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At least 1,747 records · Page 97
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Computational Enzymology and Organophosphorus Degrading Enzymes: Promising Approaches Toward Remediation Technologies of Warfare Agents and Pesticides

The re-emergence of chemical weapons as a global threat in hands of terrorist groups, together with an increasing number of pesticides intoxications and environmental contaminations worldwide, has called the attention of the scientific community for the need of improvement in the technologies for detoxification of organophosphorus (OP) compounds. A compelling strategy is the use of bioremediation by enzymes that are able to hydrolyze these molecules to harmless chemical species. Several enzymes have been studied and engineered for this purpose. However, their mechanisms of action are not well understood. Theoretical investigations may help elucidate important aspects of these mechanisms and help in the development of more efficient bio-remediators. In this review, we point out the major contributions of computational methodologies applied to enzyme based detoxification of OPs. Furthermore, we highlight the use of PTE, PON, DFP, and BuChE as enzymes used in OP detoxification process and how computational tools such as molecular docking, molecular dynamics simulations and combined quantum mechanical/molecular mechanics have and will continue to contribute to this very important area of research.The re-emergence of chemical weapons as a global threat in hands of terrorist groups, together with an increasing number of pesticides intoxications and environmental contaminations worldwide, has called the attention of the scientific community for the need of improvement in the technologies for detoxification of organophosphorus (OP) compounds. A compelling strategy is the use of bioremediation by enzymes that are able to hydrolyze these molecules to harmless chemical species. Several enzymes have been studied and engineered for this purpose. However, their mechanisms of action are not well understood. Theoretical investigations may help elucidate important aspects of these mechanisms and help in the development of more efficient bio-remediators. In this review, we point out the major contributions of computational methodologies applied to enzyme based detoxification of OPs. Furthermore, we highlight the use of PTE, PON, DFP, and BuChE as enzymes used in OP detoxification process and how computational tools such as molecular docking, molecular dynamics simulations and combined quantum mechanical/molecular mechanics have and will continue to contribute to this very important area of research.

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

CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials

In this paper, we present CTRAMER (Charge-Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory)—an opensource software package for calculating interfacial charge-transfer (CT) rate constants in organic photovoltaic (OPV) materials based on ab initio calculations and molecular dynamics simulations. The software is based on identifying representative donor/acceptor geometries within interfacial structures obtained from molecular dynamics simulation of donor/acceptor blends and calculating the corresponding Fermi’s golden rule CT rate constants within the framework of the linearized-semiclassical approximation. While the methods used are well established, the integration of these state-of-the-art tools originating from different disciplines to study photoinduced CT processes with explicit treatment of the environment, in our opinion, makes this package unique and innovative. The software also provides tools for investigating other observables of interest. After outlining the features and implementation details, the usage and performance of the software are demonstrated with results from an example OPV system.

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

Coupling Chemical Energy with Protein Conformational Changes to Translocate Small Molecules Across Membranes

EmrE is a small, homodimeric membrane transporter that exploits the established pH gradient across the E. coli inner membrane to export polyaromatic cations that might otherwise inhibit cellular growth. While herculean efforts through experimental studies have established many fundamental facts about the specificity and rate of substrate transport in EmrE, the low resolution of the available structures have hampered efforts to tie those findings to the EmrE coupling mechanism between proton and small molecule substrates. Here we present a full three-dimensional structure of EmrE optimized against available cyro-EM data to delineate the critical interactions by which EmrE regulates its conformation. We use the generated structural model to conduct equilibrium and nonequilibrium molecular dynamics simulations to probe EmrE dynamics under different substrate loading states, representing different states in the transport cycle. The model is stable under extended simulation, and reveals that water dynamics within the EmrE lumen change substantially with the loading state. The water dynamics cause hydrogen bonding networks to shift radically when the protonation states change for a pair of solvent-exposed glutamate residues (E14) within the lumen of the transporter, which are proposed to act as proton binding sites during the transport cycle. One specific hydrogen bond from a tyrosine (Y60) of one monomer to a glutamate (E14) on the opposite monomer is especially critical, as it locks the protein conformation when the glutamate is deprotonated. Furthermore, the hydrogen bond provided by Y60 lowers the pK a of the interacting glutamate relative to its partner on the opposite monomer such that it will protonate second, establishing the need for both glutamates to be protonated for the hydrogen bond to break and a substrate-free transition to take place.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Dynamic Rupture Simulations of Caldera Collapse Earthquakes: Effects of Wave Radiation, Magma Viscosity, and Evidence of Complex Nucleation at Kilauea 2018

