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At least 667 records · Page 37
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DOE OSTI2016

Design principles for high–pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures

Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures – while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute’s response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

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

Excitation energies, radiative and autoionization rates, dielectronic satellite lines, and dielectronic recombination rates for excited states of Rb-like W from Kr-like W [Relativistic atomic data for Rb-like tungsten]

Energy levels, radiative transition probabilities, and autoionization rates for [Ni]$4{s}^{2}4{p}^{6}{nl}$, [Ni]$4{s}^{2}4{p}^{5}4l^{\prime} {nl}$ ($l^{\prime} =d,f,n$ = 4–7), [Ni]$4s4{p}^{6}4l^{\prime} {nl}$, ($l^{\prime} =d,f,n$ = 4–7), [Ni]$4{s}^{2}4{p}^{5}5l^{\prime} {nl}$ (n = 5–7), and [Ni]$4s4{p}^{6}6l^{\prime} {nl}$ (n = 6–7) states in Rb-like tungsten (W37+) are calculated using the relativistic many-body perturbation theory method (RMBPT code) and the Hartree–Fock-relativistic method (COWAN code). Autoionizing levels above the [Ni]$4{s}^{2}4{p}^{6}$ threshold are considered. It is found that configuration mixing among [Ni]$4{s}^{2}4{p}^{5}4l^{\prime} {nl}$ and [Ni]$4s4{p}^{6}4l^{\prime} {nl}$ plays an important role for all atomic characteristics. Branching ratios relative to the first threshold and intensity factors are calculated for satellite lines, and dielectronic recombination (DR) rate coefficients are determined for the [Ni]$4{s}^{2}4{p}^{6}{nl}$ (n = 4–7) singly excited states, as well as the [Ni]$4{s}^{2}4{p}^{5}4{dnl}$, [Ni]$4{s}^{2}4{p}^{5}4{fnl}$, [Ni]$4s4{p}^{6}4{dnl}$, [Ni]$4{s}^{2}4{p}^{6}4{fnl}$, (n = 4–6), and [Ni]$4{s}^{2}4{p}^{5}5l^{\prime} 5l$ doubly excited nonautoionizing states in Rb-like W37+ ion. Contributions from the [Ni]$4s24{p}^{6}4{fnl}$ (n = 6–7), [Ni]$4{s}^{2}4{p}^{5}5l^{\prime} {nl}$ (n = 5–6), and [Ni]$4{s}^{2}4{p}^{5}6l^{\prime} {nl}$ (n = 6–7) doubly excited autoionizing states are evaluated numerically. The high-n state (with n up to 500) contributions are very important for high temperatures. These contributions are determined by using a scaling procedure. Synthetic dielectronic satellite spectra from Rb-like W are simulated in a broad spectral range from 8 to 70 Å. Here, these calculations provide highly accurate values for a number of W 37+ properties useful for a variety of applications including for fusion applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Ice Ih anomalies: Thermal contraction, anomalous volume isotope effect, and pressure-induced amorphization

Ice Ih displays several anomalous thermodynamic properties such as thermal contraction at low temperatures, an anomalous volume isotope effect (VIE) rendering the volume of D{sub 2}O ice greater than that of H{sub 2}O ice, and a pressure-induced transition to the high-density amorphous (HDA) phase. Furthermore, the anomalous VIE increases with temperature, despite its quantum-mechanical origin. Here, embedded-fragment ab initio second-order many-body perturbation (MP2) theory in the quasiharmonic approximation (QHA) is applied to the Gibbs energy of an infinite, proton-disordered crystal of ice Ih at wide ranges of temperatures and pressures. The quantum effect of nuclei moving in anharmonic potentials is taken into account from first principles without any empirical or nonsystematic approximation to either the electronic or vibrational Hamiltonian. MP2 predicts quantitatively correctly the thermal contraction at low temperatures, which is confirmed to originate from the volume-contracting hydrogen-bond bending modes (acoustic phonons). It qualitatively reproduces (but underestimates) the thermal expansion at higher temperatures, caused by the volume-expanding hydrogen-bond stretching (and to a lesser extent librational) modes. The anomalous VIE is found to be the result of subtle cancellations among closely competing isotope effects on volume from all modes. Consequently, even ab initio MP2 with the aug-cc-pVDZ and aug-cc-pVTZ basis sets has difficulty reproducing this anomaly, yielding qualitatively varied predictions of the sign of the VIE depending on such computational details as the choice of the embedding field. However, the temperature growth of the anomalous VIE is reproduced robustly and is ascribed to the librational modes. These solid-state MP2 calculations, as well as MP2 Born–Oppenheimer molecular dynamics, find a volume collapse and a loss of symmetry and long-range order in ice Ih upon pressure loading of 2.35 GPa or higher. Concomitantly, rapid softening of acoustic phonons is observed starting around 2 GPa. They constitute a computational detection of a mechanical instability in ice Ih and the resulting pressure-induced amorphization to HDA.

