Structure, Function, and Dynamics of the Gα Binding Domain of Ric-8A
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99 GENERAL AND MISCELLANEOUS↗
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A polarized Drell-Yan experiment to probe the dynamics of the nucleon sea
In QCD, nucleon spin comes from the sum of the quark spin, gluon spin, and the quark and gluon orbital angular momentum, but how these different components contribute and the interplay among them is not yet understood. For instance, sea quark orbital contribution remains largely unexplored. Measurements of the Sivers function for the sea quarks will provide a probe of the sea quark orbital contribution. The upcoming E1039 experiment at Fermilab will measure the Sivers asymmetry of the sea quarks via the Drell-Yan process using a 120 GeV unpolarized proton beam directed a transversely polarized ammonia target. We report on the status and plans of the E1039 polarized Drell-Yan experiment.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Water Dynamics in Nanoporous Silica: Ultrafast Vibrational Spectroscopy and Molecular Dynamics Simulations
Nanoporous silica materials are important in catalysis, energy, and materials applications in which water is an essential component. System performance is intimately connected to the water dynamics occurring in the confined environment. However, the dynamics and associated structures of water in nanoporous silica have proven challenging to measure and predict. Here, confined water dynamics are examined via the ultrafast infrared spectroscopy of selenocyanate (SeCN – ) dissolved in the hydrated ~2.4 nm silica mesopores of MCM41. Polarization selective pump–probe and two-dimensional infrared measurements on the CN stretching mode of SeCN – are used to probe the effect of confinement on orientational relaxation and spectral diffusion dynamics. Here, the dynamics of SeCN – provide information on the surrounding water hydrogen bond dynamics. The long CN stretch lifetime (~36 ps), relative to the water hydroxyl stretch (<2 ps), significantly extends the time scales that can be accessed. Complete orientational relaxation (C 2 (t), orientational correlation function) and spectral diffusion (C ω (t), frequency–frequency correlation function) dynamics are presented and compared to the simulated time correlation functions in a model silica pore of the same size. A slow decay component not present in the bulk liquid is observed in both experiments, indicating that the hydrogen bond dynamics are significantly altered by confinement. The simulations reveal a qualitative difference in the functional dependence of C 2 (t;d) and C ω (t;d) on d, the distance from the interface. The former becomes exponentially faster with distance while the latter makes an abrupt transition from slower to faster dynamics midway between the surface and pore center, d ≅ 6 Å.
14 SOLAR ENERGY↗
Extended Lagrangian Born-Oppenheimer molecular dynamics simulations of the shock-induced chemistry of phenylacetylene
The initial chemical events that occur during the shock compression of liquid phenylacetylene have been investigated using self-consistent tight binding molecular dynamics simulations. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism enabled us to compute microcanonical trajectories with precise conservation of the total energy. Our simulations revealed that the first density-increasing step under shock compression arises from the polymerization of phenylacetylene molecules at the acetylene moiety. The application of electronic structure-based molecular dynamics with long-term conservation of the total energy enabled us to identify electronic signatures of reactivity via monitoring changes in the HOMO-LUMO gap, and to capture directly adiabatic shock heating, transient non-equilibrium states, and changes in temperature arising from exothermic chemistry in classical molecular dynamics trajectories.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Nonequilibrium solvent effects in Born-Oppenheimer molecular dynamics for ground and excited electronic states
The effects of solvent on molecular processes such as excited state relaxation and photochemical reaction often occurs in a nonequilibrium regime. Dynamic processes such as these can be simulated using excited state molecular dynamics. In this work, we describe methods of simulating nonequilibrium solvent effects in excited state molecular dynamics using linear-response time-dependent density functional theory and apparent surface charge methods. These developments include a propagation method for solvent degrees of freedom and analytical energy gradients for the calculation of forces. Molecular dynamics of acetaldehyde in water or acetonitrile are demonstrated where the solute-solvent system is out of equilibrium due to photoexcitation and emission.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ensemble Kalman Filter for Dynamic State Estimation of Power Grids Stochastically Driven by Time-correlated Mechanical Input Power