All instrumented basaltic caldera collapses have generated M w > 5 very long period earthquakes. However, previous studies of source dynamics have been limited to lumped models treating the caldera block as rigid, leaving open questions related to how ruptures initiate and propagate around the ring fault, and the seismic expressions of those dynamics. Here, we present the first 3D numerical model capturing the nucleation and propagation of ring fault rupture, the mechanical coupling to the underlying viscoelastic magma, and the associated seismic wavefield. We demonstrate that seismic radiation, neglected in previous models, acts as a damping mechanism reducing coseismic slip by up to half, with effects most pronounced for large magma chamber volume/ring fault radius or highly compliant crust/compressible magma. Viscosity of basaltic magma has negligible effect on collapse dynamics. In contrast, viscosity of silicic magma significantly reduces ring fault slip. We use the model to simulate the 2018 Kilauea caldera collapse. Three stages of collapse, characterized by ring fault rupture initiation and propagation, deceleration of the downward-moving caldera block and magma column, and post-collapse resonant oscillations, in addition to chamber pressurization, are identified in simulated and observed (unfiltered) near-field seismograms. A detailed comparison of simulated and observed displacement waveforms corresponding to collapse earthquakes with hypocenters at various azimuths of the ring fault reveals a complex nucleation phase for earthquakes initiated on the northwest. Our numerical simulation framework will enhance future efforts to reconcile seismic and geodetic observations of caldera collapse with conceptual models of ring fault and magma chamber dynamics.

58 GEOSCIENCES↗
DOE OSTI2024

Machine Learning Enabled Atomistic Study of the Micro-Cold Spray Process [Poster]

Micro-cold spray is typically conducted by impacting 200-2000 nm particles at velocities of ~500 m/s. Molecular dynamics simulations have been used to study micro cold spray, but the particles that can be simulated using conventional potentials are much smaller than those used experimentally. The viewgraphs taken from molecular dynamics simulations and shown below are cross-sections of a 50 nm Ta particle with a 3 nm oxide layer impacting at 500 m/s using a machine learning enabled DeePMD potential. Using more expensive reactive interatomic potentials, the previous largest particle size for a metal/oxide impact simulation was 12 nm.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRS2002

Numerical Simulation of Rolling-Airframes Using a Multi-Level Cartesian Method

A supersonic rolling missile with two synchronous canard control surfaces is analyzed using an automated, inviscid, Cartesian method. Sequential-static and time-dependent dynamic simulations of the complete motion are computed for canard dither schedules for level flight, pitch, and yaw maneuver. The dynamic simulations are compared directly against both high-resolution viscous simulations and relevant experimental data, and are also utilized to compute dynamic stability derivatives. The results show that both the body roll rate and canard dither motion influence the roll-averaged forces and moments on the body. At the relatively, low roll rates analyzed in the current work these dynamic effects are modest, however the dynamic computations are effective in predicting the dynamic stability derivatives which can be significant for highly-maneuverable missiles.