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

Three-particle formalism for multiple channels: the ηππ + $ K\overline{K}\pi $ system in isosymmetric QCD

We generalize previous three-particle finite-volume formalisms to allow for multiple three-particle channels. For definiteness, we focus on the two-channel ηππ and $ K\overline{K}\pi $ system in isosymmetric QCD, considering the positive G parity sector of the latter channel, and neglecting the coupling to modes with four or more particles. The formalism we obtain is thus appropriate to study the b 1 (1235) and η(1295) resonances. The derivation is made in the generic relativistic field theory approach using the time-ordered perturbation theory method. We study how the resulting quantization condition reduces to that for a single three-particle channel when one drops below the upper ($ K\overline{K}\pi $) threshold. We also present parametrizations of the three-particle K matrices that enter into the formalism.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2015

A hybrid approach for quantizing complicated motion of a charged particle in time-varying magnetic field

Quantum characteristics of a charged particle subjected to a singular oscillator potential under an external magnetic field is investigated via SU(1,1) Lie algebraic approach together with the invariant operator and the unitary transformation methods. The system we managed is somewhat complicated since we considered not only the time-variation of the effective mass of the system but also the dependence of the external magnetic field on time in an arbitrary fashion. In this case, the system is a kind of time-dependent Hamiltonian systems which require more delicate treatment when we study it. The complete wave functions are obtained without relying on the methods of perturbation and/or approximation, and the global phases of the system are identified. To promote the understanding of our development, we applied it to a particular case, assuming that the effective mass slowly varies with time under a time-dependent magnetic field.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Molecular Geometry and Electronic Structure of Copper Corroles

Copper corroles are known for their unique multiconfigurational electronic structures in the ground state, which arise from the transfer of electrons from the π orbitals of the corrole to the d-orbital of copper. While density functional theory (DFT) provides reasonably good molecular geometries, the determination of the ground spin state and the associated energetics is heavily influenced by functional choice, particularly the percentage of the Hartree–Fock exchange. Using extended multireference perturbation theory methods (XMS-CASPT2), the functional choice can be assessed. The molecular geometries and electronic structures of both the unsubstituted and the meso-triphenyl copper corroles were investigated. A minimal active space was employed for structural characterization, while larger active spaces are required to examine the electronic structure. The XMS-CASPT2 investigations conclusively identify the ground electronic state as a multiconfigurational singlet (S o ) with three dominant electronic configurations in its lowest energy and characteristic saddled structure. In contrast, the planar geometry corresponds to the triplet state (T o ), which is approximately 5 kcal/mol higher in energy compared to the S o state for both the bare and substituted copper corroles. Notably, the planarity of the T o geometry is reduced in the substituted corrole compared with that in the unsubstituted one. By analyzing the potential energy surface (PES) between the S o and T o geometries using XMS-CASPT2, the multiconfigurational electronic structure is shown to transition toward a single electron configuration as the saddling angle decreases (i.e., as one approaches the planar geometry). Despite the ability of the functionals to reproduce the minimum energy structures, only the TPSSh-D 3 PES is reasonably close to the XMS-CASPT2 surface. Significant deviations along the PES are observed with other functionals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Simulation of 24,000 Electron Dynamics: Real-Time Time-Dependent Density Functional Theory (TDDFT) with the Real-Space Multigrids (RMG)

