetonitrile-water, and protic ionic liquid-water mixtures. Specifically, the turnover frequencies correlate inversely with the rates of ring inversion of the amine-containing ligand, as this dynamic process dictates the positioning of the proton relay in the second coordination sphere and therefore governs protonation at either catalytically productive or non-productive sites. This study demonstrates that the dynamic processes involved in proton delivery can be controlled through modifications of the outer coordination sphere of the catalyst, similar to the role of the protein architecture in many enzymes. The present work provides new mechanistic insight into the large rate enhancements observed in aqueous protic ionic liquid media for the [Ni(PPh2NR2)]2+ family of catalysts. The incorporation of controlled structural dynamics as a design parameter to modulate proton delivery in molecular catalysts has enabled H2 production rates that are up to three orders of magnitude faster than the [Ni(PPh2NPh2)]2+complex. The observed turnover frequencies are up to 106 s-1 in acetonitrile-water, and over 107 s-1 in protic ionic liquid-water mixtures, with a minimal increase in overpotential. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, and was performed in part using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory, a DOE national scientific user facility located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for DOE.

electrocatalysis, structural dynamics↗

Dynamics of Confined Flexible and Unentangled Polymer Melts in Highly Adsorbing Cylindrical Pores

Inspired by the recent neutron spin echo experiments (NSE) designed to address the dynamic phenomena in polymer melts that are induced by interactions with a confining surface, we performedcoarse-grained molecular dynamics simulations to replicate the experimental results in order to provide new molecular insight for the observations. The results show excellent agreement in the values obtained for the normalized coherent single chain dynamic structure factor, S(Q;Dt)/S(Q;0) , between experiments and simulations. The simulations indicate that using different chain molecular weights that are used to achieve scattering contrast results in the uneven distribution of scatterers in the radial direction because lower molecular weight chains prefer to adsorb in the confining surface. In the bulk configuration, both simulations and experiments confirm that the polymer chains follow Rouse dynamics. However, under confinement, the Rouse modes are suppressed. The mean-squared radius of gyration, R2g, and the average relative shape anisotropy k2 of the conformation of the polymer chains indicate a pancake-like conformation near the surface and a bulk-like conformation near the center of the confining cylinder. Direct visualization of the polymers in the simulation confirm the pancake-like conformation of the adsorbed chains and the presence of trains, loops and tails in the region between the adsorbed chains and the chains not in contact with the surface. Despite the presence of these different conformations, the average form factor of the confined chains still follows the Debye function which describes linear ideal chains, which is in agreement with small angle neutron scattering (SANS) experiments. The experimentally inaccessible mean squared displacement of the confined monomers, calculated as a function of radial distance from the pore surface, was obtained in the simulations. The simulation shows a gradual increase of the MSD from the adsorbed, but mobile layer, to that similar to the bulk far away from the surface.

Carrillo, Jan-Michael Y.↗

Atomic-scale imaging of ultrafast materials dynamics

The advent of short-pulse electron and x-ray sources has enabled pump-probe approaches for elucidating ultrafast materials dynamics. From such studies, a comprehensive picture of the time-dependent evolution of the initial steps of energy deposition, propagation, relaxation, and conversion in a wide range of materials can be generated. In this article, we provide an overview of the capabilities of femtosecond electron and x-ray scattering for resolving structural dynamics of materials. With such approaches, time resolutions are ultimately limited by the durations of the electron and x-ray pulses, and dynamics can be studied at length scales spanning atomic to mesoscale dimensions. The articles in this issue represent a cross section of the vigorous activity occurring in the study of light-induced ultrafast materials dynamics as it relates to charge carriers, surfaces and interfaces, lattice-coupling mechanisms, coherent structural motions, and next-generation instrument development. Here, the approaches highlighted here are leading to new physical insights, new possibilities for engineering the properties of matter, and ultimately, a new understanding of materials functionality on ultrasmall and ultrashort spatiotemporal scales.