Murman, Scott M.↗
DOE OSTI2021

An Integrated Transmission-Distribution Co-Simulation for a Distribution System with High Renewable Penetration

Traditionally, transmission and distribution system dynamic simulations are performed independently. However, dynamic co-simulation of transmission-distribution systems can be beneficial in analyzing distribution systems with high penetration of distributed renewable resources. The authors describe a framework for conducting transmission-distribution dynamic co-simulation (TDDS). A model of a real network including detailed models of solar photovoltaic units in the distribution system is constructed. The initial operating point of the network is validated against field measurements. The TDDS tool is used to simulate a single line-to-ground fault on the distribution system, highlighting the need for conducting transmission-distribution co-simulations.

14 SOLAR ENERGY↗
DOE OSTI2014

Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method

Molecular simulations of soft matter systems have been performed in recent years using a variety of systematically coarse-grained models. With these models, structural or thermodynamic properties can be quite accurately represented while the prediction of dynamic properties remains difficult, especially for multi-component systems. In this work, we use constraint molecular dynamics simulations for calculating dissipative pair forces which are used together with conditional reversible work (CRW) conservative forces in dissipative particle dynamics (DPD) simulations. The combined CRW-DPD approach aims to extend the representability of CRW models to dynamic properties and uses a bottom-up approach. Dissipative pair forces are derived from fluctuations of the direct atomistic forces between mapped groups. The conservative CRW potential is obtained from a similar series of constraint dynamics simulations and represents the reversible work performed to couple the direct atomistic interactions between the mapped atom groups. Neopentane, tetrachloromethane, cyclohexane, and n-hexane have been considered as model systems. These molecular liquids are simulated with atomistic molecular dynamics, coarse-grained molecular dynamics, and DPD. We find that the CRW-DPD models reproduce the liquid structure and diffusive dynamics of the liquid systems in reasonable agreement with the atomistic models when using single-site mapping schemes with beads containing five or six heavy atoms. For a two-site representation of n-hexane (3 carbons per bead), time scale separation can no longer be assumed and the DPD approach consequently fails to reproduce the atomistic dynamics.

2-2-DIMETHYLPROPANE↗
DOE OSTI2015

Short-range order and dynamics of atoms in liquid gallium

The features of the microscopic structure, as well as one-particle and collective dynamics of liquid gallium in the temperature range from T = 313 to 1273 K, are studied on the p = 1.0 atm isobar. Detailed analysis of the data on diffraction of neutrons and X-rays, as well as the results of atomic dynamics simulation, lead to some conclusions about the structure. In particular, for preset conditions, gallium is in the equilibrium liquid phase showing no features of any stable local crystalline clusters. The pronounced asymmetry of the principle peak of the static structure factor and the characteristic “shoulder” in its right-hand part appearing at temperatures close to the melting point, which are clearly observed in the diffraction data, are due to the fact that the arrangement of the nearest neighbors of an arbitrary atom in the system is estimated statistically from the range of correlation length values and not by a single value as in the case of simple liquids. Compactly located dimers with a very short bond make a significant contribution to the statistics of nearest neighbors. The temperature dependence of the self-diffusion coefficient calculated from atomic dynamics simulation agrees well with the results obtained from experimental spectra of the incoherent scattering function. Interpolation of the temperature dependence of the self-diffusion coefficient on a logarithmic scale reveals two linear regions with a transition temperature of about 600 K. The spectra of the dynamic structure factor and spectral densities of the local current calculated by simulating the atomic dynamics indicate the existence of acoustic vibrations with longitudinal and transverse polarizations in liquid gallium, which is confirmed by experimental data on inelastic scattering of neutrons and X-rays. It is found that the vibrational density of states is completely reproduced by the generalized Debye model, which makes it possible to decompose the total vibrational motion into individual contributions associated with the formation of acoustic waves with longitudinal and transverse polarizations. Comparison of the heights of the low-frequency component and of the high-frequency peak in the spectral density of vibrational states also indicates a temperature of T ≈ 600 K, at which the diffusion type of one-particle dynamics changes to the vibrational type upon a decrease in temperature. It is demonstrated that the modified Einstein–Stokes relation can be derived using the generalized Debye model.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2017

Induced polarization restricts the conformational distribution of a light-harvesting molecular triad in the ground state

