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DOE OSTI2017

Stable schemes for dissipative particle dynamics with conserved energy

This article presents a new numerical scheme for the discretization of dissipative particle dynamics with conserved energy. The key idea is to reduce elementary pairwise stochastic dynamics (either fluctuation/dissipation or thermal conduction) to effective single-variable dynamics, and to approximate the solution of these dynamics with one step of a Metropolis–Hastings algorithm. This ensures by construction that no negative internal energies are encountered during the simulation, and hence allows to increase the admissible timesteps to integrate the dynamics, even for systems with small heat capacities. Stability is only limited by the Hamiltonian part of the dynamics, which suggests resorting to multiple timestep strategies where the stochastic part is integrated less frequently than the Hamiltonian one.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

On the implementation of dislocation reactions in continuum dislocation dynamics modeling of mesoscale plasticity

The continuum dislocation dynamics framework for mesoscale plasticity is intended to capture the dislocation density evolution and the deformation of crystals when subjected to mechanical loading. It does so by solving a set of transport equations for dislocations concurrently with crystal mechanics equations, with the latter being cast in the form of an eigenstrain problem. Incorporating dislocation reactions in the dislocation transport equations is essential for making such continuum dislocation dynamics predictive. A formulation is proposed to incorporate dislocation reactions in the transport equations of the vector density-based continuum dislocation dynamics. This formulation aims to rigorously enforce dislocation line continuity using the concept of virtual dislocations that close all dislocation loops involved in cross slip, annihilation, and glissile and sessile junction reactions. The addition of virtual dislocations enables us to accurately enforce the divergence free condition upon the numerical solution of the dislocation transport equations for all slip systems individually. A set of tests were performed to illustrate the accuracy of the formulation and the solution of the transport equations within the vector density-based continuum dislocation dynamics. Comparing the results from these tests with an earlier approach in which the divergence free constraint was enforced on the total dislocation density tensor or the sum of two densities when only cross slip is considered shows that the new approach yields highly accurate results. Bulk simulations were performed for a face centered cubic crystal based on the new formulation and the results were compared with discrete dislocation dynamics predictions of the same. The microstructural features obtained from continuum dislocation dynamics were also analyzed with reference to relevant experimental observations.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Creating an Advanced Sensor Network to calculate real-time, mass-weighted flue gas composition and air heater leakage of a coal-fired utility boiler under dynamic operating conditions

Utilization of renewable energy sources to minimize the environmental impact of energy production has changed the way utility boilers operate, requiring frequent load cycling between full load and partial loads as low as 30%. Dynamic operation of coal-fired utility boilers significantly reduces boiler efficiency when compared to steady state at full load. Data-driven plant optimization has shown success with coal-fired utility boilers under dynamic operating conditions. The purpose of this work was to create an Advanced Sensor Network (ASN) to provide more extensive real-time data to inform dynamic plant optimization of Net Unit Heat Rate (NUHR). The ASN consists of gas sampling grids in the convective pass of the boiler and downstream of the air heater. These sampling grids allow for quantification of spatial variation of flue gas within the boiler and calculation of mass-weighted composition of flue gas through the combination of composition, velocity, and temperature measurements. The comparison of O 2 between the inlet and outlet of the air heater is used to calculate air leakage in real time. Flue gas composition and air heater leakage are both important factors in boiler efficiency and NUHR. Further, the results of this work support the value of mass-weighted averages for determining flue gas composition accurately. The measurements from the ASN show increased composition stratification during dynamic operation, with an average standard deviation 38% higher than observed during steady-state operation. Air heater leakage was also observed to increase from 2.8% to 5.1% following a load change. Prior to the installation of the ASN, these data would not have been available for dynamic control. These real-time data will be leveraged to calculate and optimize for NUHR during dynamic operation in future work.