36 MATERIALS SCIENCE↗

DCS - A high flux beamline for time resolved dynamic compression science – Design highlights

The Dynamic Compression Sector (DCS) beamline, a national user facility for time resolved dynamic compression science supported by the National Nuclear Security Administration (NNSA) of the Department of Energy (DOE), has recently completed construction and is being commissioned at Sector 35 of the Advanced Photon Source (APS) at Argonne National Laboratory (ANL). The beamline consists of a First Optics Enclosure (FOE) and four experimental enclosures. A Kirkpatrick–Baez focusing mirror system with 2.2 mrad incident angles in the FOE delivers pink beam to the experimental stations. A refocusing Kirkpatrick–Baez mirror system is situated in each of the two most downstream enclosures. Experiments can be conducted in either white, monochromatic, pink or monochromatic-reflected beam mode in any of the experimental stations by changing the position of two interlocked components in the FOE. The beamline Radiation Safety System (RSS) components have been designed to handle the continuous beam provided by two in-line revolver undulators with periods of 27 and 30 mm, at closed gap, 150 mA beam current, and passing through a power limiting aperture of 1.5 x 1.0 mm{sup 2}. A novel pink beam end station stop [1] is used to stop the continuous and focused pink beam which can achieve a peak heat flux of 105 kW/mm{sup 2}. A new millisecond shutter design [2] is used to deliver a quick pulse of beam to the sample, synchronized with the dynamic event, the microsecond shutter, and the storage ring clock.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Dynamical properties of a room temperature ionic liquid: Using molecular dynamics simulations to implement a dynamic ion cage model [plus supplemental information]

The transport behavior of ionic liquids (ILs) is pivotal for a variety of applications, especially when ILs are used as electrolytes. Many aspects of the transport dynamics of ILs remain to be understood. Here, a common ionic liquid, 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimNTf 2 ), was studied with molecular dynamics simulations. The results show that BmimNTf 2 displays typical structural relaxation, subdiffusive behavior, and a breakdown of the Stokes-Einstein diffusion relation as in glass-forming liquids. In addition, the simulations show that the translational dynamics, reorientation dynamics, and structural relaxation dynamics are well described by the Vogel-Fulcher-Tammann equation like fragile glass forming liquids. Building on previous work that employed ion cage models, it was found that the diffusion dynamics of the cations and anions were well described by a hopping process random walk where the step time is the ion cage lifetime obtained from the cage correlation function. Detailed analysis of the ion cage structures indicated that the electrostatic potential energy of the ion cage dominates the diffusion dynamics of the caged ion. The ion orientational relaxation dynamics showed that ion reorientation is a necessary step for ion cage restructuring. The dynamic ion cage model description of ion diffusion presented here may have implications for designing ILs to control their transport behavior.

36 MATERIALS SCIENCE↗

Ultrafast population and structural dynamics of a Ni-bipyridine photoredox catalyst reveal a significant deactivation pathway

The ultrafast excited state pathways and dynamics of NiII-bipyridine complexes influence the yield of photochemical processes involved in their catalytic cross-coupling reactions. Here we present ultrafast Ni K x-ray emission spectroscopy (XES) and x-ray solution scattering (XSS) of a NiII-bipyridine aryl halide complex, [Ni(t-Bubpy)(o-tol)Br], to quantify the excited state population dynamics and structural changes of the pre-catalyst. Due to the local spin-sensitivity of XES, the population dynamics of metal-to-ligand charge transfer (MLCT) and metal-centered (MC) excited states is established. A rapid ground state recovery pathway is newly identified, representing a significant deactivation pathway during photocatalysis. Furthermore, the pseudotetrahedral structure of the long-lived MC excited state is unambiguously identified and refined by XSS. The results advance our understanding of the ultrafast relaxation mechanisms that impact the photocatalytic mechanism and yield for NiII-bipyridine aryl halide cross-coupling catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Translational diffusion of water inside hydrophobic carbon micropores studied by neutron spectroscopy and molecular dynamics simulation