State and parameter estimation of power transmission networks is important for monitoring power grid operating conditions and analyzing transient stability. Wind power generation depends on fluctuating input power levels, which are correlated in time and contribute to uncertainty in turbine dynamical models. The ensemble Kalman filter (EnKF), a standard state estimation technique, uses a deterministic forecast and does not explicitly model time-correlated noise in parameters such as mechanical input power. However, this uncertainty affects the probability of fault-induced transient instability and increased prediction bias. Here a novel approach is to model input power noise with time-correlated stochastic fluctuations, and integrate them with the network dynamics during the forecast. While the EnKF has been used to calibrate constant parameters in turbine dynamical models, the calibration of a statistical model for a time-correlated parameter has not been investigated. In this study, twin experiments on a standard transmission network test case are used to validate our time-correlated noise model framework for state estimation of unsteady operating conditions and transient stability analysis, and a methodology is proposed for the inference of the mechanical input power time-correlation length parameter using time-series data from PMUs monitoring power dynamics at generator buses.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Phenomenological Model of Nonlinear Dynamics and Deterministic Chaotic Gas Migration in Bentonite: Experimental Evidence and Diagnostic Parameters
Understanding gas migration in compacted clay materials, e.g., bentonite and claystone, is important for the design and performance assessment of an engineered barrier system of a radioactive waste repository system, as well as many practical applications. Existing field and laboratory data on gas migration processes in low-permeability clay materials demonstrate the complexity of flow and transport processes, including various types of instabilities, caused by nonlinear dynamics of coupled processes of liquid–gas exchange, dilation, fracturing, fracture healing, etc., which cannot be described by classical models of fluid dynamics in porous media. We here show that the complexity of gas migration processes can be explained using a phenomenological concept of nonlinear dynamics and deterministic chaos theory. To do so, we analyzed gas pressure and gas influx (i.e., input) and outflux (i.e., output), recorded during the gas injection experiment in the compact Mx80-D bentonite sample, and calculated a set of the diagnostic parameters of nonlinear dynamics and chaos, such a global embedding dimension, a correlation dimension, an information dimension, and a spectrum of Lyapunov exponents, as well as plotted 2D and 3D pseudo-phase-space strange attractors, based on the univariate influx and outflux time series data. These results indicate the presence of phenomena of low-dimensional deterministic chaotic behavior of gas migration in bentonite. In particular, during the onset of gas influx in the bentonite core, before the breakthrough, the development of gas flow pathways is characterized by the process of chaotic gas diffusion. After the breakthrough, with inlet-to-outlet movement of gas, the prevailing process is chaotic advection. During the final phase of the experiment, with no influx to the sample, the relaxation pattern of gas outflux is resumed back to a process of chaotic diffusion. The types of data analysis and a proposed phenomenological model can be used to establish the basic principles of experimental data-gathering, modeling predictions, and a research design.
36 MATERIALS SCIENCE↗
Quantum dynamical investigation of the simplest Criegee intermediate CH{sub 2}OO and its O–O photodissociation channels
The singlet electronic potential energy surfaces for the simplest Criegee intermediate CH{sub 2}OO are computed over a two-dimensional reduced subspace of coordinates, and utilized to simulate the photo-initiated dynamics on the S{sub 2} (B) state leading to dissociation on multiple coupled excited electronic states. The adiabatic electronic potentials are evaluated using dynamically weighted state-averaged complete active space self-consistent field theory. Quasi-diabatic states are constructed from the adiabatic states by maximizing the charge separation between the states. The dissociation dynamics are then simulated on the diabatically coupled excited electronic states. The B ← X electronic transition with large oscillator strength was used to initiate dynamics on the S{sub 2} (B) excited singlet state. Diabatic coupling of the B state with other dissociative singlet states results in about 5% of the population evolving to the lowest spin-allowed asymptote, generating H{sub 2}CO (X {sup 1}A{sub 1}) and O ({sup 1}D) fragments. The remaining ∼95% of the population remains on repulsive B state and dissociates to H{sub 2}CO (a {sup 3}A″) and O ({sup 3}P) products associated with a higher asymptotic limit. Due to the dissociative nature of the B state, the simulated electronic absorption spectrum is found to be broad and devoid of any vibrational structure.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Application of a New Ensemble Conserving Quantum Dynamics Simulation Algorithm to Liquid para-Hydrogen and ortho-Deuterium
Here, we apply the Feynman-Kleinert Quasi-Classical Wigner (FK-QCW) method developed in our previous work [Smith et al., J. Chem. Phys. 142, 244112 (2015)] for the determination of the dynamic structure factor of liquid para-hydrogen and ortho-deuterium at state points of (T = 20.0 K, n = 21.24 nm -3 ) and (T = 23.0 K, n = 24.61 nm -3 ), respectively. When applied to this challenging system, it is shown that this new FK-QCW method consistently reproduces the experimental dynamic structure factor reported by Smith et al. [J. Chem. Phys. 140, 034501 (2014)] for all momentum transfers considered. Moreover, this shows that FK-QCW provides a substantial improvement over the Feynman-Kleinert linearized path-integral method, in which purely classical dynamics are used. Furthermore, for small momentum transfers, it is shown that FK-QCW provides nearly the same results as ring-polymer molecular dynamics (RPMD), thus suggesting that FK-QCW provides a potentially more appealing algorithm than RPMD since it is not formally limited to correlation functions involving linear operators.