The light-harvesting molecular triad consisting of carotenoid polyene (C), diaryl-porphyrin (P) and pyrrole-fullerene (C60) is a donor–acceptor molecule capable of absorbing incident light in the visible range. Its ability to convert solar energy to electrical excitation and charge separation energy suggests a great potential in real-world applications. The ensemble of its conformations under ambient conditions varies widely according to its electronic state. In previous work, we applied a non-polarizable model to study the conformational distribution of the molecular triad in the ground and charge separated states. However, due to the lack of polarization, which imparts subtle changes in the charge distribution on atoms, molecular simulations fail to produce accurate average dipole moments. We developed the first polarizable model for a molecular triad to investigate the structural and dynamic properties of a molecular triad in the ground state in an explicit organic solvent, tetrahydrofuran (THF). We performed first-principles electronic structure calculations of the individual components in the triad as well as THF and then fit the partial atomic charges to the electrostatic potential using the i-RESP methodology. We validated these force field parameters by comparing the thermodynamic and dynamic properties obtained from molecular dynamics simulations with those from experiments. We enhanced the sampling of the triad conformations with replica exchange molecular dynamics simulations. We characterized the effects of induced polarization on the structural stability of the triad by analyzing the free energy landscapes constructed with polarizable force fields. Furthermore, by using principal component analysis, we found that the molecular triad conformations adopted a small range of torsional angles with induced polarization. The triad conformation solvated in polar solvent with a polarizable force field qualitatively agrees with that obtained from nuclear magnetic resonance spectroscopy.

Starovoytov, Oleg N.↗
DOE OSTI2023

Dynamic Rupture Simulations of the Mw7.2 1992 Landers,California, Earthquake

An important part of the simulation technique implemented in the Recipe is the earthquake rupture characterization based on established empirical scaling relationships between source parameters and seismic moment. The scaling relationships used in the rupture characterization are derived from recorded data and are tested against dynamic and kinematic rupture models of crustal earthquakes. Currently, a revised three-stage source scaling relationship between the source rupture area and seismic moment of inland crustal earthquakes, initially proposed by Irikura and Miyake, is being used. Recent analysis of results obtained with the Recipe for the 2016 M7.1 Kumamoto earthquake performed by several researchers, including the PI, Arben Pitarka, indicate that in order to reproduce the near-fault long-period ground motions and the permanent displacements, observed during surface-rupturing earthquakes, the recipe needs modifications to the kinematic rupture parametrization in the shallow crustal weak zone. In particular, improvements are required in characterizing the slip rate function at shallow depths, above the sesimogenic zone. The main objective of this research project was the development of a dynamic rupture model for the Mw7.2 1992 Landers, California earthquake. The dynamic rupture model was used to derive kinematic rupture parameters, such as slip, slip-rate, rupture time distributions, and slip rate functions in the weak (0-4km) and seismogenic crustal zones. In addition to the knowledge gained from the dynamic rupture modeling of Chi-chi, Ridgecrest, Kumamoto and other crustal earthquakes, studied by the PI, the rupture characterization of the Landers earthquake can be helpful in updating the conventional recipe for broadband ground motion simulations of crustal earthquakes with shallow rupture. The project emphasizes the need for performing physics-based earthquake rupture modeling which ultimately will inform further improvements of rupture characterization. In particular, the modeling of rupture dynamics for recorded earthquakes, and numerical simulations for different rupture scenarios, provides physical constrains on slip evolution in time and space, used in adjustments of empirical source scaling relationships for large crustal earthquakes.