When water molecules are confined to nanoscale spacings, such as in the nanometer-size pores of activated carbon fiber (ACF), their freezing point gets suppressed down to very low temperatures (~150 K), leading to a metastable liquid state with remarkable physical properties. Here we have investigated the ambient pressure diffusive dynamics of water in microporous Kynol ACF-10 (average pore size ~11.6 Å, with primarily slit-like pores) from temperature T = 280 K in its stable liquid state down to T = 230 K into the metastable supercooled phase. The observed characteristic relaxation times and diffusion coefficients are found to be, respectively, higher and lower than those in bulk water, indicating a slowing down of the water mobility with decreasing temperature. The observed temperature-dependent average relaxation time (${{\tau}}$) when compared to previous findings indicate that it is the width of the slit pores-not their curvature-that primarily affects the dynamics of water for pore sizes larger than 10 Å. The experimental observations are compared to complementary molecular dynamics simulations of a model system, in which we studied the diffusion of water within the 11.6 Å gap of two parallel graphene sheets. We find generally a reasonable agreement between the observed and calculated relaxation times at the low momentum transfer Q (Q ≤ 0.9 Å -1) . At high Q, however, where localized dynamics becomes relevant, this ideal system does not satisfactorily reproduce the measurements. Consequently, the simulations are compared to the experiments at low Q, where the two can be best reconciled. The best agreement is obtained for the diffusion parameter D associated with the hydrogen-site when a representative stretched exponential function, rather than the standard bimodal exponential model, is used to parametrize the self-correlation function I (Q,t).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The AFDD International Dynamic Stall Workshop on Correlation of Dynamic Stall Models with 3-D Dynamic Stall Data

A variety of empirical and computational fluid dynamics two-dimensional (2-D) dynamic stall models were compared to recently obtained three-dimensional (3-D) dynamic stall data in a workshop on modeling of 3-D dynamic stall of an unswept, rectangular wing, of aspect ratio 10. Dynamic stall test data both below and above the static stall angle-of-attack were supplied to the participants, along with a 'blind' case where only the test conditions were supplied in advance, with results being compared to experimental data at the workshop itself. Detailed graphical comparisons are presented in the report, which also includes discussion of the methods and the results. The primary conclusion of the workshop was that the 3-D effects of dynamic stall on the oscillating wing studied in the workshop can be reasonably reproduced by existing semi-empirical models once 2-D dynamic stall data have been obtained. The participants also emphasized the need for improved quantification of 2-D dynamic stall.

Tan, C. M.↗

25 Mg NMR and Computational Modeling Studies of the Solvation Structures and Molecular Dynamics in Magnesium Based Liquid Electrolytes

There is increasing evidence that the solvation structure of the active components in a liquid electrolyte solution strongly impacts the performance in electrochemical applications. In this work, the nanoscale solvation structures and dynamics of Mg(BH 4 ) 2 and Mg(TFSI) 2 dissolved in diglyme (DGM) at various concentrations and ratios of Mg(BH 4 ) 2 /Mg(TFSI) 2 were investigated using a combination of natural abundance 25 Mg NMR, quantum chemistry calculations of 25 Mg NMR chemical shifts, classical molecular dynamics (MD) calculations, and electrochemical performance tests. By mixing two competing Mg salts, we were able to reduce the strong covalent interactions between Mg 2+ and BH 4 – anions. A small increase is observed in the coordination number of Mg-TFSI and a significant increase in the interaction of Mg 2+ ions with glymes. Through a combination of NMR, DFT and MD simulations, various stable species around 1 nm in size were detected in the mixed salt solution, which play key roles in the enhanced electrochemical performance of the mixed electrolyte. It is established that for the neat Mg(TFSI) 2 in DGM electrolyte at dilute concentrations the TFSI - is fully dissociated from Mg 2+ . At higher concentrations, Mg 2+ and TFSI - are only partially dissociated as contact ion pairs are formed. In contrast, at 0.01 M Mg(BH 4 ) 2 (saturated concentration) in DGM, the first solvation shell of a Mg 2+ ion contains two BH 4 - anions and one DGM molecule, while the second solvation shell consists of five to six DGM molecules. An exchange mechanism between the solvation structures in the combined electrolyte containing both Mg(BH 4 ) 2 and Mg(TFSI) 2 in DGM was found to result in the observation of a single 25 Mg NMR peak. This exchange is responsible for an increase in uncoordinated anions, as well as improved stability and ionic conductivity as compared to single anion solution. Solvent molecule rearrangement and direct Mg-ion exchange between the basic solvation structures are hypothesized as likely reasons for the exchange. We elucidate that the solvent rearrangement is energetically much more favorable than direct Mg-ion hopping and is thus suggested as the dominant exchange mechanism.

Magnesium battery, electrolytes, Mg(BH4)2, Mg(TFSI↗

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↗

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↗

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↗

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↗