42 ENGINEERING↗
DOE OSTI2017

Analysis of current-driven oscillatory dynamics of single-layer homoepitaxial islands on crystalline conducting substrates

Here we report results of a systematic study on the complex oscillatory current-driven dynamics of single-layer homoepitaxial islands on crystalline substrate surfaces and the dependence of this driven dynamical behavior on important physical parameters, including island size, substrate surface orientation, and direction of externally applied electric field. The analysis is based on a nonlinear model of driven island edge morphological evolution that accounts for curvature-driven edge diffusion, edge electromigration, and edge diffusional anisotropy. Using a linear theory of island edge morphological stability, we calculate a critical island size at which the island’s equilibrium edge shape becomes unstable, which sets a lower bound for the onset of time-periodic oscillatory dynamical response. Using direct dynamical simulations, we study the edge morphological dynamics of current-driven single-layer islands at larger-than-critical size, and determine the actual island size at which the migrating islands undergo a transition from steady to time-periodic asymptotic states through a subcritical Hopf bifurcation. At the highest symmetry of diffusional anisotropy examined, on {111} surfaces of face-centered cubic crystalline substrates, we find that more complex stable oscillatory states can be reached through period-doubling bifurcation at island sizes larger than those at the Hopf points. We characterize in detail the island morphology and dynamical response at the stable time-periodic asymptotic states, determine the range of stability of these oscillatory states terminated by island breakup, and explain the morphological features of the stable oscillating islands on the basis of linear stability theory.

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

Modulating Enzyme Activity by Altering Protein Dynamics with Solvent

Optimal enzyme activity depends on a number of factors, including structure and dynamics. The role of enzyme structure is well recognized; however, the linkage between protein dynamics and enzyme activity has given rise to a contentious debate. We have developed an approach that uses an aqueous mixture of organic solvent to control the functionally relevant enzyme dynamics (without changing the structure), which in turn modulates the enzyme activity. Using this approach, we predicted that the hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase (DHFR) from Escherichia coli in aqueous mixtures of isopropanol (IPA) with water will decrease by ~3 fold at 20% (v/v) IPA concentration. Stopped-flow kinetic measurements find that the pH-independent k hydride rate decreases by 2.2 fold. X-ray crystallographic enzyme structures show no noticeable differences, while computational studies indicate that the transition state and electrostatic effects were identical for water and mixed solvent conditions; quasi-elastic neutron scattering studies show that the dynamical enzyme motions are suppressed. Our approach provides a unique avenue to modulating enzyme activity through changes in enzyme dynamics. Further it provides vital insights that show the altered motions of DHFR cause significant changes in the enzyme's ability to access its functionally relevant conformational substates, explaining the decreased k hydride rate. This approach has important implications for obtaining fundamental insights into the role of rate-limiting dynamics in catalysis and as well as for enzyme engineering.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Nonadiabatic Molecular Dynamics by Multiconfiguration Pair-Density Functional Theory

Herein, we present the first implementation of multiconfiguration pair-density functional theory (MC-PDFT) ab initio molecular dynamics. MC-PDFT is a multireference electronic structure method that in many cases has a similar accuracy (or even better accuracy) the complete active space second-order perturbation theory (CASPT2) at a significantly lower computational cost. In this study, we introduced MC-PDFT analytical gradients into the SHARC molecular dynamics program for ab initio, nonadiabatic molecular dynamics simulations. We verify our implementation by examining the intersystem crossing dynamics of thioformaldehyde, and we observe excellent agreement with recent CASPT2 and experimental findings. Moreover, with MC-PDFT, we could perform dynamics simulations with the 12 electron in 10 orbitals active space that was computationally too expensive for direct dynamics with CASPT2.

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

Molecular dynamics force-field refinement against quasi-elastic neutron scattering data

Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulation due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. In addition, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.

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

Chain and Segmental Dynamics in Polymer–Nanoparticle Composites with High Nanoparticle Loading

Recent experimental and simulation studies have shown that polymer–nanoparticle (NP) composites (PNCs) with ultra-high NP loading (>50%) exhibit remarkable mechanical properties and dramatic increases in polymer glass-transition temperature, viscosity, and thermal stability compared to the bulk polymer. These deviations in macroscopic properties suggest a slowdown in both segmental and chain-scale polymer dynamics due to confinement. In this work, we examine the polymer conformations and dynamics in these PNCs using molecular dynamics simulations of both unentangled and entangled coarse-grained polymers in random-close-packed NP packings with varying polymer fill fractions. We find that the changes in the polymer dynamics depend on the number of NPs in contact with a polymer segment. Using the number of polymer–NP contacts and different polymer chain conformations as criteria for categorization, we further examine the polymer dynamics at multiple length scales to show the high level of dynamic heterogeneity in PNCs with ultra-high NP loading.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Crossover from Rouse to Reptation Dynamics in Salt-Free Polyelectrolyte Complex Coacervates