Here, we present the theory, implementation, and benchmarking of a real-time time-dependent density functional theory (RT-TDDFT) module within the RMG code, designed to simulate the electronic response of molecular systems to external perturbations. Our method offers insights into nonequilibrium dynamics and excited states across a diverse range of systems, from small organic molecules to large metallic nanoparticles. Benchmarking results demonstrate excellent agreement with established TDDFT implementations and showcase the superior stability of our time integration algorithm, enabling long-term simulations with minimal energy drift. The scalability and efficiency of RMG on massively parallel architectures allow for simulations of complex systems, such as plasmonic nanoparticles with thousands of atoms. Future extensions, including nuclear and spin dynamics, will broaden the applicability of this RT-TDDFT implementation, providing a powerful toolset for studies of photoactive materials, nanoscale devices, and other systems where real-time electronic dynamics is essential.

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

Prediction of Bond Dissociation Energies/Heats of Formation for Diatomic Transition Metal Compounds: CCSD(T) Works

It was recently reported that the coupled cluster singles and doubles with perturbative triples method, CCSD(T), should not be used as a benchmark tool for the prediction of dissociation energies (heats of formation) for the 1st row transition metal diatomics based on a comparison with the experimental thermodynamic values for a set of 20 diatomics. In the present work reported here, the bond dissociation energies as well as the heats of formation for those diatomics have been calculated by the Feller-Peterson-Dixon approach at the CCSD(T)/complete basis set (CBS) level of theory including scalar relativistic corrections and correlation of the outer shell of core electrons in addition to the valence electrons. Revised experimental values for the hydrides are presented that are based on new heterolytic R-H bond dissociation energies, which are needed for analysis of the mass spectrometry experiments. The agreement between the calculated bond dissociation energies and the revised experimental values of the hydrides is good. Good agreement of the calculated bond dissociation energies/heats of formation is also found for most of the chlorides, oxides, and sulfides given the experimental error bars from experiment and those of the transition metal atoms in the gas phase. Thus, reliable results can be achieved by the CCSD(T) method at the CBS limit. The use of PW91 orbitals for the CCSD(T) calculations improves the predictions for some compounds with large T 1 diagnostics at the HF-CCSD(T) level. The optimized bond distances and calculated vibrational frequencies for the diatomics also agree well with the available experimental values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II

In plants and algae, the primary antenna protein bound to photosystem II is light-harvesting complex II (LHCII), a pigment–protein complex that binds eight chlorophyll (Chl) a molecules and six Chl b molecules. Chl a and Chl b differ only in that Chl a has a methyl group (–CH 3 ) on one of its pyrrole rings, while Chl b has a formyl group (–CHO) at that position. This blue-shifts the Chl b absorbance relative to Chl a . It is not known how the protein selectively binds the right Chl type at each site. Knowing the selection criteria would allow the design of light-harvesting complexes that bind different Chl types, modifying an organism to utilize the light of different wavelengths. The difference in the binding affinity of Chl a and Chl b in pea and spinach LHCII was calculated using multiconformation continuum electrostatics and free energy perturbation. Both methods have identified some Chl sites where the bound Chl type ( a or b ) has a significantly higher affinity, especially when the protein provides a hydrogen bond for the Chl b formyl group. However, the Chl a sites often have little calculated preference for one Chl type, so they are predicted to bind a mixture of Chl a and b . The electron density of the spinach LHCII was reanalyzed, which, however, confirmed that there is negligible Chl b in the Chl a -binding sites. Finally, it is suggested that the protein chooses the correct Chl type during folding, segregating the preferred Chl to the correct binding site.

chemical calculations↗
DOE OSTI2015

Monitoring the Folding Kinetics of a β-Hairpin by Time-Resolved IR Spectroscopy in Silico