36 MATERIALS SCIENCE↗
Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling
An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Toward more realistic projections of soil carbon dynamics by Earth system models
Soil carbon (C) is a critical component of Earth system models (ESMs), and its diverse representations are a major source of the large spread across models in the terrestrial C sink from the third to fifth assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Improving soil C projections is of a high priority for Earth system modeling in the future IPCC and other assessments. To achieve this goal, we suggest that (1) model structures should reflect real-world processes, (2) parameters should be calibrated to match model outputs with observations, and (3) external forcing variables should accurately prescribe the environmental conditions that soils experience. First, most soil C cycle models simulate C input from litter production and C release through decomposition. The latter process has traditionally been represented by first-order decay functions, regulated primarily by temperature, moisture, litter quality, and soil texture. While this formulation well captures macroscopic soil organic C (SOC) dynamics, better understanding is needed of their underlying mechanisms as related to microbial processes, depth-dependent environmental controls, and other processes that strongly affect soil C dynamics. Second, incomplete use of observations in model parameterization is a major cause of bias in soil C projections from ESMs. Optimal parameter calibration with both pool-and flux-based data sets through data assimilation is among the highest priorities for near-term research to reduce biases among ESMs. Third, external variables are represented inconsistently among ESMs, leading to differences in modeled soil C dynamics. Furthermore, we recommend the implementation of traceability analyses to identify how external variables and model parameterizations influence SOC dynamics in different ESMs. Overall, projections of the terrestrial C sink can be substantially improved when reliable data sets are available to select the most representative model structure, constrain parameters, and prescribe forcing fields.
54 ENVIRONMENTAL SCIENCES↗
Dynamic Data Reconciliation and Validation of a Dynamic Model for Solvent-Based CO 2 Capture Using Pilot-Plant Data
This paper is focused on the development and validation of a dynamic model for an MEA-based CO 2 capture unit. Starting with a rigorous steady-state process model, the dynamic model is developed in Aspen Plus Dynamics ® using a modified Murphree-efficiency approach and is validated using dynamic data collected from the National Carbon Capture Center (NCCC) in Wilsonville, Alabama. The dynamic test runs were designed with due consideration of process excitation and process nonlinearities constrained by the available time to conduct the test runs and implement the experimental designs in the plant control system. The experimental data include solvent composition and loading. Since the experimental data were found to violate mass and energy balances, filtering algorithms coupled with dynamic data reconciliation techniques were used. Without adjusting any model parameters, the dynamic model satisfactorily predicted dynamic response of CO 2 capture due to step changes in the solvent flowrate, flue gas flowrate, and steam flowrates. Transient studies show that the process gain and time constants can considerably change depending on the direction of the disturbance or manipulated variables, indicating process nonlinearities. Due to a storage tank between the absorber and stripper, the time constant of the full plant can be considerably longer than the time constants of the absorber or stripper individually. Furthermore, impact of the control system on the process efficiency while following an optimal CO 2 capture schedule was also studied.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Heterogeneous nature of relaxation dynamics of room-temperature ionic liquids (EMIm) 2 [Co(NCS) 4 ] and (BMIm) 2 [Co(NCS) 4 ]
Dynamic crossover above T g has been recognized as a characteristic feature of molecular dynamics of liquids approaching glass transition. Experimentally, it is manifested as a change in Vogel Fulcher Tammann dependence or a breakdown of the Stokes Einstein and related relations. In this paper, we report the exception from this rather general pattern of behavior. By means of dielectric, ultrasonic, rheological, and calorimetric methods, dynamics of two good ionic conductors (BMIm) 2 [Co(NCS) 4 ] and (EMIm) 2 [Co(NCS) 4 ] of less common stoichiometry (2:1) was studied in a very broad temperature range. However, none of the mentioned dynamic changes was observed in the entire studied temperature range. On the contrary, the single VFT and the same fractional Walden coefficient were found for conductivity and viscosity changes over 12 decades. Furthermore, ultrasonic studies revealed that the data at temperatures which cover the normal liquid region cannot be fitted by a single exponential decay, and the Cole Cole function should be used instead.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Graph dynamical networks for unsupervised learning of atomic scale dynamics in materials
Understanding the dynamical processes that govern the performance of functional materials is essential for the design of next generation materials to tackle global energy and environmental challenges. Many of these processes involve the dynamics of individual atoms or small molecules in condensed phases, e.g. lithium ions in electrolytes, water molecules in membranes, molten atoms at interfaces, etc., which are difficult to understand due to the complexity of local environments. In this work, we develop graph dynamical networks, an unsupervised learning approach for understanding atomic scale dynamics in arbitrary phases and environments from molecular dynamics simulations. We show that important dynamical information, which would be difficult to obtain otherwise, can be learned for various multi-component amorphous material systems. With the large amounts of molecular dynamics data generated every day in nearly every aspect of materials design, this approach provides a broadly applicable, automated tool to understand atomic scale dynamics in material systems.