Considerable interest in the dynamics and rheology of polyelectrolyte complex coacervates has been motivated by their industrial application as viscosity modifiers. A central question is the extent to which classical Rouse and reptation models can be applied to systems where electrostatic interactions play a critical role on the thermodynamics. By relying on molecular simulations, we present a direct analysis of the crossover from Rouse to reptation dynamics in salt-free complex coacervates as a function of chain length. This crossover shifts to shorter chain lengths as electrostatic interactions become stronger, which corresponds to the formation of denser coacervates. To distinguish the roles of Coulomb interactions and density, here we compare the dynamics of coacervates to those of neutral, semidilute solutions at the same density. Both systems exhibit a universal dynamical behavior in the connectivity-dominated (subdiffusion and normal diffusion) regimes, but the monomer relaxation time in coacervates is much longer and increases with increasing Bjerrum length. This is similar to the cage effect observed in glass-forming polymers, but the local dynamical slowdown is caused here by strong Coulomb attractions (ion pairing) between oppositely charged monomers. Our findings provide a microscopic framework for the quantitative understanding of coacervate dynamics and rheology.

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

Probing Metastable Domain Dynamics via Automated Experimentation in Piezoresponse Force Microscopy

The dynamics of complex topological defects in ferroelectric materials is explored using automated experimentation in piezoresponse force microscopy. Specifically, a complex trigger system (i.e., “FerroBot”) is employed to study metastable domain-wall dynamics in Pb 0.6 Sr 0.4 TiO 3 thin films. Several regimes of superdomain wall dynamics have been identified, including smooth domain-wall motion and significant reconfiguration of the domain structures. We have further demonstrated that microscopic mechanisms of the domain-wall dynamics can be identified; i.e., domain-wall bending can be separated from irreversible domain reconfiguration regimes. In conjunction, phase-field modeling was used to corroborate the observed mechanisms. As such, the observed superdomain dynamics can provide a model system for classical ferroelectric dynamics, much like how colloidal crystals provide a model system for atomic and molecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Quantifying Soil Phosphorus Dynamics: A Data Assimilation Approach

The dynamics of soil phosphorus (P) control its bioavailability. Yet it remains a challenge to quantify soil P dynamics. In this work we developed a soil P dynamics (SPD) model. We then assimilated eight data sets of 426-day changes in Hedley P fractions into the SPD model, to quantify the dynamics of six major P pools in eight soil samples that are representative of a wide type of soils. The performance of our SPD model was better for labile P, secondary mineral P, and occluded P than for nonoccluded organic P (Po) and primary mineral P. All parameters describing soil P dynamics were approximately constrained by the data sets. The average turnover rates were labile P 0.040 g g -1 day-1, nonoccluded Po 0.051 g g -1 day -1 , secondary mineral P 0.023 g g -1 day -1 , primary mineral P 0.00088 g g -1 day -1 , occluded Po 0.0066 g g -1 day -1 , and occluded inorganic P 0.0065 g g -1 day -1 , in the greenhouse environment studied. Labile P was transferred on average more to nonoccluded Po (transfer coefficient of 0.42) and secondary mineral P (0.38) than to plants (0.20). Soil pH and organic C concentration were the key soil properties regulating the competition for P between plants and soil secondary minerals. The turnover rate of labile P was positively correlated with that of nonoccluded Po and secondary mineral P. The pool size of labile P was most sensitive to its turnover rate. Overall, we suggest data assimilation can contribute significantly to an improved understanding of soil P dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Dynamics, Radiation, and Overall Energy Budget of Earthquake Rupture With Coseismic Off-Fault Damage

Earthquake ruptures dynamically activate coseismic off–fault damage around fault cores. Systematic field observation efforts have shown the distribution of off–fault damage around main faults, while numerical modeling using elastic–plastic off–fault material models have demonstrated the evolution of coseismic off–fault damage during earthquake ruptures. Laboratory–scale microearthquake experiments have pointed out the enhanced high–frequency radiation due to the coseismic off–fault damage. However, the detailed off–fault fracturing mechanisms, subsequent radiation, and its contribution to the overall energy budget remain to be fully understood because of limitations of current observational techniques and model formulations. Here, we constructed a new physics–based dynamic earthquake rupture modeling framework, based on the combined finite–discrete element method, to investigate the fundamental mechanisms of coseismic off–fault damage, and its effect on the rupture dynamics, the radiation and the overall energy budget. We conducted a 2–D systematic case study with depth and showed the mechanisms of dynamic activation of the coseismic off–fault damage. We found the decrease in rupture velocity and the enhanced high–frequency radiation in near field due to the coseismic off–fault damage. We then evaluated the overall energy budget, which shows a significant contribution of the coseismic off–fault damage to the overall energy budget even at depth, where the damage zone width becomes narrower. Here, the present numerical framework for the dynamic earthquake rupture modeling thus provides new insights into earthquake rupture dynamics with the coseismic off–fault damage.