One of the most fundamental problems in modern biochemistry is protein folding. Time-resolved infrared (IR) spectroscopy in the amide I region is commonly used to monitor folding kinetics. However, associated atomic detail information on the folding mechanism requires simulations. In atomistic simulations structural order parameters are typically used to follow the folding process along the simulated trajectories. But, a rigorous test of the reliability of the mechanisms found in the simulations requires calculation of the time-dependent experimental observable, i.e., in the present case the IR signal in the amide I region. Here, we combine molecular dynamics simulation with a mixed quantum mechanics/molecular mechanics theoretical methodology, the Perturbed Matrix Method, in order to characterize the folding of a -hairpin peptide, through modeling the time-dependence of the amide I IR signal. The kinetic and thermodynamic data (folding and unfolding rate constants, and equilibrium folded- and unfolded-state probabilities) obtained from the fit of the calculated signal are in good agreement with the available experimental data [Xu et al. J. Am. Chem. Soc. 2003, 125, 15388 15394]. Furthermore, to the best of our knowledge, this is the first report of the simulation of the time-resolved IR signal of a complex process occurring on a long (microsecond) time scale.

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

Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal–Water Interfaces

We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C–C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

Chemical calculations↗
DOE OSTI2015

Deep-subwavelength imaging of both electric and magnetic localized optical fields by plasmonic campanile nanoantenna

Tailoring the electromagnetic field at the nanoscale has led to artificial materials exhibiting fascinating optical properties unavailable in naturally occurring substances. Besides having fundamental implications for classical and quantum optics, nanoscale metamaterials provide a platform for developing disruptive novel technologies, in which a combination of both the electric and magnetic radiation field components at optical frequencies is relevant to engineer the light-matter interaction. Thus, an experimental investigation of the spatial distribution of the photonic states at the nanoscale for both field components is of crucial importance. Here we experimentally demonstrate a concomitant deep-subwavelength near-field imaging of the electric and magnetic intensities of the optical modes localized in a photonic crystal nanocavity. We take advantage of the “campanile tip”, a plasmonic near-field probe that efficiently combines broadband field enhancement with strong far-field to near-field coupling. In conclusion, by exploiting the electric and magnetic polarizability components of the campanile tip along with the perturbation imaging method, we are able to map in a single measurement both the electric and magnetic localized near-field distributions.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2011

Modeling Warm Dense Matter Experiments using the 3D ALE-AMR Code and the Move Toward Exascale Computing

The Neutralized Drift Compression Experiment II (NDCX II) is an induction accelerator planned for initial commissioning in 2012. The final design calls for a 3 MeV, Li+ ion beam, delivered in a bunch with characteristic pulse duration of 1 ns, and transverse dimension of order 1 mm. The NDCX II will be used in studies of material in the warm dense matter (WDM) regime, and ion beam/hydrodynamic coupling experiments relevant to heavy ion based inertial fusion energy. We discuss recent efforts to adapt the 3D ALE-AMR code to model WDM experiments on NDCX II. The code, which combines Arbitrary Lagrangian Eulerian (ALE) hydrodynamics with Adaptive Mesh Refinement (AMR), has physics models that include ion deposition, radiation hydrodynamics, thermal diffusion, anisotropic material strength with material time history, and advanced models for fragmentation. Experiments at NDCX-II will explore the process of bubble and droplet formation (two-phase expansion) of superheated metal solids using ion beams. Experiments at higher temperatures will explore equation of state and heavy ion fusion beam-to-target energy coupling efficiency. Ion beams allow precise control of local beam energy deposition providing uniform volumetric heating on a timescale shorter than that of hydrodynamic expansion. The ALE-AMR code does not have any export control restrictions and is currently running at the National Energy Research Scientific Computing Center (NERSC) at LBNL and has been shown to scale well to thousands of CPUs. New surface tension models that are being implemented and applied to WDM experiments. Some of the approaches use a diffuse interface surface tension model that is based on the advective Cahn-Hilliard equations, which allows for droplet breakup in divergent velocity fields without the need for imposed perturbations. Other methods require seeding or other methods for droplet breakup. We also briefly discuss the effects of the move to exascale computing and related computational changes on general modeling codes in fusion energy.