58 GEOSCIENCES↗
DOE OSTI2025

Quantum simulation of Lindbladian dynamics via repeated interactions

The Lindblad equation generalizes the Schrödinger equation to quantum systems that undergo dissipative dynamics. The quantum simulation of Lindbladian dynamics is therefore non-unitary, preventing a naive application of state-of-the-art quantum algorithms. Here, we make use of an approximate correspondence between Lindbladian dynamics and evolution based on repeated interaction (RI) CPTP maps to write down a Hamiltonian formulation of the Lindblad dynamics and derive a rigorous error bound on the master equation. Specifically, we show that the number of interactions needed to simulate the Liouvillian within error e scales in most physical scenarios as . This is significant because the error in the Lindbladian approximation to the dynamics is not explicitly bounded in existing quantum algorithms for open system simulations. We then provide quantum algorithms to simulate RI maps using an iterative qubitization approach and Trotter–Suzuki formulas, and specifically show that for iterative qubitization the number of operations needed to simulate the dynamics (for a fixed value of ?) scales as in the limit where a0 (the coefficient 1-norm for the system and bath Hamiltonians) asymptotically dominates over the corresponding factor for the interaction Hamiltonian, which is often the case in weak coupling. This scaling would appear to be optimal if the complexity of ? is not considered, which underscores the importance of considering the error in the Liouvillian that we reveal in this work.

Quantum Computing↗
DOE OSTI2016

Crossover from disordered to core-shell structures of nano-oxide Y 2 O 3 dispersed particles in Fe

Here, molecular dynamic simulations of Y 2 O 3 in bcc Fe and transmission electron microscopy (TEM) observations were used to understand the structure of Y 2 O 3 nano-clusters in an oxide dispersion strengthened steel matrix. The study showed that Y 2 O 3 nano-clusters below 2 nm were completely disordered. Y 2 O 3 nano-clusters above 2 nm, however, form a core-shell structure, with a shell thickness of 0.5–0.7 nm that is independent of nano-cluster size. Y 2 O 3 nano-clusters were surrounded by off-lattice Fe atoms, further increasing the stability of these nano-clusters. TEM was used to corroborate our simulation results and showed a crossover from a disordered nano-cluster to a core-shell structure.

36 MATERIALS SCIENCE↗
NASA NTRS1990

Simulation and dynamic performance of a 20-kHz spacecraft power system

A candidate 20-kHz spacecraft power system which includes a series-parallel combination of four Mapham inverters connected to several types of loads is described. A computer simulation of the power system is used to illustrate its steady-state and dynamic performance on an end-to-end basis. Comparisons with measured data are made. It is shown that significant distortion of the 20-kHz bus voltage can occur due to the switching of the load converters. This distortion can be reduced by including a shunt-connected parallel resonant filter on the 20-kHz side of the load converter. It is also shown that the distortion can be reduced by using a pulse-density-modulated switching strategy.

Wasynczuk, O.↗
DOE OSTI2023

Driving and characterizing nucleation of urea and glycine polymorphs in water

Crystal nucleation is relevant across the domains of fundamental and applied sciences. However, in many cases, its mechanism remains unclear due to a lack of temporal or spatial resolution. To gain insights into the molecular details of nucleation, some form of molecular dynamics simulations is typically performed; these simulations, in turn, are limited by their ability to run long enough to sample the nucleation event thoroughly. To overcome the timescale limits in typical molecular dynamics simulations in a manner free of prior human bias, here, we employ the machine learning-augmented molecular dynamics framework “reweighted autoencoded variational Bayes for enhanced sampling (RAVE).” We study two molecular systems—urea and glycine—in explicit all-atom water, due to their enrichment in polymorphic structures and common utility in commercial applications. From our simulations, we observe multiple back-and-forth nucleation events of different polymorphs from homogeneous solution; from these trajectories, we calculate the relative ranking of finite-sized polymorph crystals embedded in solution, in terms of the free-energy difference between the finite-sized crystal polymorph and the original solution state. We further observe that the obtained reaction coordinates and transitions are highly nonclassical.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

A new force field including charge directionality for TMAO in aqueous solution

We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (O{sub TMAO}) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around O{sub TMAO} to mimic the O{sub TMAO} lone pairs and we migrate the negative charge on the O{sub TMAO} to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasing TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