58 GEOSCIENCES↗
DOE OSTI2025

Improved Representations of Land‐Atmosphere Interactions Over the Continental U.S. Through Dynamic Root Modeling

Previous studies have identified the oversimplified root system representation as a key factor leading to inaccuracies in vegetation‐atmosphere feedbacks. In this study, a dynamic root water uptake scheme in the Noah‐MP land surface model has been coupled to the Weather Research and Forecasting (WRF) model to investigate its impact on the surface hydroclimate variables and land‐atmosphere interactions. To evaluate the impact of the dynamic root, two coupled simulations were conducted, one with the dynamic root water uptake scheme (DynRt) and one with the static root water uptake scheme (StcRt), which is based on the default root representation in Noah‐MP, with slight modifications, primarily in vegetation‐related parameters. Both DynRt and StcRt simulations were conducted with a small ensemble of three members to account for variations in physical parameterizations, initial and boundary forcing and model setup. When compared with reference data sets, the DynRt simulations show improved results than the StcRt simulations, reducing biases in the simulated leaf area index, surface energy fluxes, soil moisture and precipitation. Two different mechanisms through which roots affect land‐atmosphere coupling have been identified. Over the transitional climate zone between the dry and wet climate, the dynamic root scheme affects surface climate and land‐atmosphere coupling mainly through changes in soil moisture through hydraulic redistribution by plant root system. Over the energy‐limited mesic zone, the dynamic root affects regional land‐atmosphere coupling mainly through changes in carbon allocation. This work highlights the importance of dynamic root representation in improving vegetation‐atmosphere simulations by enhancing predictions of water, energy, and carbon fluxes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

1 H chemical shift anisotropy: a high sensitivity solid-state NMR dynamics probe for surface studies?

We report dynamics play significant roles in chemistry and biochemistry-molecular motions impact both large- and small-scale chemical reactions in addition to biochemical processes. In many systems, including heterogeneous catalysts, the characterization of dynamics remains a challenge. The most common approaches involve the solid-state NMR measurement of anisotropic interactions, in particular 2 H quadrupolar coupling and 1 H–X dipolar coupling, which generally require isotope enrichment. Due to the high sensitivity of 1 H NMR, 1 H chemical shift anisotropy (CSA) is a particularly enticing, and underexplored, dynamics probe. We carried out 1 H CSA and 1 H– 13 C dipolar coupling measurements in a series of model supported complexes to understand how 1 H CSA can be leveraged to gain dynamic information for heterogeneous catalysts. Mathematical descriptions are given for the dynamic averaging of the CSA tensor, and its dependence on orientation and asymmetry. The variability of the orientation of the tensor in the molecular frame, in addition to its magnitude and asymmetry, negatively impacts attempts to extract quantitative dynamic information. Nevertheless, 1 H CSA measurements can reveal useful qualitative insights into the motions of a particularly dilute site, such as from a surface species.

1H chemical shift anisotropy↗
DOE OSTI2013

Extended Lagrangian Born-Oppenheimer molecular dynamics in the limit of vanishing self-consistent field optimization

We present an efficient general approach to first principles molecular dynamics simulations based on extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The reduction of the optimization requirement reduces the computational cost to a minimum, but without causing any significant loss of accuracy or long-term energy drift. The optimization-free first principles molecular dynamics requires only one single diagonalization per time step, but is still able to provide trajectories at the same level of accuracy as “exact,” fully converged, Born-Oppenheimer molecular dynamics simulations. The optimization-free limit of extended Lagrangian Born-Oppenheimer molecular dynamics therefore represents an ideal starting point for robust and efficient first principles quantum mechanical molecular dynamics simulations.