42 ENGINEERING↗
DOE OSTI2011

Final state interactions and the Sivers function

The non-vanishing of naive T-odd parton distributions function can be explained by the existence of the gauge link which emerges from the factorized description of the deep inelastic scattering cross section into perturbatively calculable and non-perturbative factors. This path ordered exponential describes initial / final-state interactions of the active parton due to soft gluon exchanges with the target remnants. Although these interactions are non-perturbative, studies of final state interactions have been approximated by perturbative one-gluon exchange in Abelian models. We include higher-order gluonic contributions from the gauge link by applying non-perturbative eikonal methods, incorporating color degrees of freedom in a calculation of the Sivers function. In this context we study the effects of color by considering the FSIs with with Abelian and non-Abelian gluon interactions. We confirm the large N{sub c} QCD scaling behavior of Sivers functions and further uncover the deviations for finite N{sub c}. Within this framework of FSIs we perform a quantitative check of approximate relations between T-odd TMDs and GPD which goes beyond the discussion of overall signs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2011

Oblique propagation of nonlinear electrostatic waves in dense astrophysical magnetoplasmas

Nonlinear quantum ion-acoustic waves in dense dissipative as well as non-dissipative magnetized plasmas are investigated employing the quantum hydrodynamic model. In this regard, Zakharov Kuznetsov Burgers equation is derived in quantum plasmas, for the first time, using the small amplitude perturbation expansion method. The unique features of nonlinear electrostatic structures in pure electron-ion quantum magnetoplasma are highlighted and the parametric domain of the applicability of the model is unequivocally expressed. The present study may be useful to understand the nonlinear propagation characteristics of electrostatic shock and solitary structures in dense astrophysical systems where the quantum effects are expected to dominate.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2012

Transition from order to chaos, and density limit, in magnetized plasmas

It is known that a plasma in a magnetic field, conceived microscopically as a system of point charges, can exist in a magnetized state, and thus remain confined, inasmuch as it is in an ordered state of motion, with the charged particles performing gyrational motions transverse to the field. Here, we give an estimate of a threshold, beyond which transverse motions become chaotic, the electrons being unable to perform even one gyration, so that a breakdown should occur, with complete loss of confinement. The estimate is obtained by the methods of perturbation theory, taking as perturbing force acting on each electron that due to the so-called microfield, i.e., the electric field produced by all the other charges. We first obtain a general relation for the threshold, which involves the fluctuations of the microfield. Then, taking for such fluctuations, the formula given by Iglesias, Lebowitz, and MacGowan for the model of a one component plasma with neutralizing background, we obtain a definite formula for the threshold, which corresponds to a density limit increasing as the square of the imposed magnetic field. Such a theoretical density limit is found to fit pretty well the empirical data for collapses of fusion machines.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2012

Numerical studies of a plasma diode with external forcing

With reference to laboratory Q-machine studies we analyze the dynamics of a plasma diode under external forcing. Assuming a strong axial magnetic field, the problem is analyzed in one spatial dimension by a particle-in-cell code. The cathode is assumed to be operated in electron rich conditions, supplying an abundance of electrons. We compare different forcing schemes with the results obtained by solving the van der Pol equation. In one method of forcing we apply an oscillation in addition to the DC end plate bias and consider both amplitude and frequency variations. An alternative method of perturbation consists of modelling an absorbing grid at some internal position. Also in this case we can have a constant frequency with varying amplitude or alternatively an oscillation with chirped frequency but constant amplitude. We find that the overall features of the forced van der Pol equation are recovered, but the details in the plasma response need more attention to the harmonic responses, requiring extensions of the model equation. The analysis is extended by introducing collisional effects, where we emphasize charge exchange collisions of ions, since these processes usually have the largest cross sections and give significant modifications of the diode performance. In particular we find a reduction in oscillator frequency, although a linear scaling of the oscillation time with the system length remains also in this case.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