36 MATERIALS SCIENCE↗
Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy
We employed ultrafast transient absorption and broadband 2DIR spectroscopy to study the vibrational dynamics of aqueous hydroxide solutions by exciting the O–H stretch vibrations of the strongly hydrogen-bonded hydroxide solvation shell water and probing the continuum absorption of the solvated ion between 1500 and 3800 cm{sup −1}. We observe rapid vibrational relaxation processes on 150–250 fs time scales across the entire probed spectral region as well as slower vibrational dynamics on 1–2 ps time scales. Furthermore, the O–H stretch excitation loses its frequency memory in 180 fs, and vibrational energy exchange between bulk-like water vibrations and hydroxide-associated water vibrations occurs in ∼200 fs. The fast dynamics in this system originate in strong nonlinear coupling between intra- and intermolecular vibrations and are explained in terms of non-adiabatic vibrational relaxation. These measurements indicate that the vibrational dynamics of the aqueous hydroxide complex are faster than the time scales reported for long-range transport of protons in aqueous hydroxide solutions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Photonic Doppler velocimetry probe used to measure grain boundaries of dynamic shocked materials
Material scientists have developed computational modeling to predict the dynamic response of materials undergoing stress, but there is still a need to make precision measurements of surfaces undergoing shock compression. Miniature photonic Doppler velocimetry (PDV) probes have been developed to measure the velocity distribution from a moving surface traveling tens of kilometers per second. These probes use hundreds of optical fibers imaged by optical relays onto different regions of this moving surface. While previous work examined large surface areas, we have now developed a PDV microscope that can interrogate 37 different spots within a field of view of <1 mm, with a standoff distance of 17 mm, to analyze the motion differences across grain boundaries of the material undergoing dynamic stress. Each PDV fiber interrogates a 10 μm spot size on the moving surface. A separate imaging system using a coherent bundle records the location of the PDV spots relative to the grain boundaries prior to the dynamic event. Designing the mounting structures for the lenses, fibers, and coherent bundle was a challenge. To minimize back reflections, the fibers are index matched onto the first relay lens, which is made of fused silica. The PDV fibers are aligned normal to the moving surface. The imaging probe views the surface at an 18° angle. The coherent bundle is tilted 11° to its optical relay. All components are assembled into a single probe head assembly. The coherent bundle is removed from the probe head to be used for the next dynamic event. Alignment issues will also be discussed.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
A computational fluid dynamics model to estimate local quantities in firebrand char oxidation
Firebrand burning is a complex phenomenon that is influenced by several parameters which are difficult to fully explore experimentally. Computational fluid dynamics models capable of predicting local quantities are essential for accurate prediction of char oxidation in firebrands. This article presents a computational fluid dynamics model to estimate firebrand mass loss, diameter change, and surface temperature during char oxidation. The model was validated using previously conducted wind tunnel experiments. These experiments were conducted for firebrands of two different aspect ratios, which were arranged in three different configurations (single, horizontal array, and vertical array), and for four different wind speeds (0.5, 1, 1.5, and 2 m/s). The computational fluid dynamics results were compared with a previous 1 D model. In all the test cases, the computational fluid dynamics model predicted the physical phenomena with significantly improved accuracy compared to a 1 D model. The char oxidation model presented in this article can be coupled with other models to study firebrand generation and trajectory, biomass pyrolysis, fluidized bed reactors, and coal combustion.
Engineering↗