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

How to remove the spurious resonances from ring polymer molecular dynamics

Two of the most successful methods that are presently available for simulating the quantum dynamics of condensed phase systems are centroid molecular dynamics (CMD) and ring polymer molecular dynamics (RPMD). Despite their conceptual differences, practical implementations of these methods differ in just two respects: the choice of the Parrinello-Rahman mass matrix and whether or not a thermostat is applied to the internal modes of the ring polymer during the dynamics. Here, we explore a method which is halfway between the two approximations: we keep the path integral bead masses equal to the physical particle masses but attach a Langevin thermostat to the internal modes of the ring polymer during the dynamics. We justify this by showing analytically that the inclusion of an internal mode thermostat does not affect any of the established features of RPMD: thermostatted RPMD is equally valid with respect to everything that has actually been proven about the method as RPMD itself. In particular, because of the choice of bead masses, the resulting method is still optimum in the short-time limit, and the transition state approximation to its reaction rate theory remains closely related to the semiclassical instanton approximation in the deep quantum tunneling regime. In effect, there is a continuous family of methods with these properties, parameterised by the strength of the Langevin friction. Here, we explore numerically how the approximation to quantum dynamics depends on this friction, with a particular emphasis on vibrational spectroscopy. We find that a broad range of frictions approaching optimal damping give similar results, and that these results are immune to both the resonance problem of RPMD and the curvature problem of CMD.

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

Communication: On the consistency of approximate quantum dynamics simulation methods for vibrational spectra in the condensed phase

Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these limitations can be traced down to two approaches: methods that treat a small subset of the degrees of freedom with rigorous quantum mechanics, considering the rest of the system as a static or classical environment, and methods that treat the whole system quantum mechanically, but using approximate dynamics. Here, we perform a systematic comparison between these two philosophies for the description of quantum effects in vibrational spectroscopy, taking the Embedded Local Monomer model and a mixed quantum-classical model as representatives of the first family of methods, and centroid molecular dynamics and thermostatted ring polymer molecular dynamics as examples of the latter. We use as benchmarks D{sub 2}O doped with HOD and pure H{sub 2}O at three distinct thermodynamic state points (ice Ih at 150 K, and the liquid at 300 K and 600 K), modeled with the simple q-TIP4P/F potential energy and dipole moment surfaces. With few exceptions the different techniques yield IR absorption frequencies that are consistent with one another within a few tens of cm{sup −1}. Comparison with classical molecular dynamics demonstrates the importance of nuclear quantum effects up to the highest temperature, and a detailed discussion of the discrepancies between the various methods let us draw some (circumstantial) conclusions about the impact of the very different approximations that underlie them. Such cross validation between radically different approaches could indicate a way forward to further improve the state of the art in simulations of condensed-phase quantum dynamics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Anomalous dynamics of aqueous solutions of di-propylene glycol methylether confined in MCM-41 by quasielastic neutron scattering

The molecular dynamics of solutions of di-propylene glycol methylether (2PGME) and H{sub 2}O (or D{sub 2}O) confined in 28 Å pores of MCM-41 have been studied by quasielastic neutron scattering and differential scanning calorimetry over the concentration range 0–90 wt.% water. This system is of particular interest due to its pronounced non-monotonic concentration dependent dynamics of 2PGME in the corresponding bulk system, showing the important role of hydrogen bonding for the dynamics. In this study we have elucidated how this non-monotonic concentration dependence is affected by the confined geometry. The results show that this behaviour is maintained in the confinement, but the slowest diffusive dynamics of 2PGME is now observed at a considerably higher water concentration; at 75 wt.% water in MCM-41 compared to 30 wt.% water in the corresponding bulk system. This difference can be explained by an improper mixing of the two confined liquids. The results suggest that water up to a concentration of about 20 wt.% is used to hydrate the hydrophilic hydroxyl surface groups of the silica pores, and that it is only at higher water contents the water becomes partly mixed with 2PGME. Hence, due to this partial micro-phase separation of the two liquids larger, and thereby slower relaxing, structural entities of hydrogen bonded water and 2PGME molecules can only be formed at higher water contents than in the bulk system. However, the Q-dependence is unchanged with confinement, showing that the nature of the molecular motions is preserved. Thus, there is no indication of localization of the dynamics at length scales of less than 20 Å. The dynamics of both water and 2PGME is strongly dominated by translational diffusion at a temperature of 280 K.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